-- dump date 20111121_010141 -- class Genbank::misc_feature -- table misc_feature_note -- id note 998088000001 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 998088000002 hypothetical protein; Validated; Region: PRK06672 998088000003 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088000004 Walker A motif; other site 998088000005 ATP binding site [chemical binding]; other site 998088000006 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088000007 Walker B motif; other site 998088000008 arginine finger; other site 998088000009 C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple...; Region: Bac_DnaA_C; cd06571 998088000010 DnaA box-binding interface [nucleotide binding]; other site 998088000011 DNA polymerase III subunit beta; Validated; Region: PRK05643 998088000012 Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the...; Region: beta_clamp; cd00140 998088000013 putative DNA binding surface [nucleotide binding]; other site 998088000014 dimer interface [polypeptide binding]; other site 998088000015 beta-clamp/clamp loader binding surface; other site 998088000016 beta-clamp/translesion DNA polymerase binding surface; other site 998088000017 recombination protein F; Reviewed; Region: recF; PRK00064 998088000018 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088000019 Walker A/P-loop; other site 998088000020 ATP binding site [chemical binding]; other site 998088000021 Q-loop/lid; other site 998088000022 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088000023 ABC transporter signature motif; other site 998088000024 Walker B; other site 998088000025 D-loop; other site 998088000026 H-loop/switch region; other site 998088000027 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 998088000028 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 998088000029 TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to the B subunits of E. coli DNA gyrase and E. coli Topoisomerase IV which are...; Region: TopoII_Trans_DNA_gyrase; cd00822 998088000030 anchoring element; other site 998088000031 dimer interface [polypeptide binding]; other site 998088000032 ATP binding site [chemical binding]; other site 998088000033 TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of...; Region: TOPRIM_TopoIIA_GyrB; cd03366 998088000034 active site 998088000035 putative metal-binding site [ion binding]; other site 998088000036 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 998088000037 transcriptional activator FtrA; Provisional; Region: ftrA; PRK09393 998088000038 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 998088000039 conserved cys residue [active] 998088000040 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088000041 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 998088000042 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 998088000043 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein...; Region: ACD_IbpA-B_like; cd06470 998088000044 putative dimer interface [polypeptide binding]; other site 998088000045 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 998088000046 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein...; Region: ACD_IbpA-B_like; cd06470 998088000047 putative dimer interface [polypeptide binding]; other site 998088000048 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 998088000049 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088000050 homodimer interface [polypeptide binding]; other site 998088000051 catalytic residue [active] 998088000052 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 998088000053 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088000054 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 998088000055 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088000056 active site 998088000057 phosphorylation site [posttranslational modification] 998088000058 intermolecular recognition site; other site 998088000059 dimerization interface [polypeptide binding]; other site 998088000060 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 998088000061 DNA binding site [nucleotide binding] 998088000062 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 998088000063 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 998088000064 USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium...; Region: USP_OKCHK; cd01987 998088000065 Ligand Binding Site [chemical binding]; other site 998088000066 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 998088000067 dimer interface [polypeptide binding]; other site 998088000068 phosphorylation site [posttranslational modification] 998088000069 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088000070 ATP binding site [chemical binding]; other site 998088000071 Mg2+ binding site [ion binding]; other site 998088000072 G-X-G motif; other site 998088000073 K+-transporting ATPase, c chain; Region: KdpC; cl00944 998088000074 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 998088000075 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 998088000076 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 998088000077 K+-transporting ATPase, A chain [Inorganic ion transport and metabolism]; Region: KdpA; cl00903 998088000078 Potassium-transporting ATPase A subunit; Region: KdpA; pfam03814 998088000079 glutathione reductase; Validated; Region: PRK06116 998088000080 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088000081 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 998088000082 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088000083 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 998088000084 PAS fold; Region: PAS_4; pfam08448 998088000085 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 998088000086 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088000087 ATP binding site [chemical binding]; other site 998088000088 Mg2+ binding site [ion binding]; other site 998088000089 G-X-G motif; other site 998088000090 multidrug efflux protein; Reviewed; Region: PRK09579 998088000091 Protein export membrane protein; Region: SecD_SecF; cl14618 998088000092 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 998088000093 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 998088000094 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088000095 Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly...; Region: RICIN; cd00161 998088000096 putative sugar binding sites [chemical binding]; other site 998088000097 Q-X-W motif; other site 998088000098 putative hydrolase; Provisional; Region: PRK10976 998088000099 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cd01427 998088000100 active site 998088000101 motif I; other site 998088000102 motif II; other site 998088000103 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 998088000104 lysophospholipase L2; Provisional; Region: PRK10749 998088000105 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 998088000106 Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and...; Region: LbH_XAT; cd03349 998088000107 trimer interface [polypeptide binding]; other site 998088000108 active site 998088000109 CoA binding site [chemical binding]; other site 998088000110 tRNA guanosine-2'-O-methyltransferase; Provisional; Region: PRK11081 998088000111 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 998088000112 C-terminal; Region: SpoU_methylas_C; pfam12105 998088000113 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional; Region: PRK11092 998088000114 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 998088000115 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 998088000116 synthetase active site [active] 998088000117 NTP binding site [chemical binding]; other site 998088000118 metal binding site [ion binding]; metal-binding site 998088000119 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named...; Region: TGS_RelA_SpoT; cd01668 998088000120 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 998088000121 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 998088000122 Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and...; Region: GMPK; cd00071 998088000123 catalytic site [active] 998088000124 G-X2-G-X-G-K; other site 998088000125 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 998088000126 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 998088000127 putative active site [active] 998088000128 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 998088000129 ATP binding site [chemical binding]; other site 998088000130 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 998088000131 substrate binding site [chemical binding]; other site 998088000132 PAS fold; Region: PAS_3; pfam08447 998088000133 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088000134 metal binding site [ion binding]; metal-binding site 998088000135 active site 998088000136 I-site; other site 998088000137 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 998088000138 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 998088000139 EamA-like transporter family; Region: EamA; cl01037 998088000140 EamA-like transporter family; Region: EamA; cl01037 998088000141 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088000142 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088000143 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 998088000144 substrate binding pocket [chemical binding]; other site 998088000145 dimerization interface [polypeptide binding]; other site 998088000146 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 998088000147 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 998088000148 active site 998088000149 HIGH motif; other site 998088000150 dimer interface [polypeptide binding]; other site 998088000151 KMSKS motif; other site 998088000152 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 998088000153 Ligand Binding Site [chemical binding]; other site 998088000154 trans-2-enoyl-CoA reductase; Provisional; Region: PRK13656 998088000155 NAD(P)H binding domain of trans-2-enoyl-CoA reductase; Region: Eno-Rase_NADH_b; pfam12242 998088000156 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088000157 Enoyl reductase FAD binding domain; Region: Eno-Rase_FAD_bd; pfam07055 998088000158 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 998088000159 Ferritin-like domain; Region: Ferritin; pfam00210 998088000160 ferroxidase diiron center [ion binding]; other site 998088000161 Predicted flavoproteins [General function prediction only]; Region: COG2081 998088000162 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088000163 Putative regulator of cell autolysis [Signal transduction mechanisms]; Region: LytS; COG3275 998088000164 Protein of unknown function (DUF1393); Region: DUF1393; cl01942 998088000165 Histidine kinase; Region: His_kinase; pfam06580 998088000166 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088000167 ATP binding site [chemical binding]; other site 998088000168 Mg2+ binding site [ion binding]; other site 998088000169 G-X-G motif; other site 998088000170 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 998088000171 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088000172 active site 998088000173 phosphorylation site [posttranslational modification] 998088000174 intermolecular recognition site; other site 998088000175 dimerization interface [polypeptide binding]; other site 998088000176 LytTr DNA-binding domain; Region: LytTR; cl04498 998088000177 Oxalate/Formate Antiporter; Region: 2A0111; TIGR00890 998088000178 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088000179 putative substrate translocation pore; other site 998088000180 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 998088000181 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 998088000182 AIR carboxylase; Region: AIRC; cl00310 998088000183 Domain of unknown function (DUF897); Region: DUF897; cl01312 998088000184 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 998088000185 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088000186 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088000187 dimerization interface [polypeptide binding]; other site 998088000188 vitamin B12/cobalamin outer membrane transporter; Provisional; Region: btuB; PRK10641 998088000189 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 998088000190 N-terminal plug; other site 998088000191 ligand-binding site [chemical binding]; other site 998088000192 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 998088000193 RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA...; Region: RRM; cd00590 998088000194 RNA/DNA binding site [nucleotide binding]; other site 998088000195 RRM dimerization site [polypeptide binding]; other site 998088000196 sulfur acceptor protein CsdL; Provisional; Region: PRK15116 998088000197 Family of activating enzymes (E1) of ubiquitin-like proteins related to the E.coli hypothetical protein ygdL. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-...; Region: YgdL_like; cd00755 998088000198 putative ATP binding site [chemical binding]; other site 998088000199 putative substrate interface [chemical binding]; other site 998088000200 Fe-S metabolism associated domain; Region: SufE; cl00951 998088000201 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 998088000202 Cysteine desulfurase (SufS)-like. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to cysteine desulfurase (SufS) and selenocysteine lyase. SufS...; Region: SufS_like; cd06453 998088000203 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 998088000204 catalytic residue [active] 998088000205 ATP-dependent DNA helicase Rep; Provisional; Region: PRK10919 998088000206 UvrD/REP helicase; Region: UvrD-helicase; cl14126 998088000207 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088000208 metal binding site [ion binding]; metal-binding site 998088000209 active site 998088000210 I-site; other site 998088000211 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 998088000212 Cytochrome c; Region: Cytochrom_C; cl11414 998088000213 L-threonine 3-dehydrogenase; Validated; Region: tdh; PRK05396 998088000214 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl14614 998088000215 NAD(P) binding site [chemical binding]; other site 998088000216 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 998088000217 KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS), 8-amino-7-...; Region: KBL_like; cd06454 998088000218 substrate-cofactor binding pocket; other site 998088000219 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088000220 catalytic residue [active] 998088000221 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 998088000222 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088000223 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 998088000224 ADP-L-glycero-D-mannoheptose-6-epimerase; Provisional; Region: rfaD; PRK11150 998088000225 NADP binding site [chemical binding]; other site 998088000226 homopentamer interface [polypeptide binding]; other site 998088000227 substrate binding site [chemical binding]; other site 998088000228 active site 998088000229 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 998088000230 This family is most closely related to the GT1 family of glycosyltransferases. WavL in Vibrio cholerae has been shown to be involved in the biosynthesis of the lipopolysaccharide core; Region: GT1_WavL_like; cd03819 998088000231 putative ADP-binding pocket [chemical binding]; other site 998088000232 Polysaccharide deacetylase; Region: Polysacc_deac_1; cl12061 998088000233 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 998088000234 O-Antigen ligase; Region: Wzy_C; cl04850 998088000235 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 998088000236 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 998088000237 Probable Catalytic site [active] 998088000238 metal binding site [ion binding]; metal-binding site 998088000239 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 998088000240 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088000241 substrate binding pocket [chemical binding]; other site 998088000242 membrane-bound complex binding site; other site 998088000243 hinge residues; other site 998088000244 Cupin domain; Region: Cupin_2; cl09118 998088000245 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 998088000246 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088000247 LysE type translocator; Region: LysE; cl00565 998088000248 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088000249 Protein of unknown function (DUF3313); Region: DUF3313; pfam11769 998088000250 Cupin domain; Region: Cupin_2; cl09118 998088000251 Domain of unknown function (DUF1993); Region: DUF1993; cl01567 998088000252 putative selenium-binding protein YdfZ; Region: YdfZ_fam; TIGR03318 998088000253 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 998088000254 UvrD/REP helicase; Region: UvrD-helicase; cl14126 998088000255 Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea; Region: PBP1_BmpA_PnrA_like; cd06354 998088000256 ligand binding site [chemical binding]; other site 998088000257 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 998088000258 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and...; Region: ABC_Carb_Monos_I; cd03216 998088000259 Walker A/P-loop; other site 998088000260 ATP binding site [chemical binding]; other site 998088000261 Q-loop/lid; other site 998088000262 ABC transporter signature motif; other site 998088000263 Walker B; other site 998088000264 D-loop; other site 998088000265 H-loop/switch region; other site 998088000266 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (; Region: ABC_Carb_Monos_II; cd03215 998088000267 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (; Region: TM_PBP1_transp_TpRbsC_like; cd06580 998088000268 TM-ABC transporter signature motif; other site 998088000269 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (; Region: TM_PBP1_transp_TpRbsC_like; cd06580 998088000270 TM-ABC transporter signature motif; other site 998088000271 bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein; Reviewed; Region: cpdB; PRK09420 998088000272 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 998088000273 active site 998088000274 metal binding site [ion binding]; metal-binding site 998088000275 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 998088000276 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 998088000277 MgtE intracellular N domain; Region: MgtE_N; cl15244 998088000278 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 998088000279 Divalent cation transporter; Region: MgtE; cl00786 998088000280 siroheme synthase; Provisional; Region: cysG; PRK10637 998088000281 precorrin-2 dehydrogenase; Validated; Region: PRK06719 998088000282 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 998088000283 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 998088000284 Formate/nitrite transporter; Region: Form_Nir_trans; cl00927 998088000285 Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium. Members include bacterial and fungal proteins. The bacterial NirD contains a single Rieske domain...; Region: Rieske_NirD; cd03529 998088000286 nitrite reductase subunit NirD; Provisional; Region: PRK14989 998088000287 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 998088000288 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 998088000289 ABC-2 type transporter; Region: ABC2_membrane; cl11417 998088000290 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 998088000291 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 998088000292 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 998088000293 daunorubicin resistance ABC transporter ATP-binding subunit; Region: drrA; TIGR01188 998088000294 Walker A/P-loop; other site 998088000295 ATP binding site [chemical binding]; other site 998088000296 Q-loop/lid; other site 998088000297 ABC transporter signature motif; other site 998088000298 Walker B; other site 998088000299 D-loop; other site 998088000300 H-loop/switch region; other site 998088000301 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 998088000302 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088000303 Walker A/P-loop; other site 998088000304 ATP binding site [chemical binding]; other site 998088000305 Q-loop/lid; other site 998088000306 ABC transporter signature motif; other site 998088000307 Walker B; other site 998088000308 D-loop; other site 998088000309 H-loop/switch region; other site 998088000310 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 998088000311 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2...; Region: Biotinyl_lipoyl_domains; cl11404 998088000312 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088000313 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 998088000314 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088000315 Walker A motif; other site 998088000316 ATP binding site [chemical binding]; other site 998088000317 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088000318 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 998088000319 Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the...; Region: protease_HslV; cd01913 998088000320 active site 998088000321 HslU subunit interaction site [polypeptide binding]; other site 998088000322 cell division protein FtsN; Provisional; Region: PRK12757 998088000323 Sporulation related domain; Region: SPOR; cl10051 998088000324 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 998088000325 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; cl04104 998088000326 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 998088000327 active site 998088000328 HIGH motif; other site 998088000329 KMSK motif region; other site 998088000330 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 998088000331 tRNA binding surface [nucleotide binding]; other site 998088000332 anticodon binding site; other site 998088000333 ATP-dependent protease La (LON) domain; Region: LON; pfam02190 998088000334 RNA polymerase sigma factor; Provisional; Region: PRK11924 998088000335 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 998088000336 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial...; Region: Sigma70_r4; cd06171 998088000337 DNA binding residues [nucleotide binding] 998088000338 Transcriptional activator [Transcription]; Region: ChrR; COG3806 998088000339 Cupin domain; Region: Cupin_2; cl09118 998088000340 Bacitracin resistance protein BacA; Region: BacA; cl00858 998088000341 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 998088000342 active site 998088000343 catalytic residues [active] 998088000344 galactokinase; Provisional; Region: PRK05101 998088000345 Galactokinase galactose-binding signature; Region: GalKase_gal_bdg; pfam10509 998088000346 GHMP kinases N terminal domain; Region: GHMP_kinases_N; cl08256 998088000347 galactose-1-phosphate uridylyltransferase; Provisional; Region: PRK11720 998088000348 Galactose-1-phosphate uridyl transferase (GalT): This enzyme plays a key role in galactose metabolism by catalysing the transfer of a uridine 5'-phosphoryl group from UDP-galactose 1-phosphate. The structure of E.coli GalT reveals that the enzyme...; Region: GalT; cd00608 998088000349 dimer interface [polypeptide binding]; other site 998088000350 active site 998088000351 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 998088000352 UDP-glucose 4-epimerase; Region: PLN02240 998088000353 NAD binding site [chemical binding]; other site 998088000354 homodimer interface [polypeptide binding]; other site 998088000355 active site 998088000356 substrate binding site [chemical binding]; other site 998088000357 DNA-binding transcriptional regulator GalR; Provisional; Region: PRK10727 998088000358 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 998088000359 DNA binding site [nucleotide binding] 998088000360 domain linker motif; other site 998088000361 Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism; Region: PBP1_GalS_like; cd06270 998088000362 dimerization interface (closed form) [polypeptide binding]; other site 998088000363 ligand binding site [chemical binding]; other site 998088000364 beta-D-galactosidase; Reviewed; Region: lacZ; PRK09525 998088000365 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 998088000366 domain; Region: Glyco_hydro_2; pfam00703 998088000367 Beta galactosidase small chain; Region: Bgal_small_N; cl03787 998088000368 Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species; Region: PBP1_GGBP; cd01539 998088000369 ligand binding site [chemical binding]; other site 998088000370 calcium binding site [ion binding]; other site 998088000371 galactose/methyl galaxtoside transporter ATP-binding protein; Provisional; Region: PRK10982 998088000372 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088000373 Walker A/P-loop; other site 998088000374 ATP binding site [chemical binding]; other site 998088000375 Q-loop/lid; other site 998088000376 ABC transporter signature motif; other site 998088000377 Walker B; other site 998088000378 D-loop; other site 998088000379 H-loop/switch region; other site 998088000380 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (; Region: ABC_Carb_Monos_II; cd03215 998088000381 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 998088000382 TM-ABC transporter signature motif; other site 998088000383 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088000384 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088000385 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088000386 tRNA (uracil-5-)-methyltransferase; Validated; Region: PRK05031 998088000387 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 998088000388 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; cl00920 998088000389 maltodextrin glucosidase; Provisional; Region: PRK10785 998088000390 CD and pullulan-degrading enzymes N-terminus domain. Members of this subgroup include: Cyclomaltodextrinase (CDase), maltogenic amylase, and neopullulanase all of which are capable of hydrolyzing all or two of the following three types of substrates:...; Region: CD_pullulan_degrading_enzymes_N_term; cd02857 998088000391 homodimer; other site 998088000392 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 998088000393 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; cl02706 998088000394 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 998088000395 aminopeptidase; Provisional; Region: PRK09795 998088000396 META domain; Region: META; cl01245 998088000397 putative chaperone; Provisional; Region: PRK11678 998088000398 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 998088000399 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088000400 CreA protein; Region: CreA; cl01154 998088000401 Protein of unknown function (DUF962); Region: DUF962; cl01879 998088000402 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088000403 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 998088000404 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 998088000405 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 998088000406 putative aminotransferase; Validated; Region: PRK07480 998088000407 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase...; Region: OAT_like; cd00610 998088000408 inhibitor-cofactor binding pocket; inhibition site 998088000409 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088000410 catalytic residue [active] 998088000411 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 998088000412 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088000413 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 998088000414 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088000415 putrescine transporter ATP-binding subunit; Provisional; Region: potG; PRK11607 998088000416 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088000417 Walker A/P-loop; other site 998088000418 ATP binding site [chemical binding]; other site 998088000419 Q-loop/lid; other site 998088000420 ABC transporter signature motif; other site 998088000421 Walker B; other site 998088000422 D-loop; other site 998088000423 H-loop/switch region; other site 998088000424 TOBE domain; Region: TOBE_2; cl01440 998088000425 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088000426 dimer interface [polypeptide binding]; other site 998088000427 conserved gate region; other site 998088000428 putative PBP binding loops; other site 998088000429 ABC-ATPase subunit interface; other site 998088000430 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088000431 dimer interface [polypeptide binding]; other site 998088000432 conserved gate region; other site 998088000433 putative PBP binding loops; other site 998088000434 ABC-ATPase subunit interface; other site 998088000435 6-N-hydroxylaminopurine resistance protein; Provisional; Region: PRK11536 998088000436 MOSC domain; Region: MOSC; pfam03473 998088000437 3-alpha domain; Region: 3-alpha; pfam03475 998088000438 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 998088000439 CoenzymeA binding site [chemical binding]; other site 998088000440 subunit interaction site [polypeptide binding]; other site 998088000441 PHB binding site; other site 998088000442 ATP-dependent DNA helicase RecQ; Provisional; Region: PRK11057 998088000443 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 998088000444 ATP binding site [chemical binding]; other site 998088000445 putative Mg++ binding site [ion binding]; other site 998088000446 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 998088000447 nucleotide binding region [chemical binding]; other site 998088000448 ATP-binding site [chemical binding]; other site 998088000449 RQC domain; Region: RQC; cl09632 998088000450 HRDC domain; Region: HRDC; cl02578 998088000451 Cytochrome c; Region: Cytochrom_C; cl11414 998088000452 Uncharacterized conserved protein [Function unknown]; Region: COG0397; cl00428 998088000453 Protein of unknown function (DUF3630); Region: DUF3630; pfam12305 998088000454 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; cl00756 998088000455 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 998088000456 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088000457 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088000458 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088000459 CpeT/CpcT family (DUF1001); Region: CpeT; pfam06206 998088000460 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 998088000461 primosome assembly protein PriA; Validated; Region: PRK05580 998088000462 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 998088000463 ATP binding site [chemical binding]; other site 998088000464 putative Mg++ binding site [ion binding]; other site 998088000465 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088000466 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088000467 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 998088000468 NAD(P) binding site [chemical binding]; other site 998088000469 active site 998088000470 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 998088000471 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 998088000472 Malic enzyme [Energy production and conversion]; Region: SfcA; COG0281 998088000473 Malic enzyme, N-terminal domain; Region: malic; pfam00390 998088000474 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 998088000475 putative NAD(P) binding site [chemical binding]; other site 998088000476 Ribonuclease BN-like family; Region: Ribonuclease_BN; cl07918 998088000477 D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but...; Region: Dtyr_deacylase; cd00563 998088000478 putative active site [active] 998088000479 dimerization interface [polypeptide binding]; other site 998088000480 putative tRNAtyr binding site [nucleotide binding]; other site 998088000481 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 998088000482 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 998088000483 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088000484 Coenzyme A binding pocket [chemical binding]; other site 998088000485 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 998088000486 AsmA family; Region: AsmA; pfam05170 998088000487 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 998088000488 Y-family of DNA polymerases; Region: PolY; cl12025 998088000489 RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-...; Region: RecG_wedge_OBF; cd04488 998088000490 ssDNA binding site; other site 998088000491 generic binding surface II; other site 998088000492 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 998088000493 ATP binding site [chemical binding]; other site 998088000494 putative Mg++ binding site [ion binding]; other site 998088000495 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 998088000496 nucleotide binding region [chemical binding]; other site 998088000497 ATP-binding site [chemical binding]; other site 998088000498 phosphatidylserine synthase; Provisional; Region: pssA; PRK09428 998088000499 Catalytic domain, repeat 1, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_1; cd09134 998088000500 domain interface [polypeptide binding]; other site 998088000501 putative active site [active] 998088000502 catalytic site [active] 998088000503 Catalytic domain, repeat 2, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_2; cd09136 998088000504 domain interface [polypeptide binding]; other site 998088000505 putative active site [active] 998088000506 catalytic site [active] 998088000507 GntP family permease; Region: GntP_permease; cl15264 998088000508 gluconate transporter; Region: gntP; TIGR00791 998088000509 Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits; Region: GntK; cd02021 998088000510 Gluconate kinase [Carbohydrate transport and metabolism]; Region: GntK; COG3265 998088000511 ATP-binding site [chemical binding]; other site 998088000512 Gluconate-6-phosphate binding site [chemical binding]; other site 998088000513 Dehydratase family; Region: ILVD_EDD; cl00340 998088000514 6-phosphogluconate dehydratase; Region: edd; TIGR01196 998088000515 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 998088000516 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 998088000517 active site 998088000518 intersubunit interface [polypeptide binding]; other site 998088000519 catalytic residue [active] 998088000520 gluconate operon transcriptional regulator; Provisional; Region: PRK14987 998088000521 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 998088000522 DNA binding site [nucleotide binding] 998088000523 domain linker motif; other site 998088000524 Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_GntR; cd01575 998088000525 putative ligand binding site [chemical binding]; other site 998088000526 putative dimerization interface [polypeptide binding]; other site 998088000527 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 998088000528 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 998088000529 Peptidase family M23; Region: Peptidase_M23; pfam01551 998088000530 Sulfatase; Region: Sulfatase; cl10460 998088000531 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 998088000532 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 998088000533 active site residue [active] 998088000534 Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent...; Region: Translocase_SecB; cd00557 998088000535 SecA binding site; other site 998088000536 Preprotein binding site; other site 998088000537 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 998088000538 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088000539 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 998088000540 Fe/S biogenesis protein NfuA; Provisional; Region: PRK11190 998088000541 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 998088000542 NifU-like domain; Region: NifU; cl00484 998088000543 DNA utilization protein GntX; Provisional; Region: PRK11595 998088000544 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 998088000545 carboxylesterase BioH; Provisional; Region: PRK10349 998088000546 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 998088000547 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 998088000548 SprA-related family; Region: SprA-related; pfam12118 998088000549 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 998088000550 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 998088000551 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cl00243 998088000552 S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin...; Region: S1_Tex; cd05685 998088000553 RNA binding site [nucleotide binding]; other site 998088000554 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 998088000555 domain; Region: GreA_GreB_N; pfam03449 998088000556 C-term; Region: GreA_GreB; pfam01272 998088000557 osmolarity response regulator; Provisional; Region: ompR; PRK09468 998088000558 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088000559 active site 998088000560 phosphorylation site [posttranslational modification] 998088000561 intermolecular recognition site; other site 998088000562 dimerization interface [polypeptide binding]; other site 998088000563 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 998088000564 DNA binding site [nucleotide binding] 998088000565 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 998088000566 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088000567 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 998088000568 dimer interface [polypeptide binding]; other site 998088000569 phosphorylation site [posttranslational modification] 998088000570 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088000571 ATP binding site [chemical binding]; other site 998088000572 Mg2+ binding site [ion binding]; other site 998088000573 G-X-G motif; other site 998088000574 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 998088000575 EamA-like transporter family; Region: EamA; cl01037 998088000576 EamA-like transporter family; Region: EamA; cl01037 998088000577 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 998088000578 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 998088000579 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 998088000580 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 998088000581 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 998088000582 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 998088000583 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 998088000584 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 998088000585 Ribosomal protein L22/L17e. L22 (L17 in eukaryotes) is a core protein of the large ribosomal subunit. It is the only ribosomal protein that interacts with all six domains of 23S rRNA, and is one of the proteins important for directing the proper...; Region: Ribosomal_L22; cd00336 998088000586 putative translocon binding site; other site 998088000587 protein-rRNA interface [nucleotide binding]; other site 998088000588 ribosomal protein S3, bacterial type; Region: rpsC_bact; TIGR01009 998088000589 K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The...; Region: 30S_S3_KH; cd02412 998088000590 G-X-X-G motif; other site 998088000591 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 998088000592 Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with...; Region: Ribosomal_L16_L10e; cd01433 998088000593 23S rRNA interface [nucleotide binding]; other site 998088000594 5S rRNA interface [nucleotide binding]; other site 998088000595 putative antibiotic binding site [chemical binding]; other site 998088000596 L25 interface [polypeptide binding]; other site 998088000597 L27 interface [polypeptide binding]; other site 998088000598 Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where...; Region: Ribosomal_L29_HIP; cd00427 998088000599 23S rRNA interface [nucleotide binding]; other site 998088000600 putative translocon interaction site; other site 998088000601 signal recognition particle (SRP54) interaction site; other site 998088000602 L23 interface [polypeptide binding]; other site 998088000603 trigger factor interaction site; other site 998088000604 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 998088000605 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 998088000606 KOW motif; Region: KOW; cl00354 998088000607 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 998088000608 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 998088000609 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 998088000610 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 998088000611 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 998088000612 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 998088000613 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 998088000614 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 998088000615 Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA...; Region: Ribosomal_L18_L5e; cd00432 998088000616 5S rRNA interface [nucleotide binding]; other site 998088000617 L5 interface [polypeptide binding]; other site 998088000618 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 998088000619 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 998088000620 Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins...; Region: Ribosomal_L30; cd01658 998088000621 23S rRNA binding site [nucleotide binding]; other site 998088000622 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 998088000623 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 998088000624 SecY translocase; Region: SecY; pfam00344 998088000625 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 998088000626 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 998088000627 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 998088000628 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 998088000629 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 998088000630 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 998088000631 RNA binding surface [nucleotide binding]; other site 998088000632 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 998088000633 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 998088000634 alphaNTD homodimer interface [polypeptide binding]; other site 998088000635 alphaNTD - beta interaction site [polypeptide binding]; other site 998088000636 alphaNTD - beta' interaction site [polypeptide binding]; other site 998088000637 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 998088000638 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 998088000639 putative outer membrane receptor; Provisional; Region: PRK13513 998088000640 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 998088000641 N-terminal plug; other site 998088000642 ligand-binding site [chemical binding]; other site 998088000643 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088000644 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088000645 substrate binding pocket [chemical binding]; other site 998088000646 membrane-bound complex binding site; other site 998088000647 hinge residues; other site 998088000648 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088000649 metal binding site [ion binding]; metal-binding site 998088000650 active site 998088000651 I-site; other site 998088000652 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 998088000653 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088000654 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 998088000655 dimer interface [polypeptide binding]; other site 998088000656 phosphorylation site [posttranslational modification] 998088000657 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088000658 ATP binding site [chemical binding]; other site 998088000659 Mg2+ binding site [ion binding]; other site 998088000660 G-X-G motif; other site 998088000661 osmolarity response regulator; Provisional; Region: ompR; PRK09468 998088000662 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088000663 active site 998088000664 phosphorylation site [posttranslational modification] 998088000665 intermolecular recognition site; other site 998088000666 dimerization interface [polypeptide binding]; other site 998088000667 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 998088000668 DNA binding site [nucleotide binding] 998088000669 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088000670 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 998088000671 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088000672 dimerization interface [polypeptide binding]; other site 998088000673 Cupin domain; Region: Cupin_2; cl09118 998088000674 DoxX; Region: DoxX; cl00976 998088000675 exonuclease V subunit gamma; Provisional; Region: recC; PRK11069 998088000676 exodeoxyribonuclease V, gamma subunit; Region: recC; TIGR01450 998088000677 exonuclease V subunit beta; Provisional; Region: recB; PRK10876 998088000678 UvrD/REP helicase; Region: UvrD-helicase; cl14126 998088000679 UvrD/REP helicase; Region: UvrD-helicase; cl14126 998088000680 exonuclease V subunit alpha; Provisional; Region: recD; PRK10875 998088000681 Putative ATPase (DUF699); Region: DUF699; pfam05127 998088000682 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088000683 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 998088000684 PAS fold; Region: PAS_3; pfam08447 998088000685 putative active site [active] 998088000686 heme pocket [chemical binding]; other site 998088000687 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088000688 metal binding site [ion binding]; metal-binding site 998088000689 active site 998088000690 I-site; other site 998088000691 Surface antigen; Region: Surface_Ag_2; cl01155 998088000692 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 998088000693 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 998088000694 transcriptional regulator protein; Region: phnR; TIGR03337 998088000695 DNA-binding site [nucleotide binding]; DNA binding site 998088000696 UTRA domain; Region: UTRA; cl01230 998088000697 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088000698 Sulfatase; Region: Sulfatase; cl10460 998088000699 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cl00427 998088000700 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088000701 dimer interface [polypeptide binding]; other site 998088000702 conserved gate region; other site 998088000703 putative PBP binding loops; other site 998088000704 ABC-ATPase subunit interface; other site 998088000705 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 998088000706 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088000707 Walker A/P-loop; other site 998088000708 ATP binding site [chemical binding]; other site 998088000709 Q-loop/lid; other site 998088000710 ABC transporter signature motif; other site 998088000711 Walker B; other site 998088000712 D-loop; other site 998088000713 H-loop/switch region; other site 998088000714 TOBE domain; Region: TOBE_2; cl01440 998088000715 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 998088000716 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 998088000717 Cache domain; Region: Cache_1; pfam02743 998088000718 regulatory protein CsrD; Provisional; Region: PRK11059 998088000719 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088000720 metal binding site [ion binding]; metal-binding site 998088000721 active site 998088000722 I-site; other site 998088000723 Predicted membrane protein (DUF2214); Region: DUF2214; cl01427 998088000724 EamA-like transporter family; Region: EamA; cl01037 998088000725 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 998088000726 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins...; Region: GST_N_GTT1_like; cd03046 998088000727 putative C-terminal domain interface [polypeptide binding]; other site 998088000728 putative GSH binding site (G-site) [chemical binding]; other site 998088000729 putative dimer interface [polypeptide binding]; other site 998088000730 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 998088000731 N-terminal domain interface [polypeptide binding]; other site 998088000732 dimer interface [polypeptide binding]; other site 998088000733 substrate binding pocket (H-site) [chemical binding]; other site 998088000734 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK06084 998088000735 CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of...; Region: CGS_like; cd00614 998088000736 homodimer interface [polypeptide binding]; other site 998088000737 substrate-cofactor binding pocket; other site 998088000738 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088000739 catalytic residue [active] 998088000740 transcriptional regulator SgrR; Provisional; Region: PRK13626 998088000741 Sugar transport-related sRNA regulator N-term; Region: SgrR_N; pfam12793 998088000742 The C-terminal solute-binding domain of DNA-binding transcriptional regulator SgrR is related to the ABC-type oligopeptide-binding proteins and contains the type 2 periplasmic-binding fold; Region: PBP2_SgrR_like; cd08507 998088000743 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 998088000744 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 998088000745 dimer interface [polypeptide binding]; other site 998088000746 active site 998088000747 heme binding site [chemical binding]; other site 998088000748 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 998088000749 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active...; Region: 4HBT; cd00586 998088000750 active site 998088000751 Proteobacterial lipase chaperone protein; Region: Lipase_chap; cl02224 998088000752 Predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold [General function prediction only]; Region: LipA; COG1075 998088000753 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 998088000754 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 998088000755 active site 998088000756 HIGH motif; other site 998088000757 dimer interface [polypeptide binding]; other site 998088000758 KMSKS motif; other site 998088000759 transcriptional regulator MalT; Provisional; Region: PRK04841 998088000760 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors...; Region: LuxR_C_like; cd06170 998088000761 DNA binding residues [nucleotide binding] 998088000762 dimerization interface [polypeptide binding]; other site 998088000763 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088000764 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088000765 substrate binding pocket [chemical binding]; other site 998088000766 membrane-bound complex binding site; other site 998088000767 hinge residues; other site 998088000768 Protein of unknown function (DUF1496); Region: DUF1496; pfam07383 998088000769 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 998088000770 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 998088000771 tetramer interface [polypeptide binding]; other site 998088000772 heme binding pocket [chemical binding]; other site 998088000773 NADPH binding site [chemical binding]; other site 998088000774 putative acetyltransferase YhhY; Provisional; Region: PRK10140 998088000775 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088000776 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 998088000777 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088000778 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; cl01368 998088000779 Ca2+/Na+ antiporter [Inorganic ion transport and metabolism]; Region: ECM27; COG0530 998088000780 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 998088000781 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 998088000782 HIGH motif; other site 998088000783 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 998088000784 active site 998088000785 KMSKS motif; other site 998088000786 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 998088000787 tRNA binding surface [nucleotide binding]; other site 998088000788 anticodon binding site; other site 998088000789 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 998088000790 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; cl01106 998088000791 multifunctional aminopeptidase A; Provisional; Region: PRK00913 998088000792 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein...; Region: Peptidase_M17; cd00433 998088000793 interface (dimer of trimers) [polypeptide binding]; other site 998088000794 Substrate-binding/catalytic site; other site 998088000795 Zn-binding sites [ion binding]; other site 998088000796 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 998088000797 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 998088000798 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 998088000799 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 998088000800 RDD family; Region: RDD; cl00746 998088000801 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 998088000802 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 998088000803 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 998088000804 N-terminal plug; other site 998088000805 ligand-binding site [chemical binding]; other site 998088000806 Predicted O-acyltransferase [General function prediction only]; Region: COG3274; cl00792 998088000807 Acyltransferase family; Region: Acyl_transf_3; pfam01757 998088000808 Beta-lactamase; Region: Beta-lactamase; cl01009 998088000809 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 998088000810 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 998088000811 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 998088000812 EamA-like transporter family; Region: EamA; cl01037 998088000813 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 998088000814 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface...; Region: gram_neg_porins; cd00342 998088000815 trimer interface [polypeptide binding]; other site 998088000816 eyelet of channel; other site 998088000817 Fructose-1,6-bisphosphatase/sedoheptulose 1,7-bisphosphatase and related proteins [Carbohydrate transport and metabolism]; Region: GlpX; COG1494 998088000818 Bacterial fructose-1,6-bisphosphatase, glpX-encoded. A dimeric enzyme dependent on Mg(2+). glpX-encoded FPBase (FBPase class II) differs from other members of the inositol-phosphatase superfamily by permutation of secondary structure elements. The core...; Region: FBPase_glpX; cd01516 998088000819 putative active site [active] 998088000820 Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]; Region: HemY; COG3071 998088000821 HemY protein N-terminus; Region: HemY_N; pfam07219 998088000822 HemX; Region: HemX; cl14667 998088000823 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 998088000824 Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations...; Region: HemD; cd06578 998088000825 active site 998088000826 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 998088000827 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cd00494 998088000828 domain interfaces; other site 998088000829 active site 998088000830 adenylate cyclase; Provisional; Region: cyaA; PRK09450 998088000831 Adenylate cyclase NT domain; Region: Adenyl_cycl_N; pfam12633 998088000832 Adenylate cyclase, class-I; Region: Adenylate_cycl; pfam01295 998088000833 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 998088000834 Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate in...; Region: Frataxin; cd00503 998088000835 putative iron binding site [ion binding]; other site 998088000836 diaminopimelate decarboxylase; Region: lysA; TIGR01048 998088000837 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 998088000838 active site 998088000839 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 998088000840 substrate binding site [chemical binding]; other site 998088000841 catalytic residues [active] 998088000842 dimer interface [polypeptide binding]; other site 998088000843 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 998088000844 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 998088000845 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 998088000846 Protein of unknown function, DUF484; Region: DUF484; cl01228 998088000847 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 998088000848 N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid...; Region: INT_XerDC; cd00798 998088000849 Int/Topo IB signature motif; other site 998088000850 active site 998088000851 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 998088000852 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cd01427 998088000853 motif II; other site 998088000854 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 998088000855 Mechanosensitive ion channel; Region: MS_channel; pfam00924 998088000856 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 998088000857 ligand binding site [chemical binding]; other site 998088000858 flexible hinge region; other site 998088000859 Peptidase C26; Region: Peptidase_C26; pfam07722 998088000860 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 998088000861 catalytic triad [active] 998088000862 Protein of unknown function (DUF615); Region: DUF615; cl01147 998088000863 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 998088000864 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 998088000865 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Validated; Region: PRK09369 998088000866 UDP-N-acetylglucosamine enolpyruvyl transferase catalyzes enolpyruvyl transfer as part of the first step in the biosynthesis of peptidoglycan, a component of the bacterial cell wall. The reaction is phosphoenolpyruvate + UDP-N-acetyl-D-glucosamine =...; Region: UdpNAET; cd01555 998088000867 hinge; other site 998088000868 active site 998088000869 BolA-like protein; Region: BolA; cl00386 998088000870 Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors; Region: STAS; cl00604 998088000871 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; cl01074 998088000872 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 998088000873 mce related protein; Region: MCE; pfam02470 998088000874 Domain of unknown function DUF140; Region: DUF140; cl00510 998088000875 putative ABC transporter ATP-binding protein YrbF; Provisional; Region: PRK11831 998088000876 ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex...; Region: ABC_Org_Solvent_Resistant; cd03261 998088000877 Walker A/P-loop; other site 998088000878 ATP binding site [chemical binding]; other site 998088000879 Q-loop/lid; other site 998088000880 ABC transporter signature motif; other site 998088000881 Walker B; other site 998088000882 D-loop; other site 998088000883 H-loop/switch region; other site 998088000884 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 998088000885 KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose 5-...; Region: SIS_Kpsf; cd05014 998088000886 putative active site [active] 998088000887 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with KpsF/GutQ domains in the API [A5P (D-arabinose 5-phosphate) isomerase] protein. These APIs catalyze the conversion of the pentose pathway...; Region: CBS_pair_KpsF_GutQ_assoc; cd04604 998088000888 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 998088000889 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 998088000890 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 998088000891 OstA-like protein; Region: OstA; cl00844 998088000892 lipopolysaccharide ABC transporter ATP-binding protein; Provisional; Region: PRK10895 998088000893 The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids. The genes yhbG and yhbN are located in a single operon and may function together in...; Region: ABC_YhbG; cd03218 998088000894 Walker A/P-loop; other site 998088000895 ATP binding site [chemical binding]; other site 998088000896 Q-loop/lid; other site 998088000897 ABC transporter signature motif; other site 998088000898 Walker B; other site 998088000899 D-loop; other site 998088000900 H-loop/switch region; other site 998088000901 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 998088000902 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 998088000903 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 998088000904 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 998088000905 RaiA ('ribosome-associated inhibitor A', also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site...; Region: RaiA; cd00552 998088000906 30S subunit binding site; other site 998088000907 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 998088000908 active site 998088000909 phosphorylation site [posttranslational modification] 998088000910 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088000911 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 998088000912 dimerization domain swap beta strand [polypeptide binding]; other site 998088000913 regulatory protein interface [polypeptide binding]; other site 998088000914 active site 998088000915 regulatory phosphorylation site [posttranslational modification]; other site 998088000916 Transcriptional antiterminator [Transcription]; Region: BglG; COG3711 998088000917 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088000918 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088000919 PRD domain; Region: PRD; pfam00874 998088000920 PTS_IIB_bgl_like: the PTS (phosphotransferase system) IIB domain of a family of sensory systems composed of a membrane-bound sugar-sensor (similar to BglF) and a transcription antiterminator (similar to BglG) which regulate expression of genes involved...; Region: PTS_IIB_bgl_like; cd05568 998088000921 P-loop; other site 998088000922 active site 998088000923 phosphorylation site [posttranslational modification] 998088000924 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 998088000925 active site 998088000926 phosphorylation site [posttranslational modification] 998088000927 Protein of unknown function (DUF1341); Region: DUF1341; cl06211 998088000928 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 998088000929 probable amidohydrolase EF_0837/AHA_3915; Region: EF_0837; TIGR03583 998088000930 Metallo-dependent hydrolases, subgroup B is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_B; cd01307 998088000931 active site 998088000932 conserved hypothetical protein EF_0833/AHA_3914; Region: EF_0833; TIGR03579 998088000933 conserved hypothetical protein EF_0832/AHA_3913; Region: EF_0832; TIGR03580 998088000934 conserved hypothetical protein EF_0831/AHA_3912; Region: EF_0831; TIGR03578 998088000935 conserved hypothetical protein EF_0830/AHA_3911; Region: EF_0830; TIGR03577 998088000936 PRD domain protein EF_0829/AHA_3910; Region: EF_0829; TIGR03582 998088000937 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 998088000938 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic...; Region: Tryp_SPc; cl00149 998088000939 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-...; Region: PDZ_serine_protease; cd00987 998088000940 protein binding site [polypeptide binding]; other site 998088000941 serine endoprotease; Provisional; Region: PRK10942 998088000942 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic...; Region: Tryp_SPc; cl00149 998088000943 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-...; Region: PDZ_serine_protease; cd00987 998088000944 protein binding site [polypeptide binding]; other site 998088000945 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-...; Region: PDZ_serine_protease; cd00987 998088000946 Protein of unknown function (DUF1043); Region: DUF1043; cl11473 998088000947 AFG1-like ATPase; Region: AFG1_ATPase; pfam03969 998088000948 Ribosomal protein L13. Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the...; Region: Ribosomal_L13; cd00392 998088000949 23S rRNA interface [nucleotide binding]; other site 998088000950 L3 interface [polypeptide binding]; other site 998088000951 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 998088000952 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 998088000953 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 998088000954 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including...; Region: Rieske_cytochrome_bc1; cd03470 998088000955 [2Fe-2S] cluster binding site [ion binding]; other site 998088000956 cytochrome b; Provisional; Region: CYTB; MTH00145 998088000957 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria...; Region: Cytochrome_b_N; cd00284 998088000958 Qi binding site; other site 998088000959 intrachain domain interface; other site 998088000960 interchain domain interface [polypeptide binding]; other site 998088000961 heme bH binding site [chemical binding]; other site 998088000962 heme bL binding site [chemical binding]; other site 998088000963 Qo binding site; other site 998088000964 Cytochrome b(C-terminus)/b6/petD: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria...; Region: cytochrome_b_C; cl00193 998088000965 interchain domain interface [polypeptide binding]; other site 998088000966 intrachain domain interface; other site 998088000967 Qi binding site; other site 998088000968 Qo binding site; other site 998088000969 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 998088000970 stringent starvation protein A; Provisional; Region: sspA; PRK09481 998088000971 GST_N family, Stringent starvation protein A (SspA) subfamily; SspA is a RNA polymerase (RNAP)-associated protein required for the lytic development of phage P1 and for stationary phase-induced acid tolerance of E. coli. It is implicated in survival...; Region: GST_N_SspA; cd03059 998088000972 C-terminal domain interface [polypeptide binding]; other site 998088000973 putative GSH binding site (G-site) [chemical binding]; other site 998088000974 dimer interface [polypeptide binding]; other site 998088000975 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 998088000976 dimer interface [polypeptide binding]; other site 998088000977 N-terminal domain interface [polypeptide binding]; other site 998088000978 Stringent starvation protein B; Region: SspB; cl01120 998088000979 BON domain; Region: BON; cl02771 998088000980 BON domain; Region: BON; cl02771 998088000981 Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of...; Region: SIS_GmhA; cd05006 998088000982 dimer interface [polypeptide binding]; other site 998088000983 active site 998088000984 Uncharacterised protein family UPF0102; Region: UPF0102; cl00516 998088000985 LppC putative lipoprotein; Region: LppC; pfam04348 998088000986 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 998088000987 putative ligand binding site [chemical binding]; other site 998088000988 Predicted methyltransferases [General function prediction only]; Region: COG0313 998088000989 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 998088000990 cell division protein MraZ; Reviewed; Region: PRK00326 998088000991 MraZ protein; Region: MraZ; pfam02381 998088000992 MraZ protein; Region: MraZ; pfam02381 998088000993 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 998088000994 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 998088000995 Septum formation initiator; Region: DivIC; cl11433 998088000996 peptidoglycan synthase FtsI; Provisional; Region: PRK15105 998088000997 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 998088000998 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 998088000999 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 998088001000 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 998088001001 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 998088001002 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 998088001003 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Reviewed; Region: murF; PRK10773 998088001004 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 998088001005 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 998088001006 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 998088001007 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 998088001008 Phospho-N-acetylmuramoyl-pentapeptide-transferase (mraY) is an enzyme responsible for the formation of the first lipid intermediate in the synthesis of bacterial cell wall peptidoglycan. It catalyzes the formation of undecaprenyl-pyrophosphoryl-N-...; Region: GT_MraY; cd06852 998088001009 Mg++ binding site [ion binding]; other site 998088001010 putative catalytic motif [active] 998088001011 putative substrate binding site [chemical binding]; other site 998088001012 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03806 998088001013 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 998088001014 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 998088001015 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 998088001016 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 998088001017 MurG is an N-acetylglucosaminyltransferase, the last enzyme involved in the intracellular phase of peptidoglycan biosynthesis. It transfers N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the C4 hydroxyl of a lipid-linked N-acetylmuramoyl...; Region: GT1_MurG; cd03785 998088001018 active site 998088001019 homodimer interface [polypeptide binding]; other site 998088001020 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 998088001021 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 998088001022 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 998088001023 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 998088001024 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 998088001025 Cell division protein FtsQ; Region: FtsQ; pfam03799 998088001026 cell division protein FtsA; Reviewed; Region: ftsA; PRK09472 998088001027 Cell division protein FtsA; Region: FtsA; cl11496 998088001028 Cell division protein FtsA; Region: FtsA; cl11496 998088001029 cell division protein FtsZ; Validated; Region: PRK09330 998088001030 FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum...; Region: FtsZ_type1; cd02201 998088001031 nucleotide binding site [chemical binding]; other site 998088001032 SulA interaction site; other site 998088001033 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 998088001034 Peptidase family M23; Region: Peptidase_M23; pfam01551 998088001035 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 998088001036 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088001037 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 998088001038 hypothetical protein; Provisional; Region: PRK00183 998088001039 SEC-C motif; Region: SEC-C; cl12132 998088001040 The MutT pyrophosphohydrolase is a prototypical Nudix hydrolase that catalyzes the hydrolysis of nucleoside and deoxynucleoside triphosphates (NTPs and dNTPs) by substitution at a beta-phosphorus to yield a nucleotide monophosphate (NMP) and inorganic...; Region: MutT_pyrophosphohydrolase; cd03425 998088001041 active site 998088001042 8-oxo-dGMP binding site [chemical binding]; other site 998088001043 nudix motif; other site 998088001044 metal binding site [ion binding]; metal-binding site 998088001045 Domain of unknown function (DUF329); Region: DUF329; cl01144 998088001046 Protein of unknown function (DUF1342); Region: DUF1342; cl01892 998088001047 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 998088001048 Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis; Region: DPCK; cd02022 998088001049 CoA-binding site [chemical binding]; other site 998088001050 Type II secretory pathway, prepilin signal peptidase PulO and related peptidases [Cell motility and secretion / Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: PulO; COG1989 998088001051 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 998088001052 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 998088001053 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 998088001054 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 998088001055 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 998088001056 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 998088001057 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 998088001058 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 998088001059 Walker A motif; other site 998088001060 ATP binding site [chemical binding]; other site 998088001061 Walker B motif; other site 998088001062 quinolinate phosphoribosyltransferase; Validated; Region: PRK09016 998088001063 Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with 5-...; Region: QPRTase; cd01572 998088001064 dimerization interface [polypeptide binding]; other site 998088001065 active site 998088001066 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 998088001067 catalytic motif [active] 998088001068 Catalytic residue [active] 998088001069 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 998088001070 substrate binding site [chemical binding]; other site 998088001071 amidase catalytic site [active] 998088001072 Zn binding residues [ion binding]; other site 998088001073 transcriptional regulator PdhR; Reviewed; Region: pdhR; PRK09464 998088001074 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 998088001075 DNA-binding site [nucleotide binding]; DNA binding site 998088001076 FCD domain; Region: FCD; cl11656 998088001077 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 998088001078 Thiamine pyrophosphate (TPP) family, E1 of E. coli PDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDC). PDC catalyzes the oxidative...; Region: TPP_E1_EcPDC_like; cd02017 998088001079 dimer interface [polypeptide binding]; other site 998088001080 TPP-binding site [chemical binding]; other site 998088001081 pyruvate dehydrogenase dihydrolipoyltransacetylase; Validated; Region: aceF; PRK11854 998088001082 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 998088001083 E3 interaction surface; other site 998088001084 lipoyl attachment site [posttranslational modification]; other site 998088001085 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 998088001086 E3 interaction surface; other site 998088001087 lipoyl attachment site [posttranslational modification]; other site 998088001088 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 998088001089 E3 interaction surface; other site 998088001090 lipoyl attachment site [posttranslational modification]; other site 998088001091 e3 binding domain; Region: E3_binding; pfam02817 998088001092 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 998088001093 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 998088001094 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088001095 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088001096 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 998088001097 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 998088001098 GAF domain; Region: GAF; cl00853 998088001099 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088001100 metal binding site [ion binding]; metal-binding site 998088001101 active site 998088001102 I-site; other site 998088001103 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088001104 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088001105 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088001106 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 998088001107 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 998088001108 active site 998088001109 nucleophile elbow; other site 998088001110 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 998088001111 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 998088001112 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 998088001113 Aconitase B swivel domain. Aconitate hydratase B is involved in energy metabolism as part of the TCA cycle. It catalyses the formation of cis-aconitate from citrate. This is the aconitase swivel domain, which undergoes swivelling conformational change...; Region: AcnB_Swivel; cd01576 998088001114 substrate binding site [chemical binding]; other site 998088001115 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 998088001116 substrate binding site [chemical binding]; other site 998088001117 ligand binding site [chemical binding]; other site 998088001118 Predicted signal transduction protein containing sensor and EAL domains [Signal transduction mechanisms]; Region: COG4943 998088001119 CSS motif domain associated with EAL; Region: CSS-motif; pfam12792 998088001120 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 998088001121 FAD-linked oxidoreductase; Region: bact_FAD_ox; TIGR01679 998088001122 FAD binding domain; Region: FAD_binding_4; pfam01565 998088001123 D-arabinono-1,4-lactone oxidase; Region: ALO; cl04370 998088001124 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 998088001125 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 998088001126 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 998088001127 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 998088001128 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 998088001129 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 998088001130 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088001131 putative transporter; Provisional; Region: PRK10504 998088001132 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088001133 putative substrate translocation pore; other site 998088001134 YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting homologs, YbaK, ProX, and PrdX. The primary function of INS is to hydrolyze...; Region: YbaK_like; cd04332 998088001135 putative deacylase active site [active] 998088001136 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after...; Region: HPPK; cd00483 998088001137 catalytic center binding site [active] 998088001138 ATP binding site [chemical binding]; other site 998088001139 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines...; Region: DHNA_DHNTPE; cd00534 998088001140 homooctamer interface [polypeptide binding]; other site 998088001141 active site 998088001142 Domain of unknown function (DUF205); Region: DUF205; cl00410 998088001143 Nucleoside recognition; Region: Gate; cl00486 998088001144 Protein of unknown function (DUF1706); Region: DUF1706; cl01748 998088001145 argininosuccinate lyase; Provisional; Region: PRK04833 998088001146 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 998088001147 active sites [active] 998088001148 tetramer interface [polypeptide binding]; other site 998088001149 Argininosuccinate synthase [Amino acid transport and metabolism]; Region: ArgG; COG0137 998088001150 Argininosuccinate synthase. The Argininosuccinate synthase is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate . In...; Region: Argininosuccinate_Synthase; cd01999 998088001151 ANP binding site [chemical binding]; other site 998088001152 Substrate Binding Site II [chemical binding]; other site 998088001153 Substrate Binding Site I [chemical binding]; other site 998088001154 ornithine carbamoyltransferase; Provisional; Region: PRK14805 998088001155 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 998088001156 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088001157 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 998088001158 nucleotide binding site [chemical binding]; other site 998088001159 substrate binding site [chemical binding]; other site 998088001160 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 998088001161 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088001162 Semialdehyde dehydrogenase, dimerisation domain; Region: Semialdhyde_dhC; pfam02774 998088001163 acetylornithine deacetylase; Provisional; Region: PRK05111 998088001164 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 998088001165 metal binding site [ion binding]; metal-binding site 998088001166 putative dimer interface [polypeptide binding]; other site 998088001167 Phosphoenolpyruvate carboxylase [Carbohydrate transport and metabolism; Energy production and conversion]; Region: COG1892; cl14656 998088001168 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 998088001169 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088001170 metal binding site [ion binding]; metal-binding site 998088001171 active site 998088001172 I-site; other site 998088001173 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 998088001174 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 998088001175 Exopolysaccharide synthesis, ExoD; Region: ExoD; cl01617 998088001176 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088001177 metal binding site [ion binding]; metal-binding site 998088001178 active site 998088001179 I-site; other site 998088001180 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 998088001181 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 998088001182 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 998088001183 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088001184 Coenzyme A binding pocket [chemical binding]; other site 998088001185 Nitrous oxide-stimulated promoter; Region: YgbA_NO; cl08119 998088001186 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 998088001187 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 998088001188 X-Prolyl Aminopeptidase 2. E.C. 3.4.11.9. Also known as X-Pro aminopeptidase, proline aminopeptidase, aminopeptidase P, and aminoacylproline aminopeptidase. Catalyses release of any N-terminal amino acid, including proline, that is linked with proline...; Region: APP; cd01085 998088001189 active site 998088001190 Transcriptional regulators [Transcription]; Region: GntR; COG1802 998088001191 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 998088001192 DNA-binding site [nucleotide binding]; DNA binding site 998088001193 FCD domain; Region: FCD; cl11656 998088001194 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_ATP; cd00484 998088001195 active site 998088001196 substrate-binding site [chemical binding]; other site 998088001197 metal-binding site [ion binding] 998088001198 ATP binding site [chemical binding]; other site 998088001199 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 998088001200 Heat shock protein 33 (Hsp33): Cytosolic protein that acts as a molecular chaperone under oxidative conditions. In normal (reducing) cytosolic conditions, four conserved Cys residues are coordinated by a Zn ion. Under oxidative stress (such as heat...; Region: Hsp33; cd00498 998088001201 dimerization interface [polypeptide binding]; other site 998088001202 domain crossover interface; other site 998088001203 redox-dependent activation switch; other site 998088001204 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 998088001205 RNA binding surface [nucleotide binding]; other site 998088001206 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or...; Region: Nudix_Hydrolase; cl00447 998088001207 nudix motif; other site 998088001208 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cl00474 998088001209 Domain of unknown function DUF20; Region: UPF0118; cl00465 998088001210 putative transposase OrfB; Reviewed; Region: PHA02517 998088001211 DNA-binding transcriptional regulator DhaR; Provisional; Region: PRK11388 998088001212 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088001213 Walker A motif; other site 998088001214 ATP binding site [chemical binding]; other site 998088001215 Walker B motif; other site 998088001216 arginine finger; other site 998088001217 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 998088001218 Glycerol dehydrogenases (GlyDH) catalyzes oxidation of glycerol to dihydroxyacetone in glycerol dissmilation; Region: GlyDH; cd08170 998088001219 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 998088001220 dimer interface [polypeptide binding]; other site 998088001221 active site 998088001222 metal binding site [ion binding]; metal-binding site 998088001223 PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_man; cl00025 998088001224 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 998088001225 dimerization domain swap beta strand [polypeptide binding]; other site 998088001226 regulatory protein interface [polypeptide binding]; other site 998088001227 active site 998088001228 regulatory phosphorylation site [posttranslational modification]; other site 998088001229 DAK2 domain; Region: Dak2; cl03685 998088001230 dihydroxyacetone kinase subunit DhaK; Provisional; Region: PRK14481; cl10557 998088001231 Dak1 domain; Region: Dak1; pfam02733 998088001232 Sulfate transporter family; Region: Sulfate_transp; cl00967 998088001233 Permease family; Region: Xan_ur_permease; pfam00860 998088001234 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein...; Region: CSP_CDS; cd04458 998088001235 DNA-binding site [nucleotide binding]; DNA binding site 998088001236 RNA-binding motif; other site 998088001237 YjbD family (DUF3811); Region: DUF3811; cl08125 998088001238 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 998088001239 Cation efflux family; Region: Cation_efflux; cl00316 998088001240 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088001241 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088001242 substrate binding pocket [chemical binding]; other site 998088001243 membrane-bound complex binding site; other site 998088001244 hinge residues; other site 998088001245 SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date...; Region: SSB_OBF; cd04496 998088001246 dimer interface [polypeptide binding]; other site 998088001247 ssDNA binding site [nucleotide binding]; other site 998088001248 tetramer (dimer of dimers) interface [polypeptide binding]; other site 998088001249 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 998088001250 DNA-binding transcriptional regulator CsgD; Provisional; Region: PRK10100 998088001251 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors...; Region: LuxR_C_like; cd06170 998088001252 DNA binding residues [nucleotide binding] 998088001253 dimerization interface [polypeptide binding]; other site 998088001254 Curli assembly protein CsgE; Region: CsgE; cl08115 998088001255 Curli production assembly/transport component CsgF; Region: Tafi-CsgF; cl08082 998088001256 Curli production assembly/transport component CsgG; Region: CsgG; cl00639 998088001257 curlin minor subunit CsgB; Provisional; Region: csgB; PRK10101 998088001258 curlin minor subunit CsgB; Provisional; Region: csgB; PRK10101 998088001259 curlin minor subunit CsgB; Provisional; Region: csgB; PRK10101 998088001260 curlin minor subunit CsgB; Provisional; Region: csgB; PRK10101 998088001261 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 998088001262 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 998088001263 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 998088001264 The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_II; cd03271 998088001265 CHASE4 domain; Region: CHASE4; cl01308 998088001266 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088001267 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088001268 metal binding site [ion binding]; metal-binding site 998088001269 active site 998088001270 I-site; other site 998088001271 Surface antigen; Region: Surface_Ag_2; cl01155 998088001272 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 998088001273 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088001274 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088001275 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088001276 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 998088001277 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088001278 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088001279 Methylenetetrahydrofolate reductase; Region: MTHFR; pfam02219 998088001280 Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine...; Region: MTHFR; cd00537 998088001281 FAD binding site [chemical binding]; other site 998088001282 Protein of unknown function (DUF3103); Region: DUF3103; pfam11301 998088001283 Sulfate transporter family; Region: Sulfate_transp; cl00967 998088001284 Uncharacterized protein involved in benzoate metabolism [Secondary metabolites biosynthesis, transport, and catabolism]; Region: BenE; COG3135 998088001285 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 998088001286 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 998088001287 non-specific DNA binding site [nucleotide binding]; other site 998088001288 salt bridge; other site 998088001289 sequence-specific DNA binding site [nucleotide binding]; other site 998088001290 Cupin domain; Region: Cupin_2; cl09118 998088001291 NnrS protein; Region: NnrS; cl01258 998088001292 Protein of unknown function (DUF496); Region: DUF496; cl09955 998088001293 Membrane carboxypeptidase (penicillin-binding protein) [Cell envelope biogenesis, outer membrane]; Region: MrcB; COG0744 998088001294 Transglycosylase; Region: Transgly; cl07896 998088001295 sugar phosphate phosphatase; Provisional; Region: PRK10513 998088001296 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cd01427 998088001297 active site 998088001298 motif I; other site 998088001299 motif II; other site 998088001300 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 998088001301 Protein of unknown function (DUF342); Region: DUF342; pfam03961 998088001302 hypothetical protein; Provisional; Region: PRK03673 998088001303 Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of...; Region: cinA; cd00885 998088001304 putative MPT binding site; other site 998088001305 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 998088001306 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088001307 Zn2+ binding site [ion binding]; other site 998088001308 Mg2+ binding site [ion binding]; other site 998088001309 Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS); Region: GATase1_HTS; cd03131 998088001310 proposed active site lysine [active] 998088001311 conserved cys residue [active] 998088001312 Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (; Region: PTPc; cl00053 998088001313 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 998088001314 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088001315 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 998088001316 Sulfatase; Region: Sulfatase; cl10460 998088001317 Protein of unknown function (DUF2442); Region: DUF2442; pfam10387 998088001318 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 998088001319 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 998088001320 N-terminal plug; other site 998088001321 ligand-binding site [chemical binding]; other site 998088001322 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 998088001323 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 998088001324 Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) [Coenzyme metabolism / Translation, ribosomal structure and biogenesis]; Region: RimK; COG0189 998088001325 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 998088001326 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 998088001327 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088001328 Protein of unknown function (DUF3624); Region: DUF3624; pfam12292 998088001329 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088001330 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 998088001331 NAD(P) binding site [chemical binding]; other site 998088001332 active site 998088001333 Peptidase family C69; Region: Peptidase_C69; cl01920 998088001334 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 998088001335 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 998088001336 dimer interface [polypeptide binding]; other site 998088001337 active site 998088001338 metal binding site [ion binding]; metal-binding site 998088001339 Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to...; Region: MGS; cd01422 998088001340 active site 998088001341 dimer interfaces [polypeptide binding]; other site 998088001342 catalytic residues [active] 998088001343 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 998088001344 Ferritin-like domain; Region: Ferritin; pfam00210 998088001345 heme binding site [chemical binding]; other site 998088001346 ferroxidase pore; other site 998088001347 ferroxidase diiron center [ion binding]; other site 998088001348 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 998088001349 Transcriptional activator HlyU; Region: HlyU; cl02273 998088001350 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088001351 NAD(P) binding site [chemical binding]; other site 998088001352 active site 998088001353 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 998088001354 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088001355 active site 998088001356 phosphorylation site [posttranslational modification] 998088001357 intermolecular recognition site; other site 998088001358 dimerization interface [polypeptide binding]; other site 998088001359 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 998088001360 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 998088001361 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 998088001362 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 998088001363 putative active site [active] 998088001364 Collagenase; Region: Peptidase_M9; pfam01752 998088001365 Fimbrial protein; Region: Fimbrial; cl01416 998088001366 pilin outer membrane usher protein SafC; Provisional; Region: PRK15223; cl14650 998088001367 Fimbrial Usher protein; Region: Usher; pfam00577 998088001368 putative periplasmic fimbrial chaperone protein SteC; Provisional; Region: PRK15274 998088001369 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 998088001370 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 998088001371 Fimbrial protein; Region: Fimbrial; cl01416 998088001372 Fimbrial protein; Region: Fimbrial; cl01416 998088001373 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 998088001374 DNA binding site [nucleotide binding] 998088001375 O-succinylbenzoic acid--CoA ligase; Provisional; Region: PRK09029 998088001376 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 998088001377 O-succinylbenzoate synthase; Provisional; Region: PRK05105 998088001378 o-Succinylbenzoate synthase (OSBS) catalyzes the conversion of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to 4-(2'-carboxyphenyl)-4-oxobutyrate (o-succinylbenzoate or OSB), a reaction in the menaquinone biosynthetic pathway...; Region: OSBS; cd03320 998088001379 active site 998088001380 dihydroxynaphthoic acid synthetase; Validated; Region: PRK07396 998088001381 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase...; Region: crotonase-like; cd06558 998088001382 substrate binding site [chemical binding]; other site 998088001383 oxyanion hole (OAH) forming residues; other site 998088001384 trimer interface [polypeptide binding]; other site 998088001385 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase; Region: menH_SHCHC; TIGR03695 998088001386 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase; Validated; Region: PRK07449 998088001387 Pyrimidine (PYR) binding domain of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1- carboxylate synthase (MenD) and related proteins; Region: TPP_PYR_MenD; cd07037 998088001388 dimer interface [polypeptide binding]; other site 998088001389 tetramer interface [polypeptide binding]; other site 998088001390 PYR/PP interface [polypeptide binding]; other site 998088001391 TPP binding site [chemical binding]; other site 998088001392 TPP-binding module; composed of proteins similar to Escherichia coli 2-succinyl-6-hydroxyl-2,4-cyclohexadiene-1-carboxylic acid (SHCHC) synthase (also called MenD). SHCHC synthase plays a key role in the menaquinone biosynthetic pathway, converting...; Region: TPP_SHCHC_synthase; cd02009 998088001393 TPP-binding site; other site 998088001394 Isochorismate synthase [Coenzyme metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: MenF; COG1169 998088001395 chorismate binding enzyme; Region: Chorismate_bind; cl10555 998088001396 UbiA prenyltransferase family; Region: UbiA; cl00337 998088001397 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 998088001398 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 998088001399 Flagellin N-methylase; Region: FliB; cl00497 998088001400 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 998088001401 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (...; Region: DEADc; cd00268 998088001402 ATP binding site [chemical binding]; other site 998088001403 Mg++ binding site [ion binding]; other site 998088001404 motif III; other site 998088001405 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 998088001406 nucleotide binding region [chemical binding]; other site 998088001407 ATP-binding site [chemical binding]; other site 998088001408 DbpA RNA binding domain; Region: DbpA; pfam03880 998088001409 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 998088001410 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 998088001411 Nucleoside recognition; Region: Gate; cl00486 998088001412 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 998088001413 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; cl00868 998088001414 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; cl00727 998088001415 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 998088001416 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 998088001417 Mechanosensitive ion channel; Region: MS_channel; pfam00924 998088001418 DNA-J related protein; Region: DNAJ_related; pfam12339 998088001419 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of...; Region: DnaJ; cd06257 998088001420 HSP70 interaction site [polypeptide binding]; other site 998088001421 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 998088001422 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 998088001423 Mannitol repressor; Region: MtlR; cl11450 998088001424 mannitol-1-phosphate 5-dehydrogenase; Provisional; Region: PRK02318 998088001425 Mannitol dehydrogenase Rossmann domain; Region: Mannitol_dh; pfam01232 998088001426 Mannitol dehydrogenase C-terminal domain; Region: Mannitol_dh_C; pfam08125 998088001427 PTS system mannitol-specific transporter subunit IICBA; Provisional; Region: PRK15083 998088001428 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 998088001429 PTS_IIB_mannitol: subunit IIB of enzyme II (EII) of the mannitol-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is a mannitol-specific permease with two cytoplasmic domains (IIA and IIB) and a...; Region: PTS_IIB_mannitol; cd05567 998088001430 active site 998088001431 P-loop; other site 998088001432 phosphorylation site [posttranslational modification] 998088001433 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 998088001434 active site 998088001435 phosphorylation site [posttranslational modification] 998088001436 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 998088001437 putative acyl-acceptor binding pocket; other site 998088001438 bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase; Provisional; Region: PRK11316 998088001439 RfaE encodes a bifunctional ADP-heptose synthase involved in the biosynthesis of the lipopolysaccharide (LPS) core precursor ADP-L-glycero-D-manno-heptose. LPS plays an important role in maintaining the structural integrity of the bacterial outer...; Region: RfaE_like; cd01172 998088001440 putative ribose interaction site [chemical binding]; other site 998088001441 putative ADP binding site [chemical binding]; other site 998088001442 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 998088001443 active site 998088001444 nucleotide binding site [chemical binding]; other site 998088001445 HIGH motif; other site 998088001446 KMSKS motif; other site 998088001447 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 998088001448 Outer membrane efflux protein; Region: OEP; pfam02321 998088001449 Outer membrane efflux protein; Region: OEP; pfam02321 998088001450 ADP-ribose pyrophosphatase NudF; Provisional; Region: nudF; PRK10729 998088001451 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as...; Region: ADPRase_NUDT5; cd03424 998088001452 dimer interface [polypeptide binding]; other site 998088001453 ADP-ribose binding site [chemical binding]; other site 998088001454 active site 998088001455 nudix motif; other site 998088001456 metal binding site [ion binding]; metal-binding site 998088001457 Protein of unknown function (DUF1249); Region: DUF1249; cl01223 998088001458 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 998088001459 Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; Region: MPP_GpdQ; cd07402 998088001460 active site 998088001461 metal binding site [ion binding]; metal-binding site 998088001462 hexamer interface [polypeptide binding]; other site 998088001463 Uncharacterised protein family (UPF0227); Region: UPF0227; cl14886 998088001464 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 998088001465 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088001466 ATP binding site [chemical binding]; other site 998088001467 Mg2+ binding site [ion binding]; other site 998088001468 G-X-G motif; other site 998088001469 TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to the B subunits of E. coli DNA gyrase and E. coli Topoisomerase IV which are...; Region: TopoII_Trans_DNA_gyrase; cd00822 998088001470 anchoring element; other site 998088001471 dimer interface [polypeptide binding]; other site 998088001472 ATP binding site [chemical binding]; other site 998088001473 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 998088001474 active site 998088001475 metal binding site [ion binding]; metal-binding site 998088001476 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 998088001477 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 998088001478 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in...; Region: TOP4c; cd00187 998088001479 CAP-like domain; other site 998088001480 Active site [active] 998088001481 primary dimer interface [polypeptide binding]; other site 998088001482 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088001483 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088001484 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 998088001485 putative effector binding pocket; other site 998088001486 dimerization interface [polypeptide binding]; other site 998088001487 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088001488 Major Facilitator Superfamily; Region: MFS_1; pfam07690 998088001489 putative substrate translocation pore; other site 998088001490 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cl11420 998088001491 amino acid/peptide transporter (Peptide:H+ symporter), bacterial; Region: yjdL_sub1_fam; TIGR00924 998088001492 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of...; Region: DnaJ; cd06257 998088001493 HSP70 interaction site [polypeptide binding]; other site 998088001494 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 998088001495 classical (c) SDRs; Region: SDR_c; cd05233 998088001496 NAD(P) binding site [chemical binding]; other site 998088001497 active site 998088001498 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 998088001499 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088001500 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088001501 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088001502 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 998088001503 TlpA-like family, suppressor for copper sensitivity D protein (ScsD) and actinobacterial DsbE homolog subfamily; composed of ScsD, the DsbE homolog of Mycobacterium tuberculosis (MtbDsbE) and similar proteins, all containing a redox-active CXXC motif...; Region: TlpA_like_ScsD_MtbDsbE; cd03011 998088001504 catalytic residues [active] 998088001505 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 998088001506 DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a...; Region: DsbA_Com1_like; cd03023 998088001507 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 998088001508 catalytic residues [active] 998088001509 Uncharacterized protein predicted to be involved in C-type cytochrome biogenesis [Posttranslational modification, protein turnover, chaperones / Energy production and conversion]; Region: COG4233 998088001510 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl00515 998088001511 DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD...; Region: DsbDgamma; cd02953 998088001512 DsbD alpha interface [polypeptide binding]; other site 998088001513 catalytic residues [active] 998088001514 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 998088001515 putative acyl-acceptor binding pocket; other site 998088001516 phage shock protein A; Region: phageshock_pspA; TIGR02977 998088001517 phage shock protein PspA; Provisional; Region: PRK10698 998088001518 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 998088001519 GIY-YIG motif/motif A; other site 998088001520 putative active site [active] 998088001521 putative metal binding site [ion binding]; other site 998088001522 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088001523 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088001524 substrate binding pocket [chemical binding]; other site 998088001525 membrane-bound complex binding site; other site 998088001526 hinge residues; other site 998088001527 Predicted permeases [General function prediction only]; Region: RarD; COG2962 998088001528 EamA-like transporter family; Region: EamA; cl01037 998088001529 Uncharacterized subfamily of Uracil-DNA glycosylases; Region: UDG_like_1; cd10033 998088001530 putative uracil binding site [chemical binding]; other site 998088001531 putative active site [active] 998088001532 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 998088001533 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 998088001534 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088001535 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088001536 dimerization interface [polypeptide binding]; other site 998088001537 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist...; Region: TM_ABC_iron-siderophores_like; cd06550 998088001538 ABC-ATPase subunit interface; other site 998088001539 dimer interface [polypeptide binding]; other site 998088001540 putative PBP binding regions; other site 998088001541 high-affinity zinc transporter ATPase; Reviewed; Region: znuC; PRK09544 998088001542 ABC component of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of iron-...; Region: ABC_Metallic_Cations; cd03235 998088001543 Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism; Region: ZnuA; cd01019 998088001544 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 998088001545 metal binding site [ion binding]; metal-binding site 998088001546 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 998088001547 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 998088001548 putative peptidase; Provisional; Region: PRK11649 998088001549 Peptidase family M23; Region: Peptidase_M23; pfam01551 998088001550 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088001551 Protein of unknown function (DUF416); Region: DUF416; cl01166 998088001552 Transcriptional regulators [Transcription]; Region: MarR; COG1846 998088001553 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088001554 BCCT family transporter; Region: BCCT; cl00569 998088001555 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 998088001556 Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins; Region: NT_Pol-beta-like; cl11966 998088001557 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 998088001558 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 998088001559 adenine DNA glycosylase; Provisional; Region: PRK10880 998088001560 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 998088001561 minor groove reading motif; other site 998088001562 helix-hairpin-helix signature motif; other site 998088001563 substrate binding pocket [chemical binding]; other site 998088001564 active site 998088001565 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 998088001566 DNA glycosylase (MutY in bacteria and hMYH in humans) is responsible for repairing misread A*oxoG residues to C*G by removing the inappropriately paired adenine base from the DNA backbone. It belongs to the Nudix hydrolase superfamily and is important...; Region: DNA_Glycosylase_C; cd03431 998088001567 DNA binding and oxoG recognition site [nucleotide binding] 998088001568 Bacterial Fe(2+) trafficking; Region: Iron_traffic; cl01104 998088001569 Domain of unknown function (DUF3393); Region: DUF3393; pfam11873 998088001570 murein transglycosylase C; Provisional; Region: mltC; PRK11671 998088001571 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 998088001572 N-acetyl-D-glucosamine binding site [chemical binding]; other site 998088001573 catalytic residue [active] 998088001574 Bacterial OB fold (BOF) protein; Region: BOF; cl01196 998088001575 Fatty acyltransferase-like subfamily of the SGNH hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its...; Region: fatty_acyltransferase_like; cd01846 998088001576 active site 998088001577 catalytic triad [active] 998088001578 oxyanion hole [active] 998088001579 outer membrane protein A; Reviewed; Region: PRK10808 998088001580 Surface antigen; Region: Surface_Ag_2; cl01155 998088001581 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088001582 ligand binding site [chemical binding]; other site 998088001583 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088001584 metal binding site [ion binding]; metal-binding site 998088001585 active site 998088001586 I-site; other site 998088001587 exoribonuclease R; Provisional; Region: PRK11642 998088001588 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain...; Region: S1_like; cl09927 998088001589 RNB domain; Region: RNB; pfam00773 998088001590 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an...; Region: S1_RNase_R; cd04471 998088001591 RNA binding site [nucleotide binding]; other site 998088001592 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 998088001593 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 998088001594 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 998088001595 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 998088001596 ligand binding site [chemical binding]; other site 998088001597 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088001598 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (...; Region: DEADc; cd00268 998088001599 DEAD-like helicases superfamily; Region: DEXDc; smart00487 998088001600 ATP binding site [chemical binding]; other site 998088001601 Mg++ binding site [ion binding]; other site 998088001602 motif III; other site 998088001603 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 998088001604 nucleotide binding region [chemical binding]; other site 998088001605 ATP-binding site [chemical binding]; other site 998088001606 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 998088001607 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cd02440 998088001608 S-adenosylmethionine binding site [chemical binding]; other site 998088001609 Branched-chain amino acid transport protein; Region: Branch_AA_trans; cl00547 998088001610 Branched-chain amino acid transport protein; Region: Branch_AA_trans; cl00547 998088001611 Predicted inhibitor of MCP methylation, homolog of CheC [Cell motility and secretion]; Region: COG1406 998088001612 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 998088001613 metal binding site 2 [ion binding]; metal-binding site 998088001614 putative DNA binding helix; other site 998088001615 metal binding site 1 [ion binding]; metal-binding site 998088001616 dimer interface [polypeptide binding]; other site 998088001617 structural Zn2+ binding site [ion binding]; other site 998088001618 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 998088001619 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and...; Region: DUS_like_FMN; cd02801 998088001620 FMN binding site [chemical binding]; other site 998088001621 active site 998088001622 catalytic residues [active] 998088001623 substrate binding site [chemical binding]; other site 998088001624 nitrogen fixation negative regulator NifL; Region: nifL_nitrog; TIGR02938 998088001625 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 998088001626 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088001627 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088001628 oligopeptide ABC transporter substrate-binding protein OppA; Provisional; Region: PRK15104 998088001629 The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; Region: PBP2_OppA; cd08504 998088001630 peptide binding site [polypeptide binding]; other site 998088001631 Putative ParB-like nuclease; Region: ParBc_2; cl01772 998088001632 Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and...; Region: LbH_XAT; cd03349 998088001633 trimer interface [polypeptide binding]; other site 998088001634 active site 998088001635 substrate binding site [chemical binding]; other site 998088001636 CoA binding site [chemical binding]; other site 998088001637 Protein of unknown function (DUF2753); Region: DUF2753; pfam10952 998088001638 enoyl-CoA hydratase; Provisional; Region: PRK06688 998088001639 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase...; Region: crotonase-like; cd06558 998088001640 substrate binding site [chemical binding]; other site 998088001641 oxyanion hole (OAH) forming residues; other site 998088001642 trimer interface [polypeptide binding]; other site 998088001643 Protein of unknown function (DUF461); Region: DUF461; cl01071 998088001644 3-ketodihydrosphingosine reductase (KDSR) and related proteins, classical (c) SDR; Region: KDSR-like_SDR_c; cd08939 998088001645 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 998088001646 putative NAD(P) binding site [chemical binding]; other site 998088001647 homotetramer interface [polypeptide binding]; other site 998088001648 active site 998088001649 homodimer interface [polypeptide binding]; other site 998088001650 prolyl-tRNA synthetase; Provisional; Region: PRK09194 998088001651 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation...; Region: ProRS_core_prok; cd00779 998088001652 dimer interface [polypeptide binding]; other site 998088001653 motif 1; other site 998088001654 active site 998088001655 motif 2; other site 998088001656 INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and single-...; Region: ProRS-INS; cd04334 998088001657 putative deacylase active site [active] 998088001658 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 998088001659 active site 998088001660 motif 3; other site 998088001661 ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-...; Region: ProRS_anticodon_short; cd00861 998088001662 anticodon binding site; other site 998088001663 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 998088001664 TRAM domain; Region: TRAM; cl01282 998088001665 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cd02440 998088001666 S-adenosylmethionine binding site [chemical binding]; other site 998088001667 Protein of unknown function (DUF330); Region: DUF330; cl01135 998088001668 paraquat-inducible protein B; Provisional; Region: PRK10807 998088001669 mce related protein; Region: MCE; pfam02470 998088001670 mce related protein; Region: MCE; pfam02470 998088001671 paraquat-inducible membrane protein A; Provisional; Region: PRK15103 998088001672 Paraquat-inducible protein A; Region: PqiA; pfam04403 998088001673 Paraquat-inducible protein A; Region: PqiA; pfam04403 998088001674 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members...; Region: Sm_like; cl00259 998088001675 Sm1 motif; other site 998088001676 D3 - B interaction site; other site 998088001677 D1 - D2 interaction site; other site 998088001678 Hfq - Hfq interaction site; other site 998088001679 RNA binding pocket [nucleotide binding]; other site 998088001680 Sm2 motif; other site 998088001681 beta-phosphoglucomutase family hydrolase; Region: PGMB-YQAB-SF; TIGR02009 998088001682 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cd01427 998088001683 motif II; other site 998088001684 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 998088001685 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 998088001686 GAF domain; Region: GAF; cl00853 998088001687 two component system sensor kinase SsrA; Provisional; Region: PRK15347 998088001688 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088001689 metal binding site [ion binding]; metal-binding site 998088001690 active site 998088001691 I-site; other site 998088001692 exoribonuclease II; Provisional; Region: PRK05054 998088001693 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain...; Region: S1_like; cl09927 998088001694 RNB domain; Region: RNB; pfam00773 998088001695 chromosome replication initiation inhibitor protein; Validated; Region: PRK03635 998088001696 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088001697 The C-terminal substrate binding domain of LysR-type transcriptional regulator, ArgP (IciA), for arginine exporter (ArgO); contains the type 2 periplasmic binding fold; Region: PBP2_IciA_ArgP; cd08428 998088001698 putative dimerization interface [polypeptide binding]; other site 998088001699 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088001700 DNA-binding transcriptional activator SdiA; Provisional; Region: PRK10188 998088001701 Autoinducer binding domain; Region: Autoind_bind; pfam03472 998088001702 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors...; Region: LuxR_C_like; cd06170 998088001703 DNA binding residues [nucleotide binding] 998088001704 dimerization interface [polypeptide binding]; other site 998088001705 LysE type translocator; Region: LysE; cl00565 998088001706 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 998088001707 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088001708 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088001709 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 998088001710 RuvA N terminal domain; Region: RuvA_N; pfam01330 998088001711 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 998088001712 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 998088001713 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088001714 Walker A motif; other site 998088001715 ATP binding site [chemical binding]; other site 998088001716 Walker B motif; other site 998088001717 arginine finger; other site 998088001718 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 998088001719 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 998088001720 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 998088001721 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 998088001722 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 998088001723 Membrane bound YbgT-like protein; Region: YbgT_YccB; cl02039 998088001724 Cyd operon protein YbgE (Cyd_oper_YbgE); Region: Cyd_oper_YbgE; cl11451 998088001725 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active...; Region: 4HBT; cd00586 998088001726 active site 998088001727 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 998088001728 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 998088001729 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 998088001730 Gram-negative bacterial tonB protein; Region: TonB; cl10048 998088001731 translocation protein TolB; Provisional; Region: tolB; PRK04792 998088001732 TolB amino-terminal domain; Region: TolB_N; pfam04052 998088001733 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 998088001734 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 998088001735 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 998088001736 peptidoglycan-associated outer membrane lipoprotein; Provisional; Region: PRK10802 998088001737 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088001738 ligand binding site [chemical binding]; other site 998088001739 tol-pal system protein YbgF; Provisional; Region: PRK10803 998088001740 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi...; Region: TPR; cd00189 998088001741 binding surface 998088001742 TPR motif; other site 998088001743 Sodium:neurotransmitter symporter family; Region: SNF; cl11976 998088001744 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cl15306 998088001745 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088001746 substrate binding pocket [chemical binding]; other site 998088001747 membrane-bound complex binding site; other site 998088001748 hinge residues; other site 998088001749 Sodium:neurotransmitter symporter family; Region: SNF; cl11976 998088001750 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 998088001751 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl01206 998088001752 Protein of unknown function (DUF2799); Region: DUF2799; pfam10973 998088001753 pyridoxal phosphate (PLP) phosphatase; Provisional; Region: PRK10530 998088001754 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cd01427 998088001755 active site 998088001756 motif I; other site 998088001757 motif II; other site 998088001758 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 998088001759 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 998088001760 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088001761 putative substrate translocation pore; other site 998088001762 Predicted transcriptional regulator [Transcription]; Region: COG2345 998088001763 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 998088001764 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088001765 Bacterial OB fold (BOF) protein; Region: BOF; cl01196 998088001766 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_19; cd04678 998088001767 nudix motif; other site 998088001768 Chromate transporter; Region: Chromate_transp; pfam02417 998088001769 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 998088001770 Chromate transporter; Region: Chromate_transp; pfam02417 998088001771 SelR domain; Region: SelR; cl00369 998088001772 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 998088001773 E or 'early' set of sugar utilizing enzymes which may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end; Region: E_set; cl09101 998088001774 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 998088001775 The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-...; Region: GH31; cl11402 998088001776 catalytic site [active] 998088001777 glycogen branching enzyme; Provisional; Region: PRK05402 998088001778 Glycogen branching enzyme N-terminus domain. Glycogen branching enzyme (AKA 1,4 alpha glucan branching enzyme) catalyzes the formation of alpha-1,6 branch points in either glycogen or starch by cleavage of the alpha-1,4 glucosidic linkage yielding a...; Region: Glycogen_branching_enzyme_N_term; cd02855 998088001779 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 998088001780 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; cl02706 998088001781 4-alpha-glucanotransferase; Provisional; Region: malQ; PRK11052 998088001782 4-alpha-glucanotransferase; Region: Glyco_hydro_77; cl00711 998088001783 glyceraldehyde-3-phosphate dehydrogenase A; Provisional; Region: gapA; PRK15425 998088001784 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; cl15267 998088001785 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 998088001786 Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism]; Region: GalM; COG2017 998088001787 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 998088001788 active site 998088001789 phosphate binding residues; other site 998088001790 catalytic residues [active] 998088001791 Quinolinate synthetase A protein; Region: NadA; cl00420 998088001792 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088001793 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088001794 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088001795 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 998088001796 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 998088001797 Band_7_stomatin_like: A subgroup of the band 7 domain of flotillin (reggie) like proteins similar to stomatin and podicin (two lipid raft-associated integral membrane proteins). Individual proteins of this band 7 domain family may cluster to form...; Region: Band_7_stomatin_like; cd03403 998088001798 siroheme synthase; Provisional; Region: cysG; PRK10637 998088001799 precorrin-2 dehydrogenase; Validated; Region: PRK06719 998088001800 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 998088001801 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 998088001802 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 998088001803 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 998088001804 Active Sites [active] 998088001805 sulfate adenylyltransferase subunit 1; Provisional; Region: cysN; PRK05124 998088001806 CysN_ATPS subfamily. CysN, together with protein CysD, form the ATP sulfurylase (ATPS) complex in some bacteria and lower eukaryotes. ATPS catalyzes the production of ATP sulfurylase (APS) and pyrophosphate (PPi) from ATP and sulfate. CysD, which...; Region: CysN_ATPS; cd04166 998088001807 CysD dimerization site [polypeptide binding]; other site 998088001808 G1 box; other site 998088001809 putative GEF interaction site [polypeptide binding]; other site 998088001810 GTP/Mg2+ binding site [chemical binding]; other site 998088001811 Switch I region; other site 998088001812 G2 box; other site 998088001813 G3 box; other site 998088001814 Switch II region; other site 998088001815 G4 box; other site 998088001816 G5 box; other site 998088001817 CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of...; Region: CysN_NodQ_II; cd03695 998088001818 TCysN_NoDQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of...; Region: CysN_NoDQ_III; cd04095 998088001819 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088001820 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088001821 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088001822 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088001823 Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically 'activated' sulfate form important for the assimilation...; Region: APSK; cd02027 998088001824 ligand-binding site [chemical binding]; other site 998088001825 FRG domain; Region: FRG; cl07460 998088001826 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 998088001827 PAS fold; Region: PAS_3; pfam08447 998088001828 putative active site [active] 998088001829 heme pocket [chemical binding]; other site 998088001830 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088001831 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088001832 Protein of unknown function (DUF2806); Region: DUF2806; cl12560 998088001833 Protein of unknown function (DUF3299); Region: DUF3299; cl01387 998088001834 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 998088001835 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 998088001836 FtsX-like permease family; Region: FtsX; pfam02687 998088001837 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 998088001838 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 998088001839 Walker A/P-loop; other site 998088001840 ATP binding site [chemical binding]; other site 998088001841 Q-loop/lid; other site 998088001842 ABC transporter signature motif; other site 998088001843 Walker B; other site 998088001844 D-loop; other site 998088001845 H-loop/switch region; other site 998088001846 Protein of unknown function (DUF2796); Region: DUF2796; pfam10986 998088001847 Bacterial protein of unknown function (YtfJ_HI0045); Region: YtfJ_HI0045; cl01158 998088001848 Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers; Region: pyrophosphatase; cd00412 998088001849 dimer interface [polypeptide binding]; other site 998088001850 substrate binding site [chemical binding]; other site 998088001851 metal binding sites [ion binding]; metal-binding site 998088001852 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 998088001853 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088001854 active site 998088001855 phosphorylation site [posttranslational modification] 998088001856 intermolecular recognition site; other site 998088001857 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 998088001858 Domain of unknown function (DUF3369); Region: DUF3369; pfam11849 998088001859 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088001860 Zn2+ binding site [ion binding]; other site 998088001861 Mg2+ binding site [ion binding]; other site 998088001862 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088001863 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088001864 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 998088001865 dimerization interface [polypeptide binding]; other site 998088001866 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 998088001867 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 998088001868 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_1; cd08352 998088001869 putative metal binding site [ion binding]; other site 998088001870 penicillin-binding protein 1B; Region: PBP_1b; TIGR02071 998088001871 Transglycosylase; Region: Transgly; cl07896 998088001872 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 998088001873 ATP-dependent RNA helicase HrpB; Provisional; Region: PRK11664 998088001874 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 998088001875 ATP binding site [chemical binding]; other site 998088001876 putative Mg++ binding site [ion binding]; other site 998088001877 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 998088001878 nucleotide binding region [chemical binding]; other site 998088001879 ATP-binding site [chemical binding]; other site 998088001880 ATP-dependent helicase C-terminal; Region: HrpB_C; pfam08482 998088001881 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 998088001882 2',5' RNA ligase family; Region: 2_5_RNA_ligase; pfam02834 998088001883 RNA:NAD 2'-phosphotransferase [Translation, ribosomal structure and biogenesis]; Region: KptA; COG1859 998088001884 Sugar fermentation stimulation protein; Region: SfsA; cl00647 998088001885 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 998088001886 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 998088001887 active site 998088001888 nucleotide binding site [chemical binding]; other site 998088001889 HIGH motif; other site 998088001890 KMSKS motif; other site 998088001891 poly(A) polymerase I; Provisional; Region: pcnB; PRK11623 998088001892 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 998088001893 active site 998088001894 NTP binding site [chemical binding]; other site 998088001895 metal binding triad [ion binding]; metal-binding site 998088001896 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 998088001897 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 998088001898 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after...; Region: HPPK; cd00483 998088001899 catalytic center binding site [active] 998088001900 ATP binding site [chemical binding]; other site 998088001901 Ketopantoate hydroxymethyltransferase (KPHMT) is the first enzyme in the pantothenate biosynthesis pathway. Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate (vitamin B5), which is a...; Region: KPHMT-like; cd06557 998088001902 oligomerization interface [polypeptide binding]; other site 998088001903 active site 998088001904 metal binding site [ion binding]; metal-binding site 998088001905 pantoate--beta-alanine ligase; Region: panC; TIGR00018 998088001906 Pantoate-beta-alanine ligase; Region: PanC; cd00560 998088001907 active site 998088001908 ATP-binding site [chemical binding]; other site 998088001909 pantoate-binding site; other site 998088001910 HXXH motif; other site 998088001911 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 998088001912 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 998088001913 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 998088001914 active site residue [active] 998088001915 exonuclease subunit SbcC; Provisional; Region: PRK10246 998088001916 ABC-2 type transporter; Region: ABC2_membrane; cl11417 998088001917 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 998088001918 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088001919 Walker A/P-loop; other site 998088001920 ATP binding site [chemical binding]; other site 998088001921 Q-loop/lid; other site 998088001922 ABC transporter signature motif; other site 998088001923 Walker B; other site 998088001924 D-loop; other site 998088001925 H-loop/switch region; other site 998088001926 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 998088001927 transcriptional repressor BetI; Region: betaine_BetI; TIGR03384 998088001928 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088001929 aromatic acid decarboxylase; Validated; Region: PRK05920 998088001930 Flavoprotein; Region: Flavoprotein; cl08021 998088001931 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 998088001932 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 998088001933 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 998088001934 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 998088001935 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cl00474 998088001936 UDP-glucose 4-epimerase; Region: PLN02240 998088001937 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 998088001938 NAD binding site [chemical binding]; other site 998088001939 homodimer interface [polypeptide binding]; other site 998088001940 active site 998088001941 substrate binding site [chemical binding]; other site 998088001942 HCP oxidoreductase, NADH-dependent; Provisional; Region: PRK10684 998088001943 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron...; Region: FNR_iron_sulfur_binding_1; cd06215 998088001944 FAD binding pocket [chemical binding]; other site 998088001945 FAD binding motif [chemical binding]; other site 998088001946 phosphate binding motif [ion binding]; other site 998088001947 beta-alpha-beta structure motif; other site 998088001948 NAD binding pocket [chemical binding]; other site 998088001949 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 998088001950 catalytic loop [active] 998088001951 iron binding site [ion binding]; other site 998088001952 hybrid cluster protein; Provisional; Region: PRK05290 998088001953 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved alpha-; Region: HCP_like; cl14655 998088001954 ACS interaction site; other site 998088001955 CODH interaction site; other site 998088001956 Hybrid cluster protein (HCP), formerly known as prismane, is thought to play a role in nitrogen metabolism but its specific function is unknown. HCP has three structural domains, an N-terminal alpha-helical domain, and two similar domains comprising a...; Region: HCP; cd01914 998088001957 hybrid metal cluster; other site 998088001958 Ferritin-like domain; Region: Ferritin; pfam00210 998088001959 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 998088001960 dimerization interface [polypeptide binding]; other site 998088001961 DPS ferroxidase diiron center [ion binding]; other site 998088001962 ion pore; other site 998088001963 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 998088001964 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 998088001965 amidase catalytic site [active] 998088001966 Zn binding residues [ion binding]; other site 998088001967 substrate binding site [chemical binding]; other site 998088001968 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4807 998088001969 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 998088001970 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 998088001971 hybrid sensory histidine kinase BarA; Provisional; Region: PRK11107 998088001972 Uncharacterized signal transduction histidine kinase domain (DUF2222); Region: DUF2222; pfam09984 998088001973 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088001974 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 998088001975 dimer interface [polypeptide binding]; other site 998088001976 phosphorylation site [posttranslational modification] 998088001977 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088001978 ATP binding site [chemical binding]; other site 998088001979 Mg2+ binding site [ion binding]; other site 998088001980 G-X-G motif; other site 998088001981 Uncharacterized domain of BarA-like signal transduction histidine kinases [Signal transduction mechanisms]; Region: COG4999 998088001982 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088001983 active site 998088001984 phosphorylation site [posttranslational modification] 998088001985 intermolecular recognition site; other site 998088001986 dimerization interface [polypeptide binding]; other site 998088001987 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 998088001988 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 998088001989 TRAM domain; Region: TRAM; cl01282 998088001990 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cd02440 998088001991 S-adenosylmethionine binding site [chemical binding]; other site 998088001992 (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional; Region: relA; PRK10872 998088001993 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 998088001994 synthetase active site [active] 998088001995 NTP binding site [chemical binding]; other site 998088001996 metal binding site [ion binding]; metal-binding site 998088001997 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named...; Region: TGS_RelA_SpoT; cd01668 998088001998 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 998088001999 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 998088002000 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 998088002001 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 998088002002 CTP synthetase; Validated; Region: pyrG; PRK05380 998088002003 CTP synthetase (CTPs) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer...; Region: CTGs; cd03113 998088002004 Catalytic site [active] 998088002005 Active site [active] 998088002006 UTP binding site [chemical binding]; other site 998088002007 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 998088002008 active site 998088002009 putative oxyanion hole; other site 998088002010 catalytic triad [active] 998088002011 enolase; Provisional; Region: eno; PRK00077 998088002012 Enolase: Enolases are homodimeric enzymes that catalyse the reversible dehydration of 2-phospho-D-glycerate to phosphoenolpyruvate as part of the glycolytic and gluconeogenesis pathways. The reaction is facilitated by the presence of metal ions; Region: enolase; cd03313 998088002013 dimer interface [polypeptide binding]; other site 998088002014 metal binding site [ion binding]; metal-binding site 998088002015 substrate binding pocket [chemical binding]; other site 998088002016 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 998088002017 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088002018 Protein of unknown function (DUF2971); Region: DUF2971; pfam11185 998088002019 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 998088002020 catalytic motif [active] 998088002021 Catalytic residue [active] 998088002022 Protein of unknown function (DUF1311); Region: DUF1311; cl01530 998088002023 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; cl01604 998088002024 Predicted membrane protein (DUF2061); Region: DUF2061; cl01257 998088002025 Predicted membrane protein (DUF2061); Region: DUF2061; cl01257 998088002026 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 998088002027 Protein of unknown function (DUF2390); Region: DUF2390; cl02376 998088002028 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 998088002029 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 998088002030 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 998088002031 ABC transporter; Region: ABC_tran_2; pfam12848 998088002032 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 998088002033 FOG: CBS domain [General function prediction only]; Region: COG0517 998088002034 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-...; Region: CBS_pair_24; cd04637 998088002035 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 998088002036 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 998088002037 DNA-binding site [nucleotide binding]; DNA binding site 998088002038 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 998088002039 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088002040 homodimer interface [polypeptide binding]; other site 998088002041 catalytic residue [active] 998088002042 LysE type translocator; Region: LysE; cl00565 998088002043 LysE type translocator; Region: LysE; cl00565 998088002044 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 998088002045 aspartate racemase; Region: asp_race; TIGR00035 998088002046 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088002047 putative acyl-acceptor binding pocket; other site 998088002048 Domain of unknown function (DUF386); Region: DUF386; cl01047 998088002049 Acetokinase family; Region: Acetate_kinase; cl01029 998088002050 Mechanosensitive ion channel; Region: MS_channel; pfam00924 998088002051 L,D-transpeptidase; Provisional; Region: PRK10190 998088002052 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 998088002053 putative peptidoglycan binding site; other site 998088002054 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 998088002055 Protein of unknown function (DUF535); Region: DUF535; cl01128 998088002056 Sodium:solute symporter family; Region: SSF; cl00456 998088002057 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 998088002058 Septum formation initiator; Region: DivIC; cl11433 998088002059 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 998088002060 substrate binding site [chemical binding]; other site 998088002061 dimer interface [polypeptide binding]; other site 998088002062 MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid...; Region: MECDP_synthase; cd00554 998088002063 homotrimer interaction site [polypeptide binding]; other site 998088002064 zinc binding site [ion binding]; other site 998088002065 CDP-binding sites; other site 998088002066 tRNA pseudouridine synthase D (TruD); Region: TruD; pfam01142 998088002067 PseudoU_synth_EcTruD: Pseudouridine synthase, TruD family. This group consists of bacterial pseudouridine synthases similar to Escherichia coli TruD. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to...; Region: PseudoU_synth_EcTruD; cd02575 998088002068 Permutation of conserved domain; other site 998088002069 active site 998088002070 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 998088002071 Survival protein SurE; Region: SurE; cl00448 998088002072 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 998088002073 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 998088002074 lipoprotein NlpD; Provisional; Region: nlpD; PRK10871 998088002075 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 998088002076 putative peptidoglycan binding site; other site 998088002077 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 998088002078 putative peptidoglycan binding site; other site 998088002079 Peptidase family M23; Region: Peptidase_M23; pfam01551 998088002080 RNA polymerase sigma factor RpoS; Region: rpoS_proteo; TIGR02394 998088002081 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 998088002082 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 998088002083 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 998088002084 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial...; Region: Sigma70_r4; cd06171 998088002085 DNA binding residues [nucleotide binding] 998088002086 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 998088002087 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN; cd02933 998088002088 FMN binding site [chemical binding]; other site 998088002089 active site 998088002090 substrate binding site [chemical binding]; other site 998088002091 catalytic residue [active] 998088002092 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 998088002093 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088002094 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088002095 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088002096 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 998088002097 substrate binding pocket [chemical binding]; other site 998088002098 dimerization interface [polypeptide binding]; other site 998088002099 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; cl01113 998088002100 agmatine deiminase; Region: agmatine_aguA; TIGR03380 998088002101 amidase; Validated; Region: PRK06565 998088002102 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl11426 998088002103 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl11426 998088002104 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 998088002105 helicase 45; Provisional; Region: PTZ00424 998088002106 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (...; Region: DEADc; cd00268 998088002107 ATP binding site [chemical binding]; other site 998088002108 Mg++ binding site [ion binding]; other site 998088002109 motif III; other site 998088002110 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 998088002111 nucleotide binding region [chemical binding]; other site 998088002112 ATP-binding site [chemical binding]; other site 998088002113 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088002114 metal binding site [ion binding]; metal-binding site 998088002115 active site 998088002116 I-site; other site 998088002117 Uncharacterized conserved protein [Function unknown]; Region: COG1912 998088002118 S-adenosyl-l-methionine hydroxide adenosyltransferase; Region: SAM_adeno_trans; pfam01887 998088002119 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 998088002120 Protein of unknown function (DUF1566); Region: DUF1566; pfam07603 998088002121 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 998088002122 Gamma carbonic anhydrases (CA): Carbonic anhydrases are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism, involving the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide...; Region: LbH_gamma_CA; cd00710 998088002123 trimer interface [polypeptide binding]; other site 998088002124 active site 998088002125 Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far. This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases). Plant T2 RNases are expressed during leaf...; Region: RNase_T2_prok; cd01062 998088002126 B1 nucleotide binding pocket [chemical binding]; other site 998088002127 B2 nucleotide binding pocket [chemical binding]; other site 998088002128 CAS motifs; other site 998088002129 Active site [active] 998088002130 Nitronate monooxygenase; Region: NMO; pfam03060 998088002131 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin...; Region: NPD_like; cd04730 998088002132 FMN binding site [chemical binding]; other site 998088002133 substrate binding site [chemical binding]; other site 998088002134 putative catalytic residue [active] 998088002135 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_22; cd04681 998088002136 nudix motif; other site 998088002137 AsmA family; Region: AsmA; pfam05170 998088002138 putative assembly protein; Provisional; Region: PRK10833 998088002139 Domain of unknown function (DUF3404); Region: DUF3404; pfam11884 998088002140 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cl00080 998088002141 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 998088002142 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088002143 active site 998088002144 phosphorylation site [posttranslational modification] 998088002145 intermolecular recognition site; other site 998088002146 dimerization interface [polypeptide binding]; other site 998088002147 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 998088002148 DNA binding site [nucleotide binding] 998088002149 Protein of unknown function (DUF2861); Region: DUF2861; pfam11060 998088002150 Protein of unknown function (DUF3111); Region: DUF3111; pfam11308 998088002151 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088002152 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 998088002153 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 998088002154 metal binding triad; other site 998088002155 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 998088002156 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 998088002157 metal binding triad; other site 998088002158 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 998088002159 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088002160 Coenzyme A binding pocket [chemical binding]; other site 998088002161 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088002162 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088002163 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088002164 Ion channel; Region: Ion_trans_2; cl11596 998088002165 SH3 domain-containing protein; Provisional; Region: PRK10884 998088002166 Bacterial SH3 domain; Region: SH3_3; cl02551 998088002167 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11904 998088002168 Proline dehydrogenase; Region: Pro_dh; cl03282 998088002169 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 998088002170 Glutamate binding site [chemical binding]; other site 998088002171 NAD binding site [chemical binding]; other site 998088002172 catalytic residues [active] 998088002173 NADH pyrophosphatase-like rudimentary NUDIX domain; Region: NUDIX-like; pfam09296 998088002174 NADH pyrophosphatase; Reviewed; Region: nudC; PRK00241 998088002175 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 998088002176 NADH pyrophosphatase, a member of the Nudix hydrolase superfamily, catalyzes the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for...; Region: NADH_pyrophosphatase; cd03429 998088002177 putative NADH binding site [chemical binding]; other site 998088002178 putative active site [active] 998088002179 nudix motif; other site 998088002180 putative metal binding site [ion binding]; other site 998088002181 Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This...; Region: URO-D; cd00717 998088002182 substrate binding site [chemical binding]; other site 998088002183 active site 998088002184 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 998088002185 fructokinase; Reviewed; Region: PRK09557 998088002186 erythrose 4-phosphate dehydrogenase; Provisional; Region: PRK13535 998088002187 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; cl15267 998088002188 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 998088002189 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cl00198 998088002190 substrate binding site [chemical binding]; other site 998088002191 hinge regions; other site 998088002192 ADP binding site [chemical binding]; other site 998088002193 catalytic site [active] 998088002194 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 998088002195 Class II Type A, Fructose-1,6-bisphosphate (FBP) aldolases. The enzyme catalyses the zinc-dependent, reversible aldol condensation of dihydroxyacetone phosphate with glyceraldehyde-3-phosphate to form fructose-1,6-bisphosphate. FBP aldolase is...; Region: FBP_aldolase_IIA; cd00946 998088002196 active site 998088002197 intersubunit interface [polypeptide binding]; other site 998088002198 zinc binding site [ion binding]; other site 998088002199 Na+ binding site [ion binding]; other site 998088002200 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 998088002201 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 998088002202 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088002203 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 998088002204 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 998088002205 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl00515 998088002206 DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD...; Region: DsbDgamma; cd02953 998088002207 DsbD alpha interface [polypeptide binding]; other site 998088002208 catalytic residues [active] 998088002209 CutA1 divalent ion tolerance protein; Region: CutA1; cl00584 998088002210 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 998088002211 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 998088002212 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088002213 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088002214 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 998088002215 dimerization interface [polypeptide binding]; other site 998088002216 putative global regulator; Reviewed; Region: PRK09559 998088002217 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 998088002218 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 998088002219 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088002220 domain; Region: Succ_DH_flav_C; pfam02910 998088002221 RNA polymerase sigma factor AlgU; Provisional; Region: algU; PRK11923 998088002222 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 998088002223 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial...; Region: Sigma70_r4; cd06171 998088002224 DNA binding residues [nucleotide binding] 998088002225 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 998088002226 Anti sigma-E protein RseA, C-terminal domain; Region: RseA_C; pfam03873 998088002227 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 998088002228 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; cl01178 998088002229 GTP-binding protein LepA; Provisional; Region: PRK05433 998088002230 LepA subfamily. LepA belongs to the GTPase family of and exhibits significant homology to the translation factors EF-G and EF-Tu, indicating its possible involvement in translation and association with the ribosome. LepA is ubiquitous in bacteria and...; Region: LepA; cd01890 998088002231 G1 box; other site 998088002232 putative GEF interaction site [polypeptide binding]; other site 998088002233 GTP/Mg2+ binding site [chemical binding]; other site 998088002234 Switch I region; other site 998088002235 G2 box; other site 998088002236 G3 box; other site 998088002237 Switch II region; other site 998088002238 G4 box; other site 998088002239 G5 box; other site 998088002240 lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-...; Region: lepA_II; cd03699 998088002241 lepA_C: This family represents the C-terminal region of LepA, a GTP-binding protein localized in the cytoplasmic membrane. LepA is ubiquitous in Bacteria and Eukaryota (e.g. Saccharomyces cerevisiae GUF1p), but is missing from Archaea. LepA exhibits...; Region: lepA_C; cd03709 998088002242 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 998088002243 signal peptidase I; Provisional; Region: PRK10861 998088002244 The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are...; Region: S26_SPase_I; cd06530 998088002245 Catalytic site [active] 998088002246 The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are...; Region: S26_SPase_I; cd06530 998088002247 ribonuclease III; Reviewed; Region: rnc; PRK00102 998088002248 RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-...; Region: RIBOc; cd00593 998088002249 dimerization interface [polypeptide binding]; other site 998088002250 active site 998088002251 metal binding site [ion binding]; metal-binding site 998088002252 Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase...; Region: DSRM; cd00048 998088002253 dsRNA binding site [nucleotide binding]; other site 998088002254 GTPase Era; Reviewed; Region: era; PRK00089 998088002255 Era subfamily. Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit...; Region: Era; cd04163 998088002256 G1 box; other site 998088002257 GTP/Mg2+ binding site [chemical binding]; other site 998088002258 Switch I region; other site 998088002259 G2 box; other site 998088002260 Switch II region; other site 998088002261 G3 box; other site 998088002262 G4 box; other site 998088002263 G5 box; other site 998088002264 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains...; Region: KH-I; cl00098 998088002265 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 998088002266 Recombination protein O N terminal; Region: RecO_N; pfam11967 998088002267 Recombination protein O C terminal; Region: RecO_C; pfam02565 998088002268 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in the...; Region: PNPsynthase; cd00003 998088002269 active site 998088002270 hydrophilic channel; other site 998088002271 dimerization interface [polypeptide binding]; other site 998088002272 catalytic residues [active] 998088002273 active site lid [active] 998088002274 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose...; Region: TBP_aldolase_IIB; cd00947 998088002275 intersubunit interface [polypeptide binding]; other site 998088002276 active site 998088002277 zinc binding site [ion binding]; other site 998088002278 Na+ binding site [ion binding]; other site 998088002279 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of N-acetyl-glucosamine-6-phosphate (GlcNAc-6-P) to glucosamine 6-phosphate and acetate. This is the first committed step in the biosynthetic pathway to...; Region: NagA; cd00854 998088002280 N-acetylglucosamine-6-phosphate deacetylase; Region: nagA; TIGR00221 998088002281 active site 998088002282 dimer interface [polypeptide binding]; other site 998088002283 PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_man; cd00006 998088002284 active pocket/dimerization site; other site 998088002285 active site 998088002286 phosphorylation site [posttranslational modification] 998088002287 PTS system mannose/fructose/sorbose family IID component; Region: EIID-AGA; cl01507 998088002288 PTS system sorbose-specific iic component; Region: EII-Sor; cl01506 998088002289 Mannose/sorbose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four...; Region: PTS_IIB_man; cd00001 998088002290 active site 998088002291 phosphorylation site [posttranslational modification] 998088002292 putative sugar isomerase, AgaS family; Region: agaS_fam; TIGR02815 998088002293 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_1; cd05008 998088002294 dimer interface [polypeptide binding]; other site 998088002295 active site 998088002296 AgaS-like protein. AgaS contains a SIS (Sugar ISomerase) domain which is found in many phosphosugar isomerases and phosphosugar binding proteins. AgaS is a putative isomerase in Escherichia coli. It is similar to the glucosamine-6-phosphate synthases (...; Region: SIS_AgaS_like; cd05010 998088002297 putative active site [active] 998088002298 Tagatose 6 phosphate kinase; Region: Tagatose_6_P_K; cl09211 998088002299 DNA-binding transcriptional regulator AgaR; Provisional; Region: PRK09802 998088002300 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088002301 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 998088002302 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in cysteine...; Region: CysQ; cd01638 998088002303 active site 998088002304 YCII-related domain; Region: YCII; cl00999 998088002305 Intracellular septation protein A; Region: IspA; cl01098 998088002306 Glutamate decarboxylase and related PLP-dependent proteins [Amino acid transport and metabolism]; Region: GadB; COG0076 998088002307 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 998088002308 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 998088002309 catalytic residue [active] 998088002310 Haemolysin-III related; Region: HlyIII; cl03831 998088002311 putative transporter; Validated; Region: PRK03818 998088002312 Predicted Permease Membrane Region; Region: Asp-Al_Ex; cl06061 998088002313 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088002314 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088002315 Predicted Permease Membrane Region; Region: Asp-Al_Ex; cl06061 998088002316 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 998088002317 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 998088002318 metal ion-dependent adhesion site (MIDAS); other site 998088002319 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 998088002320 PAS fold; Region: PAS_4; pfam08448 998088002321 aerobic respiration control sensor protein ArcB; Provisional; Region: PRK11091 998088002322 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088002323 metal binding site [ion binding]; metal-binding site 998088002324 active site 998088002325 I-site; other site 998088002326 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 998088002327 Protein of unknown function (DUF1260); Region: DUF1260; cl01170 998088002328 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 998088002329 Carbonic anhydrase alpha, prokaryotic-like subfamily. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon...; Region: alpha_CA_prokaryotic_like; cd03124 998088002330 active site 998088002331 zinc binding site [ion binding]; other site 998088002332 Indigoidine synthase A like protein; Region: Indigoidine_A; cl00983 998088002333 putative kinase; Provisional; Region: PRK09954 998088002334 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088002335 YeiC-like sugar kinase. Found in eukaryotes and bacteria, YeiC-like kinase is part of the ribokinase/pfkB sugar kinase superfamily. Its oligomerization state is unknown at this time; Region: YeiC_kinase_like; cd01941 998088002336 substrate binding site [chemical binding]; other site 998088002337 ATP binding site [chemical binding]; other site 998088002338 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 998088002339 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 998088002340 Ligand Binding Site [chemical binding]; other site 998088002341 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface...; Region: gram_neg_porins; cd00342 998088002342 trimer interface [polypeptide binding]; other site 998088002343 eyelet of channel; other site 998088002344 23S rRNA methyltransferase A; Provisional; Region: rrmA; PRK11088 998088002345 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 998088002346 DNA-binding transcriptional dual regulator Crp; Provisional; Region: PRK11753 998088002347 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 998088002348 ligand binding site [chemical binding]; other site 998088002349 flexible hinge region; other site 998088002350 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 998088002351 putative switch regulator; other site 998088002352 non-specific DNA interactions [nucleotide binding]; other site 998088002353 DNA binding site [nucleotide binding] 998088002354 sequence specific DNA binding site [nucleotide binding]; other site 998088002355 putative cAMP binding site [chemical binding]; other site 998088002356 OsmC-like protein; Region: OsmC; cl00767 998088002357 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; cl01604 998088002358 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088002359 Active site [active] 998088002360 Uncharacterised protein family (UPF0270); Region: UPF0270; cl01180 998088002361 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088002362 metal binding site [ion binding]; metal-binding site 998088002363 active site 998088002364 I-site; other site 998088002365 putative hydrolase; Provisional; Region: PRK10985 998088002366 Serine carboxypeptidase S28; Region: Peptidase_S28; cl15279 998088002367 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 998088002368 Response regulator receiver domain; Region: Response_reg; pfam00072 998088002369 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088002370 active site 998088002371 phosphorylation site [posttranslational modification] 998088002372 intermolecular recognition site; other site 998088002373 dimerization interface [polypeptide binding]; other site 998088002374 Probable metal-binding protein (DUF2387); Region: DUF2387; cl01410 998088002375 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 998088002376 Tim44-like domain; Region: Tim44; cl09208 998088002377 replicative DNA helicase; Provisional; Region: PRK08840 998088002378 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 998088002379 DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a...; Region: DnaB_C; cd00984 998088002380 Walker A motif; other site 998088002381 ATP binding site [chemical binding]; other site 998088002382 Walker B motif; other site 998088002383 DNA binding loops [nucleotide binding] 998088002384 alanine racemase; Reviewed; Region: alr; PRK00053 998088002385 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 998088002386 active site 998088002387 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 998088002388 substrate binding site [chemical binding]; other site 998088002389 catalytic residues [active] 998088002390 dimer interface [polypeptide binding]; other site 998088002391 Uncharacterised protein family UPF0047; Region: UPF0047; cl00439 998088002392 Type 1 glutamine amidotransferase (GATase1)-like domain found in peptidase E; Region: GAT1_Peptidase_E; cd03146 998088002393 active site pocket [active] 998088002394 oxyanion hole [active] 998088002395 catalytic triad [active] 998088002396 active site nucleophile [active] 998088002397 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 998088002398 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 998088002399 Walker A/P-loop; other site 998088002400 ATP binding site [chemical binding]; other site 998088002401 Q-loop/lid; other site 998088002402 ABC transporter signature motif; other site 998088002403 Walker B; other site 998088002404 D-loop; other site 998088002405 H-loop/switch region; other site 998088002406 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist...; Region: TM_ABC_iron-siderophores_like; cd06550 998088002407 ABC-ATPase subunit interface; other site 998088002408 dimer interface [polypeptide binding]; other site 998088002409 putative PBP binding regions; other site 998088002410 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface...; Region: TroA-like; cl00262 998088002411 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 998088002412 intersubunit interface [polypeptide binding]; other site 998088002413 ChuX-like family; Region: DUF1008; cl01509 998088002414 Putative heme iron utilization protein [Inorganic ion transport and metabolism]; Region: HugZ; COG0748 998088002415 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 998088002416 Nicotinamidase_ related amidohydrolases. Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia; Region: nicotinamidase_related; cd01014 998088002417 Isochorismatase family; Region: Isochorismatase; pfam00857 998088002418 catalytic triad [active] 998088002419 conserved cis-peptide bond; other site 998088002420 Protein of unknown function, DUF399; Region: DUF399; cl01139 998088002421 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 998088002422 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 998088002423 N-terminal plug; other site 998088002424 ligand-binding site [chemical binding]; other site 998088002425 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 998088002426 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 998088002427 Zn binding site [ion binding]; other site 998088002428 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 998088002429 Protein of unknown function (DUF2975); Region: DUF2975; pfam11188 998088002430 Sodium:solute symporter family; Region: SSF; cl00456 998088002431 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 998088002432 PAS fold; Region: PAS_7; pfam12860 998088002433 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 998088002434 dimer interface [polypeptide binding]; other site 998088002435 phosphorylation site [posttranslational modification] 998088002436 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088002437 ATP binding site [chemical binding]; other site 998088002438 Mg2+ binding site [ion binding]; other site 998088002439 G-X-G motif; other site 998088002440 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 998088002441 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088002442 active site 998088002443 phosphorylation site [posttranslational modification] 998088002444 intermolecular recognition site; other site 998088002445 dimerization interface [polypeptide binding]; other site 998088002446 Chitinase N-terminus domain. Chitinases hydrolyze the abundant natural biopolymer chitin, producing smaller chito-oligosaccharides. Chitin consists of multiple N-acetyl-D-glucosamine (NAG) residues connected via beta-1,4-glycosidic linkages and is an...; Region: Chitinase_N_term; cd02848 998088002447 Glyco_18 domain; Region: Glyco_18; smart00636 998088002448 The GH18 (glycosyl hydrolases, family 18) type II chitinases hydrolyze chitin, an abundant polymer of N-acetylglucosamine and have been identified in bacteria, fungi, insects, plants, viruses, and protozoan parasites. The structure of this domain is...; Region: GH18_chitinase; cd06548 998088002449 active site 998088002450 REJ domain; Region: REJ; pfam02010 998088002451 Chitin/cellulose binding domain. Putative carbohydrate binding domain found in many different glycosyl hydrolase enzymes. May occur in tandem arrangements; Region: ChtBD3; cl00046 998088002452 Chitin/cellulose binding domain. Putative carbohydrate binding domain found in many different glycosyl hydrolase enzymes. May occur in tandem arrangements; Region: ChtBD3; cl00046 998088002453 GAF domain; Region: GAF; cl00853 998088002454 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088002455 metal binding site [ion binding]; metal-binding site 998088002456 active site 998088002457 I-site; other site 998088002458 Chitinase N-terminus domain. Chitinases hydrolyze the abundant natural biopolymer chitin, producing smaller chito-oligosaccharides. Chitin consists of multiple N-acetyl-D-glucosamine (NAG) residues connected via beta-1,4-glycosidic linkages and is an...; Region: Chitinase_N_term; cd02848 998088002459 Glyco_18 domain; Region: Glyco_18; smart00636 998088002460 The GH18 (glycosyl hydrolases, family 18) type II chitinases hydrolyze chitin, an abundant polymer of N-acetylglucosamine and have been identified in bacteria, fungi, insects, plants, viruses, and protozoan parasites. The structure of this domain is...; Region: GH18_chitinase; cd06548 998088002461 active site 998088002462 REJ domain; Region: REJ; pfam02010 998088002463 Chitin/cellulose binding domain. Putative carbohydrate binding domain found in many different glycosyl hydrolase enzymes. May occur in tandem arrangements; Region: ChtBD3; cd00036 998088002464 chitin/cellulose binding site [chemical binding]; other site 998088002465 Chitin/cellulose binding domain. Putative carbohydrate binding domain found in many different glycosyl hydrolase enzymes. May occur in tandem arrangements; Region: ChtBD3; cd00036 998088002466 chitin/cellulose binding site [chemical binding]; other site 998088002467 Peptidase M66; Region: Peptidase_M66; pfam10462 998088002468 Chitin/cellulose binding domain. Putative carbohydrate binding domain found in many different glycosyl hydrolase enzymes. May occur in tandem arrangements; Region: ChtBD3; cd00036 998088002469 chitin/cellulose binding site [chemical binding]; other site 998088002470 Chitin/cellulose binding domain. Putative carbohydrate binding domain found in many different glycosyl hydrolase enzymes. May occur in tandem arrangements; Region: ChtBD3; cd00036 998088002471 chitin/cellulose binding site [chemical binding]; other site 998088002472 Chitin/cellulose binding domain. Putative carbohydrate binding domain found in many different glycosyl hydrolase enzymes. May occur in tandem arrangements; Region: ChtBD3; cl00046 998088002473 Uncharacterized protein contain chitin-binding domain type 3 [General function prediction only]; Region: COG3979 998088002474 Glycoside hydrolase family 19 chitinase domain. Chitinases are enzymes that catalyze the hydrolysis of the beta-1,4-N-acetyl-D-glucosamine linkages in chitin polymers. Family 19 chitinases are found primarily in plants (classes I, III, and IV), but...; Region: chitinase_glyco_hydro_19; cd00325 998088002475 putative sugar binding site [chemical binding]; other site 998088002476 catalytic residues [active] 998088002477 N-acetylglucosamine-binding protein A; Reviewed; Region: PRK13211 998088002478 Chitin/cellulose binding domain. Putative carbohydrate binding domain found in many different glycosyl hydrolase enzymes. May occur in tandem arrangements; Region: ChtBD3; cl00046 998088002479 YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate...; Region: YhcR_OBF_like; cd04486 998088002480 generic binding surface II; other site 998088002481 generic binding surface I; other site 998088002482 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 998088002483 putative catalytic site [active] 998088002484 putative metal binding site [ion binding]; other site 998088002485 putative phosphate binding site [ion binding]; other site 998088002486 N-acetylglucosamine-binding protein A; Reviewed; Region: PRK13211 998088002487 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 998088002488 Chitinase [Carbohydrate transport and metabolism]; Region: ChiA; COG3325 998088002489 The GH18 (glycosyl hydrolases, family 18) type II chitinases hydrolyze chitin, an abundant polymer of N-acetylglucosamine and have been identified in bacteria, fungi, insects, plants, viruses, and protozoan parasites. The structure of this domain is...; Region: GH18_chitinase; cd06548 998088002490 active site 998088002491 The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have...; Region: GH18_chitinase-like; cl10447 998088002492 Chitinase C; Region: ChiC; pfam06483 998088002493 Chitin/cellulose binding domain. Putative carbohydrate binding domain found in many different glycosyl hydrolase enzymes. May occur in tandem arrangements; Region: ChtBD3; cl00046 998088002494 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 998088002495 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 998088002496 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088002497 active site 998088002498 phosphorylation site [posttranslational modification] 998088002499 intermolecular recognition site; other site 998088002500 dimerization interface [polypeptide binding]; other site 998088002501 Lysophospholipase L1-like subgroup of SGNH-hydrolases. The best characterized member in this family is TesA, an E. coli periplasmic protein with thioesterase, esterase, arylesterase, protease and lysophospholipase activity; Region: Lysophospholipase_L1_like; cd01822 998088002502 active site 998088002503 catalytic triad [active] 998088002504 oxyanion hole [active] 998088002505 switch loop; other site 998088002506 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 998088002507 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 998088002508 Walker A/P-loop; other site 998088002509 ATP binding site [chemical binding]; other site 998088002510 Q-loop/lid; other site 998088002511 ABC transporter signature motif; other site 998088002512 Walker B; other site 998088002513 D-loop; other site 998088002514 H-loop/switch region; other site 998088002515 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 998088002516 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 998088002517 FtsX-like permease family; Region: FtsX; pfam02687 998088002518 atypical (a) SDRs, subgroup 8; Region: SDR_a8; cd05242 998088002519 TIGR01777 family protein; Region: yfcH 998088002520 putative NAD(P) binding site [chemical binding]; other site 998088002521 putative active site [active] 998088002522 Predicted signal transduction protein containing sensor and EAL domains [Signal transduction mechanisms]; Region: COG4943 998088002523 CSS motif domain associated with EAL; Region: CSS-motif; pfam12792 998088002524 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 998088002525 aspartate aminotransferase; Provisional; Region: PRK08361 998088002526 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 998088002527 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088002528 homodimer interface [polypeptide binding]; other site 998088002529 catalytic residue [active] 998088002530 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 998088002531 Protein with unknown function (DUF469); Region: DUF469; cl01237 998088002532 Glutaminase; Region: Glutaminase; cl00907 998088002533 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 998088002534 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 998088002535 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 998088002536 active site residue [active] 998088002537 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue; Region: TST_Repeat_2; cd01449 998088002538 active site residue [active] 998088002539 Bacterial protein of unknown function (DUF903); Region: DUF903; pfam06004 998088002540 Protein of unknown function (DUF2541); Region: DUF2541; cl08090 998088002541 MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea...; Region: MogA_MoaB; cd00886 998088002542 MPT binding site; other site 998088002543 trimer interface [polypeptide binding]; other site 998088002544 Protein of unknown function (DUF3135); Region: DUF3135; pfam11333 998088002545 Uncharacterized conserved protein [Function unknown]; Region: COG2966 998088002546 Protein of unknown function (DUF1212); Region: DUF1212; cl01118 998088002547 Protein of unknown function (DUF1212); Region: DUF1212; cl01118 998088002548 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5,10-...; Region: DHFR; cd00209 998088002549 folate binding site [chemical binding]; other site 998088002550 NADP+ binding site [chemical binding]; other site 998088002551 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 998088002552 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 998088002553 Active Sites [active] 998088002554 sulfite reductase subunit beta; Provisional; Region: PRK13504 998088002555 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 998088002556 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 998088002557 sulfite reductase [NADPH] flavoprotein, alpha-component; Region: cysJ; TIGR01931 998088002558 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 998088002559 Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ...; Region: SiR; cd06199 998088002560 FAD binding pocket [chemical binding]; other site 998088002561 FAD binding motif [chemical binding]; other site 998088002562 catalytic residues [active] 998088002563 NAD binding pocket [chemical binding]; other site 998088002564 phosphate binding motif [ion binding]; other site 998088002565 beta-alpha-beta structure motif; other site 998088002566 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 998088002567 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 998088002568 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 998088002569 LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-...; Region: LysRS_N; cd04322 998088002570 dimer interface [polypeptide binding]; other site 998088002571 putative anticodon binding site; other site 998088002572 Lys_tRNA synthetase (LysRS) class II core domain. Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three...; Region: LysRS_core; cd00775 998088002573 motif 1; other site 998088002574 active site 998088002575 motif 2; other site 998088002576 motif 3; other site 998088002577 peptide chain release factor 2; Provisional; Region: PRK08787 998088002578 RF-1 domain; Region: RF-1; cl02875 998088002579 RF-1 domain; Region: RF-1; cl02875 998088002580 Cache domain; Region: Cache_1; pfam02743 998088002581 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 998088002582 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cd06225 998088002583 dimerization interface [polypeptide binding]; other site 998088002584 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088002585 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088002586 sodium--glutamate symport carrier (gltS); Region: gltS; TIGR00210 998088002587 Asparaginase (amidohydrolase): Asparaginases are tetrameric enzymes that catalyze the hydrolysis of asparagine to aspartic acid and ammonia. In bacteria, there are two classes of amidohydrolases, one highly specific for asparagine and localised to the...; Region: Asparaginase; cl00216 998088002588 active site/substrate binding site [active] 998088002589 tetramer interface [polypeptide binding]; other site 998088002590 Protein of unknown function (DUF1315); Region: DUF1315; cl01215 998088002591 glyceraldehyde-3-phosphate dehydrogenase; Reviewed; Region: PRK08289 998088002592 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; cl15267 998088002593 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 998088002594 Protein of unknown function (DUF2989); Region: DUF2989; pfam11207 998088002595 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or...; Region: Nudix_Hydrolase; cl00447 998088002596 nudix motif; other site 998088002597 lipoyl synthase; Provisional; Region: PRK05481 998088002598 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster...; Region: Radical_SAM; cd01335 998088002599 FeS/SAM binding site; other site 998088002600 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 998088002601 Protein of unknown function (DUF493); Region: DUF493; cl01102 998088002602 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 998088002603 Beta-lactamase; Region: Beta-lactamase; cl01009 998088002604 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; cl06814 998088002605 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 998088002606 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 998088002607 Sporulation related domain; Region: SPOR; cl10051 998088002608 lytic murein transglycosylase; Region: MltB_2; TIGR02283 998088002609 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 998088002610 N-acetyl-D-glucosamine binding site [chemical binding]; other site 998088002611 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 998088002612 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 998088002613 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 998088002614 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 998088002615 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; cl00679 998088002616 Domain of unknown function DUF143; Region: DUF143; cl00519 998088002617 Nicotinic acid mononucleotide adenylyltransferase [Coenzyme metabolism]; Region: NadD; COG1057 998088002618 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 998088002619 active site 998088002620 (T/H)XGH motif; other site 998088002621 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 998088002622 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 998088002623 Lipopolysaccharide-assembly; Region: LptE; cl01125 998088002624 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 998088002625 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 998088002626 HIGH motif; other site 998088002627 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 998088002628 active site 998088002629 KMSKS motif; other site 998088002630 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 998088002631 tRNA binding surface [nucleotide binding]; other site 998088002632 hypothetical protein; Provisional; Region: PRK11032 998088002633 Protein of unknown function (DUF1451); Region: DUF1451; pfam07295 998088002634 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 998088002635 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 998088002636 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 998088002637 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 998088002638 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 998088002639 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 998088002640 N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid...; Region: INT_XerDC; cd00798 998088002641 Int/Topo IB signature motif; other site 998088002642 active site 998088002643 Cache domain; Region: Cache_1; pfam02743 998088002644 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088002645 metal binding site [ion binding]; metal-binding site 998088002646 active site 998088002647 I-site; other site 998088002648 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 998088002649 protein disulfide isomerase II DsbC; Provisional; Region: PRK10877 998088002650 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide...; Region: DsbA_DsbC_DsbG; cd03020 998088002651 dimerization domain [polypeptide binding]; other site 998088002652 dimer interface [polypeptide binding]; other site 998088002653 catalytic residues [active] 998088002654 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 998088002655 DHH family; Region: DHH; pfam01368 998088002656 DHHA1 domain; Region: DHHA1; pfam02272 998088002657 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 998088002658 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 998088002659 putative active site [active] 998088002660 catalytic triad [active] 998088002661 putative dimer interface [polypeptide binding]; other site 998088002662 magnesium/cobalt efflux protein CorC; Provisional; Region: PRK15094 998088002663 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in...; Region: CBS_pair_CorC_HlyC_assoc; cd04590 998088002664 Transporter associated domain; Region: CorC_HlyC; cl08393 998088002665 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 998088002666 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 998088002667 PhoH-like protein; Region: PhoH; cl12134 998088002668 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 998088002669 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 998088002670 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster...; Region: Radical_SAM; cd01335 998088002671 FeS/SAM binding site; other site 998088002672 TRAM domain; Region: TRAM; cl01282 998088002673 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088002674 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Reviewed; Region: ubiF; PRK08020 998088002675 Isochorismatase family; Region: Isochorismatase; pfam00857 998088002676 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cd00431 998088002677 catalytic triad [active] 998088002678 conserved cis-peptide bond; other site 998088002679 PAS domain S-box; Region: sensory_box; TIGR00229 998088002680 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088002681 metal binding site [ion binding]; metal-binding site 998088002682 active site 998088002683 I-site; other site 998088002684 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088002685 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088002686 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 998088002687 dimerization interface [polypeptide binding]; other site 998088002688 substrate binding pocket [chemical binding]; other site 998088002689 beta-phosphoglucomutase family hydrolase; Region: PGMB-YQAB-SF; TIGR02009 998088002690 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cd01427 998088002691 active site 998088002692 motif I; other site 998088002693 motif II; other site 998088002694 Nitroreductase-like family 4. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_4; cd02140 998088002695 dimer interface [polypeptide binding]; other site 998088002696 FMN binding site [chemical binding]; other site 998088002697 glycerate dehydrogenase; Provisional; Region: PRK06487 998088002698 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088002699 Protein of unknown function (DUF3530); Region: DUF3530; pfam12048 998088002700 elongation factor P; Validated; Region: PRK00529 998088002701 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 998088002702 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-...; Region: S1_EF-P_repeat_1; cd04470 998088002703 RNA binding site [nucleotide binding]; other site 998088002704 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-...; Region: S1_EF-P_repeat_2; cd05794 998088002705 RNA binding site [nucleotide binding]; other site 998088002706 Uncharacterized protein conserved in bacteria (DUF2331); Region: DUF2331; cl01823 998088002707 guanosine 5'-monophosphate oxidoreductase; Provisional; Region: PRK05096 998088002708 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of the...; Region: IMPDH; cd00381 998088002709 active site 998088002710 Protein of unknown function (DUF785); Region: DUF785; cl01682 998088002711 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 998088002712 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 998088002713 dimer interface [polypeptide binding]; other site 998088002714 phosphorylation site [posttranslational modification] 998088002715 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088002716 ATP binding site [chemical binding]; other site 998088002717 Mg2+ binding site [ion binding]; other site 998088002718 G-X-G motif; other site 998088002719 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 998088002720 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088002721 active site 998088002722 phosphorylation site [posttranslational modification] 998088002723 intermolecular recognition site; other site 998088002724 dimerization interface [polypeptide binding]; other site 998088002725 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 998088002726 DNA binding site [nucleotide binding] 998088002727 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi...; Region: TPR; cl02429 998088002728 binding surface 998088002729 TPR motif; other site 998088002730 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 998088002731 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088002732 NAD(P) binding site [chemical binding]; other site 998088002733 active site 998088002734 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cd00232 998088002735 heme binding pocket [chemical binding]; other site 998088002736 heme ligand [chemical binding]; other site 998088002737 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 998088002738 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 998088002739 Thermostable hemolysin; Region: T_hemolysin; pfam12261 998088002740 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 998088002741 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 998088002742 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 998088002743 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 998088002744 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 998088002745 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088002746 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3214 998088002747 Protein of unknown function (DUF1006); Region: DUF1006; pfam06224 998088002748 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088002749 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cl15306 998088002750 substrate binding pocket [chemical binding]; other site 998088002751 membrane-bound complex binding site; other site 998088002752 hinge residues; other site 998088002753 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 998088002754 hypothetical protein; Provisional; Region: PRK07338 998088002755 metal binding site [ion binding]; metal-binding site 998088002756 dimer interface [polypeptide binding]; other site 998088002757 Nucleoside recognition; Region: Gate; cl00486 998088002758 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3314 998088002759 Nucleoside recognition; Region: Gate; cl00486 998088002760 Quinol:fumarate reductase (QFR) Type D subfamily, 13kD hydrophobic subunit D; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinine...; Region: QFR_TypeD_subunitD; cd00547 998088002761 Iron-sulfur protein interface; other site 998088002762 proximal quinone binding site [chemical binding]; other site 998088002763 C-subunit interface; other site 998088002764 distal quinone binding site; other site 998088002765 Quinol:fumarate reductase (QFR) Type D subfamily, 15kD hydrophobic subunit C; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinine...; Region: QFR_TypeD_subunitC; cd00546 998088002766 D-subunit interface [polypeptide binding]; other site 998088002767 Iron-sulfur protein interface; other site 998088002768 proximal quinone binding site [chemical binding]; other site 998088002769 fumarate reductase iron-sulfur subunit; Provisional; Region: PRK12385 998088002770 fumarate reductase flavoprotein subunit; Validated; Region: PRK09231 998088002771 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088002772 domain; Region: Succ_DH_flav_C; pfam02910 998088002773 Cache domain; Region: Cache_1; pfam02743 998088002774 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088002775 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088002776 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088002777 Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins; Region: GDPD; cd08556 998088002778 Glycerophosphoryl diester phosphodiesterase family; Region: GDPD; pfam03009 998088002779 active site 998088002780 catalytic site [active] 998088002781 metal binding site [ion binding]; metal-binding site 998088002782 putative mechanosensitive channel protein; Provisional; Region: PRK10929 998088002783 Mechanosensitive ion channel inner membrane domain 1; Region: MscS_TM; pfam12794 998088002784 Mechanosensitive ion channel; Region: MS_channel; pfam00924 998088002785 multidrug efflux pump VmrA; Reviewed; Region: vmrA; PRK09575 998088002786 MatE; Region: MatE; cl10513 998088002787 MatE; Region: MatE; cl10513 998088002788 Peptidase family M23; Region: Peptidase_M23; pfam01551 998088002789 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088002790 transcriptional activator TtdR; Provisional; Region: PRK09801 998088002791 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 998088002792 putative effector binding pocket; other site 998088002793 dimerization interface [polypeptide binding]; other site 998088002794 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 998088002795 Predicted protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: COG3531 998088002796 DsbA family, FrnE-like subfamily; composed of uncharacterized proteins containing a CXXC motif with similarity to DsbA and FrnE. FrnE is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the...; Region: DsbA_FrnE_like; cd03025 998088002797 catalytic residues [active] 998088002798 CHASE3 domain; Region: CHASE3; cl05000 998088002799 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 998088002800 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088002801 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088002802 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088002803 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 998088002804 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088002805 The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_OxyR; cd08411 998088002806 dimerization interface [polypeptide binding]; other site 998088002807 penicillin-binding protein 1a; Provisional; Region: mrcA; PRK11636 998088002808 Transglycosylase; Region: Transgly; cl07896 998088002809 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 998088002810 Competence protein A; Region: Competence_A; pfam11104 998088002811 Cell division protein FtsA; Region: FtsA; cl11496 998088002812 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 998088002813 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 998088002814 Pilus assembly protein, PilO; Region: PilO; cl01234 998088002815 Pilus assembly protein, PilP; Region: PilP; cl01235 998088002816 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 998088002817 Secretin and TonB N terminus short domain; Region: STN; cl06624 998088002818 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 998088002819 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 998088002820 shikimate kinase; Reviewed; Region: aroK; PRK00131 998088002821 Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the...; Region: SK; cd00464 998088002822 ADP binding site [chemical binding]; other site 998088002823 magnesium binding site [ion binding]; other site 998088002824 putative shikimate binding site; other site 998088002825 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 998088002826 active site 998088002827 dimer interface [polypeptide binding]; other site 998088002828 metal binding site [ion binding]; metal-binding site 998088002829 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 998088002830 hypothetical protein; Reviewed; Region: PRK11901 998088002831 Sporulation related domain; Region: SPOR; cl10051 998088002832 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl00408 998088002833 Ribulose-5-phosphate 3-epimerase (RPE). This enzyme catalyses the interconversion of D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate, as part of the Calvin cycle (reductive pentose phosphate pathway) in chloroplasts and in the oxidative...; Region: RPE; cd00429 998088002834 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 998088002835 substrate binding site [chemical binding]; other site 998088002836 hexamer interface [polypeptide binding]; other site 998088002837 metal binding site [ion binding]; metal-binding site 998088002838 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 998088002839 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cd01427 998088002840 motif II; other site 998088002841 tryptophanyl-tRNA synthetase; Region: trpS; TIGR00233 998088002842 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 998088002843 active site 998088002844 HIGH motif; other site 998088002845 dimer interface [polypeptide binding]; other site 998088002846 KMSKS motif; other site 998088002847 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 998088002848 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 998088002849 glutamine binding [chemical binding]; other site 998088002850 catalytic triad [active] 998088002851 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein; Reviewed; Region: argD; PRK05093 998088002852 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase...; Region: OAT_like; cd00610 998088002853 inhibitor-cofactor binding pocket; inhibition site 998088002854 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088002855 catalytic residue [active] 998088002856 Arginine/ornithine N-succinyltransferase beta subunit [Amino acid transport and metabolism]; Region: AstA; COG3138 998088002857 Arginine N-succinyltransferase beta subunit; Region: AstA; cl11440 998088002858 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 998088002859 N-succinylglutamate 5-semialdehyde dehydrogenase, AstD-like; Region: ALDH_SGSD_AstD; cd07095 998088002860 NAD(P) binding site [chemical binding]; other site 998088002861 catalytic residues [active] 998088002862 Domain of unknown function (DUF1338); Region: DUF1338; cl02226 998088002863 beta-phosphoglucomutase family hydrolase; Region: PGMB-YQAB-SF; TIGR02009 998088002864 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cd01427 998088002865 active site 998088002866 motif I; other site 998088002867 motif II; other site 998088002868 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088002869 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088002870 pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric; Region: pyruv_ox_red; TIGR02176 998088002871 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 998088002872 dimer interface [polypeptide binding]; other site 998088002873 PYR/PP interface [polypeptide binding]; other site 998088002874 TPP binding site [chemical binding]; other site 998088002875 substrate binding site [chemical binding]; other site 998088002876 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 998088002877 Domain of unknown function; Region: EKR; cl11037 998088002878 4Fe-4S binding domain; Region: Fer4; cl02805 998088002879 TPP-binding module; composed of proteins similar to the single subunit pyruvate ferredoxin oxidoreductase (PFOR) of Desulfovibrio Africanus, present in bacteria and amitochondriate eukaryotes. This subfamily also includes proteins characterized as...; Region: TPP_PFOR_PNO; cd03377 998088002880 TPP-binding site [chemical binding]; other site 998088002881 dimer interface [polypeptide binding]; other site 998088002882 trehalose-6-phosphate hydrolase; Provisional; Region: PRK10933 998088002883 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 998088002884 Protein of unknown function (DUF1622); Region: DUF1622; cl01991 998088002885 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 998088002886 ASC-1 homology domain, subfamily similar to Escherichia coli Yqfb. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function...; Region: ASCH_yqfb_like; cd06552 998088002887 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 998088002888 ligand binding site [chemical binding]; other site 998088002889 flexible hinge region; other site 998088002890 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 998088002891 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 998088002892 Nicotinamide mononucleotide transporter; Region: NMN_transporter; cl01256 998088002893 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 998088002894 transmembrane helices; other site 998088002895 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 998088002896 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088002897 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088002898 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 998088002899 GTP-binding protein YchF; Reviewed; Region: PRK09601 998088002900 YchF subfamily. YchF is a member of the Obg family, which includes four other subfamilies of GTPases: Obg, DRG, Ygr210, and NOG1. Obg is an essential gene that is involved in DNA replication in C. crescentus and Streptomyces griseus and is associated...; Region: YchF; cd01900 998088002901 G1 box; other site 998088002902 GTP/Mg2+ binding site [chemical binding]; other site 998088002903 Switch I region; other site 998088002904 G2 box; other site 998088002905 Switch II region; other site 998088002906 G3 box; other site 998088002907 G4 box; other site 998088002908 G5 box; other site 998088002909 TGS_YchF_C: This subfamily represents TGS domain-containing YchF GTP-binding protein, a universally conserved GTPase whose function is unknown. The N-terminal domain of the YchF protein belongs to the Obg-like family of GTPases, and some members of the...; Region: TGS_YchF_C; cd04867 998088002910 Peptidyl-tRNA hydrolase (PTH) is a monomeric protein that cleaves the ester bond linking the nascent peptide and tRNA when peptidyl-tRNA is released prematurely from the ribosome. This ensures the recycling of peptidyl-tRNAs into tRNAs produced through...; Region: PTH; cd00462 998088002911 putative active site [active] 998088002912 catalytic residue [active] 998088002913 NAD pyrophosphatase/5'-nucleotidase NadN; Region: nadN; TIGR01530 998088002914 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 998088002915 active site 998088002916 metal binding site [ion binding]; metal-binding site 998088002917 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 998088002918 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK04923 998088002919 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 998088002920 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 998088002921 GHMP kinases N terminal domain; Region: GHMP_kinases_N; cl08256 998088002922 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 998088002923 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 998088002924 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 998088002925 tRNA; other site 998088002926 putative tRNA binding site [nucleotide binding]; other site 998088002927 putative NADP binding site [chemical binding]; other site 998088002928 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 998088002929 peptide chain release factor 1; Validated; Region: prfA; PRK00591 998088002930 RF-1 domain; Region: RF-1; cl02875 998088002931 RF-1 domain; Region: RF-1; cl02875 998088002932 protein-(glutamine-N5) methyltransferase, release factor-specific; Region: RF_mod_PrmC; TIGR03534 998088002933 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 998088002934 Invasion gene expression up-regulator, SirB; Region: SirB; cl01184 998088002935 Uncharacterized conserved protein [Function unknown]; Region: COG2912 998088002936 hypothetical protein; Provisional; Region: PRK10941 998088002937 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 998088002938 NeuB family; Region: NeuB; cl00496 998088002939 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 998088002940 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 998088002941 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088002942 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088002943 substrate binding pocket [chemical binding]; other site 998088002944 membrane-bound complex binding site; other site 998088002945 hinge residues; other site 998088002946 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 998088002947 ligand binding site [chemical binding]; other site 998088002948 active site 998088002949 UGI interface [polypeptide binding]; other site 998088002950 catalytic site [active] 998088002951 Uncharacterized conserved protein [Function unknown]; Region: COG3945 998088002952 alpha-glucosidase; Provisional; Region: PRK10137 998088002953 Bacterial alpha-L-rhamnosidase; Region: Bac_rhamnosid; cl01801 998088002954 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 998088002955 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088002956 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 998088002957 substrate binding site [chemical binding]; other site 998088002958 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 998088002959 Adenylosuccinate synthetase (AdSS) catalyzes the first step in the de novo biosynthesis of AMP. IMP and L-aspartate are conjugated in a two-step reaction accompanied by the hydrolysis of GTP to GDP in the presence of Mg2+. In the first step, the r-...; Region: AdSS; cd03108 998088002960 GDP-binding site [chemical binding]; other site 998088002961 ACT binding site; other site 998088002962 IMP binding site; other site 998088002963 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088002964 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088002965 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 998088002966 dimerization interface [polypeptide binding]; other site 998088002967 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 998088002968 aspartate aminotransferase; Provisional; Region: PRK08361 998088002969 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 998088002970 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088002971 homodimer interface [polypeptide binding]; other site 998088002972 catalytic residue [active] 998088002973 sugar efflux transporter B; Provisional; Region: PRK15011 998088002974 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088002975 putative substrate translocation pore; other site 998088002976 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088002977 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088002978 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088002979 dimerization interface [polypeptide binding]; other site 998088002980 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088002981 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 998088002982 NAD(P) binding site [chemical binding]; other site 998088002983 active site 998088002984 Peptidase family S49 N-terminal; Region: Peptidase_S49_N; pfam08496 998088002985 putative inner membrane peptidase; Provisional; Region: PRK11778 998088002986 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 998088002987 tandem repeat interface [polypeptide binding]; other site 998088002988 oligomer interface [polypeptide binding]; other site 998088002989 active site residues [active] 998088002990 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088002991 DsrE/DsrF-like family; Region: DrsE; cl00672 998088002992 Protein of unknown function (DUF1090); Region: DUF1090; pfam06476 998088002993 ferredoxin; Validated; Region: PRK07118 998088002994 putative protease; Provisional; Region: PRK15452 998088002995 Peptidase family U32; Region: Peptidase_U32; cl03113 998088002996 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 998088002997 putative fimbrial protein TcfA; Provisional; Region: PRK15308 998088002998 fimbrial outer membrane usher protein TcfC; Provisional; Region: PRK15310 998088002999 transcriptional regulator RcsB; Provisional; Region: PRK10840 998088003000 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088003001 active site 998088003002 phosphorylation site [posttranslational modification] 998088003003 intermolecular recognition site; other site 998088003004 dimerization interface [polypeptide binding]; other site 998088003005 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors...; Region: LuxR_C_like; cd06170 998088003006 DNA binding residues [nucleotide binding] 998088003007 dimerization interface [polypeptide binding]; other site 998088003008 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088003009 substrate binding pocket [chemical binding]; other site 998088003010 membrane-bound complex binding site; other site 998088003011 hinge residues; other site 998088003012 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 998088003013 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088003014 substrate binding pocket [chemical binding]; other site 998088003015 membrane-bound complex binding site; other site 998088003016 hinge residues; other site 998088003017 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 998088003018 dimer interface [polypeptide binding]; other site 998088003019 phosphorylation site [posttranslational modification] 998088003020 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088003021 ATP binding site [chemical binding]; other site 998088003022 Mg2+ binding site [ion binding]; other site 998088003023 G-X-G motif; other site 998088003024 Response regulator receiver domain; Region: Response_reg; pfam00072 998088003025 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088003026 active site 998088003027 phosphorylation site [posttranslational modification] 998088003028 intermolecular recognition site; other site 998088003029 dimerization interface [polypeptide binding]; other site 998088003030 Succinylarginine dihydrolase; Region: AstB; cl01511 998088003031 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 998088003032 TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in...; Region: TOPRIM_TopoIA_TopoI; cd03363 998088003033 active site 998088003034 interdomain interaction site; other site 998088003035 putative metal-binding site [ion binding]; other site 998088003036 nucleotide binding site [chemical binding]; other site 998088003037 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded...; Region: TOP1Ac; cd00186 998088003038 domain I; other site 998088003039 DNA binding groove [nucleotide binding] 998088003040 phosphate binding site [ion binding]; other site 998088003041 domain II; other site 998088003042 domain III; other site 998088003043 nucleotide binding site [chemical binding]; other site 998088003044 catalytic site [active] 998088003045 domain IV; other site 998088003046 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 998088003047 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 998088003048 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 998088003049 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 998088003050 The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases...; Region: ATase; cd06445 998088003051 active site 998088003052 DNA binding site [nucleotide binding] 998088003053 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 998088003054 PAS fold; Region: PAS_3; pfam08447 998088003055 putative active site [active] 998088003056 heme pocket [chemical binding]; other site 998088003057 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088003058 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 998088003059 The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i); Region: GH20_chitobiase-like; cd06563 998088003060 active site 998088003061 Predicted N-acetylglucosamine kinase [Carbohydrate transport and metabolism]; Region: COG2971 998088003062 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 998088003063 E or 'early' set of sugar utilizing enzymes which may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end; Region: E_set; cl09101 998088003064 endoglucanase; Region: PLN02420 998088003065 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 998088003066 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 998088003067 Walker A/P-loop; other site 998088003068 ATP binding site [chemical binding]; other site 998088003069 Q-loop/lid; other site 998088003070 ABC transporter signature motif; other site 998088003071 Walker B; other site 998088003072 D-loop; other site 998088003073 H-loop/switch region; other site 998088003074 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 998088003075 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 998088003076 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 998088003077 Walker A/P-loop; other site 998088003078 ATP binding site [chemical binding]; other site 998088003079 Q-loop/lid; other site 998088003080 ABC transporter signature motif; other site 998088003081 Walker B; other site 998088003082 D-loop; other site 998088003083 H-loop/switch region; other site 998088003084 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 998088003085 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 998088003086 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088003087 dimer interface [polypeptide binding]; other site 998088003088 conserved gate region; other site 998088003089 putative PBP binding loops; other site 998088003090 ABC-ATPase subunit interface; other site 998088003091 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 998088003092 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088003093 dimer interface [polypeptide binding]; other site 998088003094 conserved gate region; other site 998088003095 putative PBP binding loops; other site 998088003096 ABC-ATPase subunit interface; other site 998088003097 The substrate binding domain of a cellulose-binding protein from Thermotoga maritima contains the type 2 periplasmic binding fold; Region: PBP2_TmCBP_oligosaccharides_like; cd08509 998088003098 substrate binding site [chemical binding]; other site 998088003099 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 998088003100 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 998088003101 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cd06225 998088003102 dimerization interface [polypeptide binding]; other site 998088003103 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 998088003104 dimer interface [polypeptide binding]; other site 998088003105 phosphorylation site [posttranslational modification] 998088003106 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088003107 ATP binding site [chemical binding]; other site 998088003108 Mg2+ binding site [ion binding]; other site 998088003109 G-X-G motif; other site 998088003110 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088003111 Response regulator receiver domain; Region: Response_reg; pfam00072 998088003112 active site 998088003113 phosphorylation site [posttranslational modification] 998088003114 intermolecular recognition site; other site 998088003115 dimerization interface [polypeptide binding]; other site 998088003116 PAS fold; Region: PAS_4; pfam08448 998088003117 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 998088003118 Protein of unknown function (DUF2517); Region: DUF2517; pfam10725 998088003119 Predicted integral membrane protein (DUF2282); Region: DUF2282; cl02366 998088003120 hypothetical protein; Provisional; Region: PRK05409 998088003121 Protein of unknown function (DUF692); Region: DUF692; cl01263 998088003122 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 998088003123 DoxX; Region: DoxX; cl00976 998088003124 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088003125 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 998088003126 PAS domain S-box; Region: sensory_box; TIGR00229 998088003127 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 998088003128 PAS fold; Region: PAS_3; pfam08447 998088003129 putative active site [active] 998088003130 heme pocket [chemical binding]; other site 998088003131 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088003132 Domain of unknown function (DUF3332); Region: DUF3332; pfam11810 998088003133 Predicted membrane protein [Function unknown]; Region: COG1289 998088003134 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoeA; Provisional; Region: PRK14491 998088003135 Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa...; Region: MobB; cd03116 998088003136 Walker A motif; other site 998088003137 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 998088003138 dimer interface [polypeptide binding]; other site 998088003139 putative functional site; other site 998088003140 putative MPT binding site; other site 998088003141 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 998088003142 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 998088003143 GTP binding site [chemical binding]; other site 998088003144 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 998088003145 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This...; Region: ABC_cobalt_CbiO_domain1; cd03225 998088003146 Walker A/P-loop; other site 998088003147 ATP binding site [chemical binding]; other site 998088003148 Q-loop/lid; other site 998088003149 ABC transporter signature motif; other site 998088003150 Walker B; other site 998088003151 D-loop; other site 998088003152 H-loop/switch region; other site 998088003153 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cl00427 998088003154 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 998088003155 dimerization interface [polypeptide binding]; other site 998088003156 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 998088003157 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088003158 active site 998088003159 phosphorylation site [posttranslational modification] 998088003160 intermolecular recognition site; other site 998088003161 dimerization interface [polypeptide binding]; other site 998088003162 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088003163 Walker A motif; other site 998088003164 ATP binding site [chemical binding]; other site 998088003165 Walker B motif; other site 998088003166 arginine finger; other site 998088003167 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 998088003168 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 998088003169 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 998088003170 dimer interface [polypeptide binding]; other site 998088003171 phosphorylation site [posttranslational modification] 998088003172 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088003173 ATP binding site [chemical binding]; other site 998088003174 G-X-G motif; other site 998088003175 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 998088003176 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088003177 FdhD/NarQ family; Region: FdhD-NarQ; cl00659 998088003178 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster...; Region: Radical_SAM; cd01335 998088003179 FeS/SAM binding site; other site 998088003180 Protein of unknown function (DUF3305); Region: DUF3305; pfam11749 998088003181 Protein of unknown function (DUF3306); Region: DUF3306; pfam11748 998088003182 ferredoxin; Validated; Region: PRK07118 998088003183 formate hydrogenlyase complex iron-sulfur subunit; Provisional; Region: PRK12387 998088003184 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved alpha-; Region: HCP_like; cl14655 998088003185 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 998088003186 formate dehydrogenase region TAT target; Region: formate_TAT; TIGR02811 998088003187 formate dehydrogenase, alpha subunit, proteobacterial-type; Region: formate-DH-alph; TIGR01553 998088003188 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_Formate-Dh-Na-like; cd02752 998088003189 [4Fe-4S] binding site [ion binding]; other site 998088003190 molybdopterin cofactor binding site; other site 998088003191 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-...; Region: Molybdopterin-Binding; cl09928 998088003192 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_CT_Formate-Dh-Na-like; cd02792 998088003193 molybdopterin cofactor binding site; other site 998088003194 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 998088003195 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria...; Region: Cytochrome_b_N; cl00859 998088003196 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088003197 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cl15306 998088003198 substrate binding pocket [chemical binding]; other site 998088003199 membrane-bound complex binding site; other site 998088003200 hinge residues; other site 998088003201 malate dehydrogenase; Provisional; Region: PRK13529 998088003202 Malic enzyme, N-terminal domain; Region: malic; pfam00390 998088003203 NAD(P) binding domain of malic enzyme (ME), subgroup 1; Region: NAD_bind_1_malic_enz; cd05312 998088003204 NAD(P) binding site [chemical binding]; other site 998088003205 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 998088003206 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a...; Region: Hint; cl12032 998088003207 Sulfate transporter family; Region: Sulfate_transp; cl00967 998088003208 Permease family; Region: Xan_ur_permease; pfam00860 998088003209 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088003210 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088003211 substrate binding pocket [chemical binding]; other site 998088003212 membrane-bound complex binding site; other site 998088003213 hinge residues; other site 998088003214 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088003215 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088003216 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088003217 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088003218 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088003219 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088003220 Coenzyme A binding pocket [chemical binding]; other site 998088003221 Putative hydrophobic ligand-binding SRPBCC domain of Micromonospora echinospora CalC, human Aha1, and related proteins; Region: SRPBCC_CalC_Aha1-like; cd07814 998088003222 putative hydrophobic ligand binding site [chemical binding]; other site 998088003223 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 998088003224 DNA-binding transcriptional regulator HexR; Provisional; Region: PRK11302 998088003225 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose...; Region: SIS_RpiR; cd05013 998088003226 putative active site [active] 998088003227 pyruvate kinase; Provisional; Region: PRK05826 998088003228 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 998088003229 domain interfaces; other site 998088003230 active site 998088003231 Family of unknown function (DUF500); Region: DUF500; cl01109 998088003232 Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]; Region: COG1574 998088003233 YtcJ_like metal dependent amidohydrolases. YtcJ is a Bacillus subtilis ORF of unknown function. The Arabidopsis homolog LAF3 has been identified as a factor required for photochrome A signalling; Region: YtcJ_like; cd01300 998088003234 active site 998088003235 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have...; Region: metallo-dependent_hydrolases; cl00281 998088003236 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 998088003237 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088003238 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; cl01368 998088003239 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 998088003240 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 998088003241 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 998088003242 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 998088003243 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 998088003244 MgtE intracellular N domain; Region: MgtE_N; cl15244 998088003245 FliG C-terminal domain; Region: FliG_C; pfam01706 998088003246 type III secretion apparatus protein, HrpE/YscL family; Region: HrpE_YscL_not; TIGR02499 998088003247 Essential protein Yae1, N terminal; Region: Yae1_N; pfam09811 998088003248 Flagellar assembly protein FliH; Region: FliH; pfam02108 998088003249 flagellum-specific ATP synthase; Validated; Region: fliI; PRK08972 998088003250 Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they...; Region: ATPase_flagellum-secretory_path_III; cd01136 998088003251 Walker A motif/ATP binding site; other site 998088003252 Walker B motif; other site 998088003253 Flagellar FliJ protein; Region: FliJ; cl09161 998088003254 flagellar export protein FliJ; Region: flagell_FliJ; TIGR02473 998088003255 Flagellar hook-length control protein [Cell motility and secretion]; Region: FliK; COG3144 998088003256 Flagellar hook-length control protein FliK; Region: Flg_hook; cl15269 998088003257 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 998088003258 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 998088003259 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 998088003260 flagellar motor switch protein; Validated; Region: fliN; PRK05698 998088003261 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 998088003262 Flagellar biosynthesis protein, FliO; Region: FliO; cl01247 998088003263 FliP family; Region: FliP; cl00593 998088003264 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 998088003265 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 998088003266 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 998088003267 Flagellar biosynthesis pathway, component FlhB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlhB; cl12017 998088003268 Flagellar biosynthesis pathway, component FlhA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlhA; cl07980 998088003269 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 998088003270 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 998088003271 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 998088003272 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 998088003273 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 998088003274 FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by...; Region: FleN-like; cd02038 998088003275 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 998088003276 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 998088003277 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 998088003278 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial...; Region: Sigma70_r4; cd06171 998088003279 DNA binding residues [nucleotide binding] 998088003280 Response regulator receiver domain; Region: Response_reg; pfam00072 998088003281 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088003282 active site 998088003283 phosphorylation site [posttranslational modification] 998088003284 intermolecular recognition site; other site 998088003285 dimerization interface [polypeptide binding]; other site 998088003286 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 998088003287 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 998088003288 putative binding surface; other site 998088003289 active site 998088003290 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 998088003291 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088003292 ATP binding site [chemical binding]; other site 998088003293 Mg2+ binding site [ion binding]; other site 998088003294 G-X-G motif; other site 998088003295 CheA regulatory domain; CheA is a histidine protein kinase present in bacteria and archea. Activated by the chemotaxis receptor a histidine phosphoryl group from CheA is passed directly to an aspartate in the response regulator CheY. This signalling...; Region: CheA_reg; cd00731 998088003296 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 998088003297 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088003298 active site 998088003299 phosphorylation site [posttranslational modification] 998088003300 intermolecular recognition site; other site 998088003301 CheB methylesterase; Region: CheB_methylest; pfam01339 998088003302 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 998088003303 flagellar motor protein MotD; Reviewed; Region: PRK09038 998088003304 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088003305 ligand binding site [chemical binding]; other site 998088003306 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 998088003307 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following...; Region: ParA; cd02042 998088003308 P-loop; other site 998088003309 Magnesium ion binding site [ion binding]; other site 998088003310 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following...; Region: ParA; cd02042 998088003311 Magnesium ion binding site [ion binding]; other site 998088003312 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cd00588 998088003313 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 998088003314 putative CheA interaction surface; other site 998088003315 HemX; Region: HemX; cl14667 998088003316 Protein of unknown function (DUF2802); Region: DUF2802; pfam10975 998088003317 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13538 998088003318 CcmA, the ATP-binding component of the bacterial CcmAB transporter. The CCM family is involved in bacterial cytochrome c biogenesis. Cytochrome c maturation in E. coli requires the ccm operon, which encodes eight membrane proteins (CcmABCDEFGH); Region: ABC_CcmA_heme_exporter; cd03231 998088003319 Walker A/P-loop; other site 998088003320 ATP binding site [chemical binding]; other site 998088003321 Q-loop/lid; other site 998088003322 ABC transporter signature motif; other site 998088003323 Walker B; other site 998088003324 D-loop; other site 998088003325 H-loop/switch region; other site 998088003326 CcmB protein; Region: CcmB; cl01016 998088003327 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 998088003328 Heme exporter protein D (CcmD); Region: CcmD; cl11475 998088003329 CcmE; Region: CcmE; cl00994 998088003330 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 998088003331 TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c...; Region: TlpA_like_DsbE; cd03010 998088003332 catalytic residues [active] 998088003333 central insert; other site 998088003334 Cytochrome C biogenesis protein; Region: CcmH; cl01179 998088003335 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 998088003336 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 998088003337 VacJ like lipoprotein; Region: VacJ; cl01073 998088003338 superoxide dismutase; Provisional; Region: PRK10543 998088003339 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 998088003340 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 998088003341 Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain...; Region: GRX_PICOT_like; cd03028 998088003342 putative GSH binding site [chemical binding]; other site 998088003343 catalytic residues [active] 998088003344 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 998088003345 Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly...; Region: Thr-dehyd; cd01562 998088003346 tetramer interface [polypeptide binding]; other site 998088003347 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088003348 catalytic residue [active] 998088003349 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 998088003350 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 998088003351 Acetokinase family; Region: Acetate_kinase; cl01029 998088003352 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 998088003353 Pyruvate formate lyase 1; Region: PFL1; cd01678 998088003354 coenzyme A binding site [chemical binding]; other site 998088003355 active site 998088003356 catalytic residues [active] 998088003357 glycine loop; other site 998088003358 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 998088003359 homotrimer interaction site [polypeptide binding]; other site 998088003360 putative active site [active] 998088003361 16S rRNA methyltransferase B; Provisional; Region: PRK14902 998088003362 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cd02440 998088003363 S-adenosylmethionine binding site [chemical binding]; other site 998088003364 Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families...; Region: ZnMc; cl00064 998088003365 active site 998088003366 Ser-Thr-rich glycosyl-phosphatidyl-inositol-anchored membrane family; Region: GPI-anchored; pfam10342 998088003367 Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families...; Region: ZnMc; cl00064 998088003368 active site 998088003369 Ser-Thr-rich glycosyl-phosphatidyl-inositol-anchored membrane family; Region: GPI-anchored; pfam10342 998088003370 Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families...; Region: ZnMc; cl00064 998088003371 active site 998088003372 Ser-Thr-rich glycosyl-phosphatidyl-inositol-anchored membrane family; Region: GPI-anchored; pfam10342 998088003373 pyridoxamine 5'-phosphate oxidase; Provisional; Region: PRK05679 998088003374 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 998088003375 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 998088003376 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 998088003377 GST_N family, unknown subfamily 4; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_4; cd03056 998088003378 putative C-terminal domain interface [polypeptide binding]; other site 998088003379 putative GSH binding site (G-site) [chemical binding]; other site 998088003380 putative dimer interface [polypeptide binding]; other site 998088003381 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 998088003382 N-terminal domain interface [polypeptide binding]; other site 998088003383 dimer interface [polypeptide binding]; other site 998088003384 substrate binding pocket (H-site) [chemical binding]; other site 998088003385 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 998088003386 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088003387 Uncharacterized conserved protein [Function unknown]; Region: COG2850 998088003388 adenylosuccinate lyase; Provisional; Region: PRK09285 998088003389 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 998088003390 tetramer interface [polypeptide binding]; other site 998088003391 active site 998088003392 Protein of unknown function (DUF489); Region: DUF489; cl01097 998088003393 tRNA methyl transferase. This family represents tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs...; Region: tRNA_Me_trans; cd01998 998088003394 tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase; Region: trmU; TIGR00420 998088003395 Contains a crystal structure of the Nudix hydrolase from Nitrosomonas europaea, which has an unknown function. In general, members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X...; Region: Nudix_Hydrolase_2; cd03675 998088003396 nudix motif; other site 998088003397 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 998088003398 active site 998088003399 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 998088003400 regulatory protein interface [polypeptide binding]; other site 998088003401 active site 998088003402 regulatory phosphorylation site [posttranslational modification]; other site 998088003403 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 998088003404 active site 998088003405 phosphorylation site [posttranslational modification] 998088003406 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA...; Region: PTS_IIB_fructose; cd05569 998088003407 P-loop; other site 998088003408 active site 998088003409 phosphorylation site [posttranslational modification] 998088003410 sugar phosphate antiporter; Reviewed; Region: uhpT; PRK09556 998088003411 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088003412 putative substrate translocation pore; other site 998088003413 PTS system 2-O-a-mannosyl-D-glycerate specific transporter subunit IIABC; Provisional; Region: PRK09765 998088003414 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 998088003415 active site 998088003416 phosphorylation site [posttranslational modification] 998088003417 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA...; Region: PTS_IIB_fructose; cd05569 998088003418 P-loop; other site 998088003419 active site 998088003420 phosphorylation site [posttranslational modification] 998088003421 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 998088003422 This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme; Region: NifX_NifB; cl00252 998088003423 Tellurite-resistance/Dicarboxylate Transporter (TDT) family includes SLAC1 (Slow Anion Channel-Associated 1); Region: TDT_SLAC1_like; cd09323 998088003424 gating phenylalanine in ion channel; other site 998088003425 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 998088003426 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 998088003427 CoenzymeA binding site [chemical binding]; other site 998088003428 subunit interaction site [polypeptide binding]; other site 998088003429 PHB binding site; other site 998088003430 Ferritin-like domain; Region: Ferritin; pfam00210 998088003431 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 998088003432 dimerization interface [polypeptide binding]; other site 998088003433 DPS ferroxidase diiron center [ion binding]; other site 998088003434 ion pore; other site 998088003435 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 998088003436 Predicted aminoglycoside phosphotransferase [General function prediction only]; Region: COG3173 998088003437 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088003438 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 998088003439 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088003440 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088003441 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088003442 Coenzyme A binding pocket [chemical binding]; other site 998088003443 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088003444 Coenzyme A binding pocket [chemical binding]; other site 998088003445 Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/...; Region: BRCT; cl00038 998088003446 DNA-binding transcriptional repressor MalI; Provisional; Region: PRK10014 998088003447 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 998088003448 DNA binding site [nucleotide binding] 998088003449 domain linker motif; other site 998088003450 Ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria; Region: PBP1_MalI_like; cd06289 998088003451 putative dimerization interface [polypeptide binding]; other site 998088003452 putative ligand binding site [chemical binding]; other site 998088003453 bifunctional PTS system maltose and glucose-specific transporter subunits IICB; Provisional; Region: PRK10110 998088003454 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 998088003455 PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIB_glc; cd00212 998088003456 active site turn [active] 998088003457 phosphorylation site [posttranslational modification] 998088003458 aspartate aminotransferase; Provisional; Region: PRK08361 998088003459 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 998088003460 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088003461 homodimer interface [polypeptide binding]; other site 998088003462 catalytic residue [active] 998088003463 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cd00529 998088003464 active site 998088003465 putative DNA-binding cleft [nucleotide binding]; other site 998088003466 dimer interface [polypeptide binding]; other site 998088003467 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 998088003468 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 998088003469 acyl-CoA dehydrogenase; Reviewed; Region: PRK13026 998088003470 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 998088003471 active site 998088003472 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 998088003473 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088003474 putative hydrolase; Validated; Region: PRK09248 998088003475 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 998088003476 RNase P subunit p30; Region: RNase_P_p30; cl03389 998088003477 putative NADPH-dependent glutamate synthase small subunit; Provisional; Region: PRK12814 998088003478 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088003479 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088003480 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved alpha-; Region: HCP_like; cl14655 998088003481 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 998088003482 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H)...; Region: MopB_Formate-Dh-H; cd02753 998088003483 [4Fe-4S] binding site [ion binding]; other site 998088003484 molybdopterin cofactor binding site; other site 998088003485 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H)...; Region: MopB_CT_Formate-Dh_H; cd02790 998088003486 molybdopterin cofactor binding site; other site 998088003487 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088003488 Response regulator receiver domain; Region: Response_reg; pfam00072 998088003489 active site 998088003490 phosphorylation site [posttranslational modification] 998088003491 intermolecular recognition site; other site 998088003492 dimerization interface [polypeptide binding]; other site 998088003493 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 998088003494 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088003495 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088003496 substrate binding pocket [chemical binding]; other site 998088003497 membrane-bound complex binding site; other site 998088003498 hinge residues; other site 998088003499 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 998088003500 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088003501 substrate binding pocket [chemical binding]; other site 998088003502 membrane-bound complex binding site; other site 998088003503 hinge residues; other site 998088003504 hypothetical protein; Provisional; Region: PRK13560 998088003505 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: VicK; COG5002 998088003506 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 998088003507 dimer interface [polypeptide binding]; other site 998088003508 phosphorylation site [posttranslational modification] 998088003509 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088003510 ATP binding site [chemical binding]; other site 998088003511 Mg2+ binding site [ion binding]; other site 998088003512 G-X-G motif; other site 998088003513 Response regulator receiver domain; Region: Response_reg; pfam00072 998088003514 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088003515 active site 998088003516 phosphorylation site [posttranslational modification] 998088003517 intermolecular recognition site; other site 998088003518 dimerization interface [polypeptide binding]; other site 998088003519 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 998088003520 Small protein B (SmpB) is a component of the trans-translation system in prokaryotes for releasing stalled ribosome from damaged messenger RNAs; Region: SmpB; cd09294 998088003521 SmpB-tmRNA interface; other site 998088003522 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 998088003523 putative coenzyme Q binding site [chemical binding]; other site 998088003524 Uncharacterised protein family (UPF0125); Region: UPF0125; cl01096 998088003525 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 998088003526 M20 Peptidases Aminoacyclase-1 indole-3-acetic-L-aspartic acid hydrolase from bacteria and archaea; Region: M20_Acy1_IAAspH_bact; cd05665 998088003527 putative metal binding site [ion binding]; other site 998088003528 dimer interface [polypeptide binding]; other site 998088003529 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 998088003530 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 998088003531 active site 998088003532 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 998088003533 Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of...; Region: SIS_GmhA; cd05006 998088003534 dimer interface [polypeptide binding]; other site 998088003535 active site 998088003536 Glutamine amidotransferases class-II (Gn-AT)_YafJ-type. YafJ is a glutamine amidotransferase-like protein of unknown function found in prokaryotes, eukaryotes and archaea. YafJ has a conserved structural fold similar to those of other class II...; Region: YafJ; cd01908 998088003537 putative active site [active] 998088003538 putative dimer interface [polypeptide binding]; other site 998088003539 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 998088003540 Uncharacterised protein family UPF0052; Region: UPF0052; pfam01933 998088003541 family of mostly uncharacterized proteins similar to B.subtilis YvcK; Region: YvcK_like; cd07187 998088003542 phosphate binding site [ion binding]; other site 998088003543 putative substrate binding pocket [chemical binding]; other site 998088003544 dimer interface [polypeptide binding]; other site 998088003545 Uncharacterized conserved protein [Function unknown]; Region: COG3287 998088003546 FIST N domain; Region: FIST; cl10701 998088003547 FIST C domain; Region: FIST_C; pfam10442 998088003548 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 998088003549 dimer interface [polypeptide binding]; other site 998088003550 phosphorylation site [posttranslational modification] 998088003551 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088003552 ATP binding site [chemical binding]; other site 998088003553 Mg2+ binding site [ion binding]; other site 998088003554 G-X-G motif; other site 998088003555 Response regulator receiver domain; Region: Response_reg; pfam00072 998088003556 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088003557 active site 998088003558 phosphorylation site [posttranslational modification] 998088003559 intermolecular recognition site; other site 998088003560 dimerization interface [polypeptide binding]; other site 998088003561 Uncharacterized protein, similar to the N-terminal domain of Lon protease [General function prediction only]; Region: COG2802 998088003562 transcriptional regulator NarL; Provisional; Region: PRK10651 998088003563 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088003564 active site 998088003565 phosphorylation site [posttranslational modification] 998088003566 intermolecular recognition site; other site 998088003567 dimerization interface [polypeptide binding]; other site 998088003568 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors...; Region: LuxR_C_like; cd06170 998088003569 DNA binding residues [nucleotide binding] 998088003570 dimerization interface [polypeptide binding]; other site 998088003571 nitrate/nitrite sensor protein NarQ; Provisional; Region: PRK10935 998088003572 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088003573 Histidine kinase; Region: HisKA_3; pfam07730 998088003574 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088003575 ATP binding site [chemical binding]; other site 998088003576 Mg2+ binding site [ion binding]; other site 998088003577 G-X-G motif; other site 998088003578 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 998088003579 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster...; Region: Radical_SAM; cd01335 998088003580 FeS/SAM binding site; other site 998088003581 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 998088003582 ferredoxin-type protein; Provisional; Region: PRK10194 998088003583 NapD protein; Region: NapD; cl01163 998088003584 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 998088003585 NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored...; Region: MopB_Nitrate-R-NapA-like; cd02754 998088003586 [4Fe-4S] binding site [ion binding]; other site 998088003587 molybdopterin cofactor binding site; other site 998088003588 NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 998088003589 molybdopterin cofactor binding site; other site 998088003590 quinol dehydrogenase periplasmic component; Provisional; Region: napG; PRK09476 998088003591 quinol dehydrogenase membrane component; Provisional; Region: napH; PRK09477 998088003592 4Fe-4S binding domain; Region: Fer4_5; pfam12801 998088003593 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved alpha-; Region: HCP_like; cl14655 998088003594 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; cl01153 998088003595 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl09485 998088003596 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 998088003597 MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea...; Region: MogA_MoaB; cd00886 998088003598 MPT binding site; other site 998088003599 trimer interface [polypeptide binding]; other site 998088003600 MoaC family, prokaryotic and eukaryotic. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a...; Region: MoaC_PE; cd01420 998088003601 trimer interface [polypeptide binding]; other site 998088003602 dimer interface [polypeptide binding]; other site 998088003603 putative active site [active] 998088003604 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 998088003605 MoaE interaction surface [polypeptide binding]; other site 998088003606 MoeB interaction surface [polypeptide binding]; other site 998088003607 thiocarboxylated glycine; other site 998088003608 MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoaE; cd00756 998088003609 MoaE homodimer interface [polypeptide binding]; other site 998088003610 MoaD interaction [polypeptide binding]; other site 998088003611 active site residues [active] 998088003612 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088003613 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088003614 dimer interface [polypeptide binding]; other site 998088003615 ABC-ATPase subunit interface; other site 998088003616 putative PBP binding loops; other site 998088003617 molybdenum ABC transporter, ATP-binding protein; Region: modC_ABC; TIGR02142 998088003618 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088003619 Walker A/P-loop; other site 998088003620 ATP binding site [chemical binding]; other site 998088003621 Q-loop/lid; other site 998088003622 ABC transporter signature motif; other site 998088003623 Walker B; other site 998088003624 D-loop; other site 998088003625 H-loop/switch region; other site 998088003626 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 998088003627 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 998088003628 ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of...; Region: ThiF_MoeB_HesA_family; cd00757 998088003629 ATP binding site [chemical binding]; other site 998088003630 substrate interface [chemical binding]; other site 998088003631 molybdopterin biosynthesis protein MoeA; Provisional; Region: PRK10680 998088003632 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 998088003633 dimer interface [polypeptide binding]; other site 998088003634 putative functional site; other site 998088003635 putative MPT binding site; other site 998088003636 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 998088003637 GTP cyclohydrolase I; Provisional; Region: PLN03044 998088003638 active site 998088003639 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 998088003640 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088003641 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088003642 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088003643 formate--tetrahydrofolate ligase; Provisional; Region: PRK13506 998088003644 Formyltetrahydrofolate synthetase (FTHFS) catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2...; Region: FTHFS; cd00477 998088003645 Potassium binding sites [ion binding]; other site 998088003646 Cesium cation binding sites [ion binding]; other site 998088003647 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088003648 transcriptional activator TtdR; Provisional; Region: PRK09801 998088003649 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 998088003650 putative effector binding pocket; other site 998088003651 dimerization interface [polypeptide binding]; other site 998088003652 YceI-like domain; Region: YceI; cl01001 998088003653 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088003654 active site 998088003655 NAD+ binding site [chemical binding]; other site 998088003656 oligomerization interface [polypeptide binding]; other site 998088003657 Rdx family; Region: Rdx; cl01407 998088003658 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088003659 putative acyl-acceptor binding pocket; other site 998088003660 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088003661 peptidase T; Region: peptidase-T; TIGR01882 998088003662 M20 Peptidase T specifically cleaves tripeptides; Region: M20_peptT; cd03892 998088003663 metal binding site [ion binding]; metal-binding site 998088003664 dimer interface [polypeptide binding]; other site 998088003665 arginine decarboxylase; Provisional; Region: PRK05354 998088003666 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 998088003667 dimer interface [polypeptide binding]; other site 998088003668 active site 998088003669 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 998088003670 catalytic residues [active] 998088003671 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 998088003672 Alkyl sulfatase and related hydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2015 998088003673 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 998088003674 SCP-2 sterol transfer family; Region: SCP2; cl01225 998088003675 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088003676 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088003677 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088003678 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 998088003679 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 998088003680 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 998088003681 homotrimer interaction site [polypeptide binding]; other site 998088003682 putative active site [active] 998088003683 L-cysteine desulfidase [Amino acid transport and metabolism]; Region: COG3681 998088003684 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 998088003685 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2964 998088003686 YheO-like PAS domain; Region: PAS_6; pfam08348 998088003687 Histidine phosphatase superfamily (branch 1); Region: His_Phos_1; pfam00300 998088003688 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 998088003689 catalytic core [active] 998088003690 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 998088003691 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (...; Region: S24_LexA-like; cd06529 998088003692 Catalytic site [active] 998088003693 Mu DNA-binding domain; Region: HTH_Tnp_Mu_1; pfam02316 998088003694 Integrase core domain; Region: rve; cl01316 998088003695 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088003696 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 998088003697 Protein of unknown function (DUF3164); Region: DUF3164; pfam11363 998088003698 Protein of unknown function (DUF1018); Region: DUF1018; cl01815 998088003699 Mor transcription activator family; Region: Mor; cl02360 998088003700 Lysozyme family protein [General function prediction only]; Region: zliS; COG3926 998088003701 Predicted lysozyme (DUF847); Region: DUF847; pfam05838 998088003702 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 998088003703 Protein of unknown function (DUF2730); Region: DUF2730; pfam10805 998088003704 Protein of unknown function (DUF3486); Region: DUF3486; pfam11985 998088003705 Mu-like prophage FluMu protein gp28 [General function prediction only]; Region: COG4373 998088003706 Mu-like prophage protein gp29 [Function unknown]; Region: COG4383 998088003707 Phage virion morphogenesis family; Region: Phage_tail_S; cl02089 998088003708 Mu-like prophage I protein [General function prediction only]; Region: COG4388 998088003709 Mu-like prophage I protein; Region: Mu-like_Pro; pfam10123 998088003710 Mu-like prophage major head subunit gpT; Region: Mu-like_gpT; cl01826 998088003711 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 998088003712 Protein of unknown function (DUF1320); Region: DUF1320; cl01818 998088003713 trans-2-enoyl-CoA reductase; Provisional; Region: PRK13656 998088003714 NAD(P)H binding domain of trans-2-enoyl-CoA reductase; Region: Eno-Rase_NADH_b; pfam12242 998088003715 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088003716 Enoyl reductase FAD binding domain; Region: Eno-Rase_FAD_bd; pfam07055 998088003717 alanine aminotransferase; Provisional; Region: PTZ00377 998088003718 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 998088003719 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088003720 homodimer interface [polypeptide binding]; other site 998088003721 catalytic residue [active] 998088003722 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 998088003723 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-...; Region: MIP; cd00333 998088003724 amphipathic channel; other site 998088003725 Asn-Pro-Ala signature motifs; other site 998088003726 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 998088003727 N-acetyl-D-glucosamine binding site [chemical binding]; other site 998088003728 catalytic residue [active] 998088003729 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088003730 Protein of unknown function (DUF1439); Region: DUF1439; cl06345 998088003731 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 998088003732 Catalytic domain, repeat 1, of Escherichia coli cardiolipin synthase and similar proteins; Region: PLDc_EcCLS_like_1; cd09152 998088003733 putative active site [active] 998088003734 catalytic site [active] 998088003735 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase and similar proteins; Region: PLDc_EcCLS_like_2; cd09158 998088003736 putative active site [active] 998088003737 catalytic site [active] 998088003738 Bacterial protein of unknown function (DUF945); Region: DUF945; pfam06097 998088003739 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 998088003740 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 998088003741 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 998088003742 putative active site [active] 998088003743 putative substrate binding site [chemical binding]; other site 998088003744 putative cosubstrate binding site; other site 998088003745 catalytic site [active] 998088003746 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 998088003747 Murein lipoprotein [Cell envelope biogenesis, outer membrane]; Region: COG4238; cl11539 998088003748 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 998088003749 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 998088003750 Phosphopantetheinyl transferase [Coenzyme metabolism]; Region: Sfp; COG2091 998088003751 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 998088003752 NlpC/P60 family; Region: NLPC_P60; cl11438 998088003753 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 998088003754 Protein of unknown function (DUF890); Region: Methyltransf_10; pfam05971 998088003755 NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. Rhizobium and related species form nodules on the roots of their...; Region: NodN; cd03450 998088003756 putative active site [active] 998088003757 putative catalytic site [active] 998088003758 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 998088003759 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088003760 transmembrane helices; other site 998088003761 Protein of unknown function, DUF481; Region: DUF481; cl01213 998088003762 L,D-transpeptidase; Provisional; Region: PRK10190 998088003763 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 998088003764 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 998088003765 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 998088003766 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 998088003767 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088003768 active site 998088003769 phosphorylation site [posttranslational modification] 998088003770 intermolecular recognition site; other site 998088003771 dimerization interface [polypeptide binding]; other site 998088003772 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 998088003773 DNA binding site [nucleotide binding] 998088003774 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 998088003775 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088003776 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 998088003777 dimer interface [polypeptide binding]; other site 998088003778 phosphorylation site [posttranslational modification] 998088003779 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088003780 ATP binding site [chemical binding]; other site 998088003781 Mg2+ binding site [ion binding]; other site 998088003782 G-X-G motif; other site 998088003783 Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]; Region: HepA; COG0553 998088003784 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 998088003785 ATP binding site [chemical binding]; other site 998088003786 putative Mg++ binding site [ion binding]; other site 998088003787 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 998088003788 nucleotide binding region [chemical binding]; other site 998088003789 ATP-binding site [chemical binding]; other site 998088003790 DNA replication terminus site-binding protein (Ter protein); Region: Ter; cl11502 998088003791 Domain of unknown function (DUF1127); Region: DUF1127; cl02276 998088003792 Peptidase M14 Succinylglutamate desuccinylase (ASTE, also known as N-succinyl-L-glutamate amidohydrolase, N2-succinylglutamate desuccinylase, and SGDS; EC 3.5.1.96) belongs to the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily...; Region: M14_ASTE; cd03855 998088003793 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 998088003794 putative active site [active] 998088003795 Zn-binding site [ion binding]; other site 998088003796 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 998088003797 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 998088003798 N-acetyl-D-glucosamine binding site [chemical binding]; other site 998088003799 catalytic residue [active] 998088003800 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 998088003801 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 998088003802 putative peptidoglycan binding site; other site 998088003803 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 998088003804 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 998088003805 putative peptidoglycan binding site; other site 998088003806 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 998088003807 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 998088003808 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 998088003809 RNA/DNA hybrid binding site [nucleotide binding]; other site 998088003810 active site 998088003811 Proteobacterial; Region: dnaQ_proteo; TIGR01406 998088003812 DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; Region: DNA_pol_III_epsilon_Ecoli_like; cd06131 998088003813 active site 998088003814 substrate binding site [chemical binding]; other site 998088003815 catalytic site [active] 998088003816 TIGR03503 family protein; Region: TIGR03503 998088003817 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 998088003818 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cl09944 998088003819 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 998088003820 Domain of unknown function (DUF3369); Region: DUF3369; pfam11849 998088003821 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088003822 Zn2+ binding site [ion binding]; other site 998088003823 Mg2+ binding site [ion binding]; other site 998088003824 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 998088003825 Siderophore interacting proteins share the domain structure of the ferredoxin reductase like family. Siderophores are produced in various bacteria (and some plants) to extract iron from hosts. Binding constants are high, so iron can be pilfered from...; Region: siderophore_interacting; cd06193 998088003826 FAD binding pocket [chemical binding]; other site 998088003827 FAD binding motif [chemical binding]; other site 998088003828 phosphate binding motif [ion binding]; other site 998088003829 NAD binding pocket [chemical binding]; other site 998088003830 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist...; Region: TM_ABC_iron-siderophores_like; cd06550 998088003831 ABC-ATPase subunit interface; other site 998088003832 dimer interface [polypeptide binding]; other site 998088003833 putative PBP binding regions; other site 998088003834 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist...; Region: TM_ABC_iron-siderophores_like; cd06550 998088003835 ABC-ATPase subunit interface; other site 998088003836 dimer interface [polypeptide binding]; other site 998088003837 putative PBP binding regions; other site 998088003838 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 998088003839 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 998088003840 Walker A/P-loop; other site 998088003841 ATP binding site [chemical binding]; other site 998088003842 Q-loop/lid; other site 998088003843 ABC transporter signature motif; other site 998088003844 Walker B; other site 998088003845 D-loop; other site 998088003846 H-loop/switch region; other site 998088003847 Fe3+-siderophore binding domain FhuD. These proteins have been shown to function as initial receptors in ABC transport of Fe3+-siderophores in many eubacterial species. They belong to the TroA-like superfamily of helical backbone metal receptor...; Region: FhuD; cd01146 998088003848 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 998088003849 siderophore binding site; other site 998088003850 Copper binding periplasmic protein CusF; Region: CusF_Ec; cl02363 998088003851 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 998088003852 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 998088003853 Copper binding periplasmic protein CusF; Region: CusF_Ec; cl02363 998088003854 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl09488 998088003855 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 998088003856 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 998088003857 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 998088003858 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 998088003859 putative phosphate binding site [ion binding]; other site 998088003860 putative catalytic site [active] 998088003861 active site 998088003862 metal binding site A [ion binding]; metal-binding site 998088003863 DNA binding site [nucleotide binding] 998088003864 putative AP binding site [nucleotide binding]; other site 998088003865 putative metal binding site B [ion binding]; other site 998088003866 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 998088003867 Ion channel; Region: Ion_trans_2; cl11596 998088003868 Response regulator receiver domain; Region: Response_reg; pfam00072 998088003869 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088003870 active site 998088003871 phosphorylation site [posttranslational modification] 998088003872 intermolecular recognition site; other site 998088003873 dimerization interface [polypeptide binding]; other site 998088003874 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 998088003875 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi...; Region: TPR; cd00189 998088003876 TPR motif; other site 998088003877 binding surface 998088003878 ApbE family; Region: ApbE; cl00643 998088003879 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 998088003880 HutD; Region: HutD; cl01532 998088003881 hypothetical protein; Provisional; Region: PRK11239 998088003882 Protein of unknown function, DUF480; Region: DUF480; cl01209 998088003883 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088003884 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088003885 metal binding site [ion binding]; metal-binding site 998088003886 active site 998088003887 I-site; other site 998088003888 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088003889 Protein of unknown function (DUF465); Region: DUF465; cl01070 998088003890 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 998088003891 MatE; Region: MatE; cl10513 998088003892 MatE; Region: MatE; cl10513 998088003893 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 998088003894 Sulfate transporter family; Region: Sulfate_transp; cl00967 998088003895 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 998088003896 Bacterial protein of unknown function (DUF925); Region: DUF925; cl01435 998088003897 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088003898 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 998088003899 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 998088003900 active site 998088003901 NAD binding site [chemical binding]; other site 998088003902 metal binding site [ion binding]; metal-binding site 998088003903 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 998088003904 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088003905 aldehyde dehydrogenase family protein; Provisional; Region: PTZ00381 998088003906 Coniferyl aldehyde dehydrogenase-like; Region: ALDH_CALDH_CalB; cd07133 998088003907 NAD(P) binding site [chemical binding]; other site 998088003908 catalytic residues [active] 998088003909 NH_hydro_CaPnhB: A subgroup of nucleoside hydrolases similar to Corynebacterium ammoniagenes Purine/pyrimidine nucleoside hydrolase (pnhB). Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base...; Region: nuc_hydro_CaPnhB; cd02650 998088003910 active site 998088003911 Protein of unknown function (DUF3634); Region: DUF3634; pfam12321 998088003912 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 998088003913 Cytochrome c; Region: Cytochrom_C; cl11414 998088003914 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088003915 Protoporphyrinogen oxidase [Coenzyme metabolism]; Region: HemY; COG1232 998088003916 Protein of unknown function (DUF805); Region: DUF805; cl01224 998088003917 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 998088003918 putative active site [active] 998088003919 DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases. They exists as monomers and homodimers; Region: NUC; cd00091 998088003920 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 998088003921 active site 998088003922 substrate binding site [chemical binding]; other site 998088003923 Mg2+ binding site [ion binding]; other site 998088003924 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 998088003925 active site 998088003926 phosphorylation site [posttranslational modification] 998088003927 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 998088003928 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA...; Region: PTS_IIB_fructose; cd05569 998088003929 P-loop; other site 998088003930 active site 998088003931 phosphorylation site [posttranslational modification] 998088003932 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 998088003933 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 998088003934 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088003935 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088003936 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088003937 mannose-6-phosphate isomerase, class I; Region: manA; TIGR00218 998088003938 mannose-6-phosphate isomerase; Provisional; Region: PRK15131 998088003939 mannose-6-phosphate isomerase, class I; Region: manA; TIGR00218 998088003940 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 998088003941 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088003942 isocitrate dehydrogenase; Validated; Region: PRK07362 998088003943 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 998088003944 D-Serine dehydratase is a pyridoxal phosphate (PLP)-dependent enzyme which catalyzes the conversion of L- or D-serine to pyruvate and ammonia. D-serine dehydratase serves as a detoxifying enzyme in most E. coli strains where D-serine is a competitive...; Region: D-Ser-dehyd; cd06447 998088003945 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 998088003946 catalytic residue [active] 998088003947 GntP family permease; Region: GntP_permease; cl15264 998088003948 gluconate transporter; Region: gntP; TIGR00791 998088003949 DNA-binding transcriptional regulator DsdC; Provisional; Region: PRK10086 998088003950 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088003951 HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 998088003952 dimerization interface [polypeptide binding]; other site 998088003953 substrate binding pocket [chemical binding]; other site 998088003954 NlpC/P60 family; Region: NLPC_P60; cl11438 998088003955 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 998088003956 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088003957 The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_OxyR; cd08411 998088003958 dimerization interface [polypeptide binding]; other site 998088003959 peroxidase; Provisional; Region: PRK15000 998088003960 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic...; Region: PRX_Typ2cys; cd03015 998088003961 dimer interface [polypeptide binding]; other site 998088003962 decamer (pentamer of dimers) interface [polypeptide binding]; other site 998088003963 catalytic triad [active] 998088003964 peroxidatic and resolving cysteines [active] 998088003965 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 998088003966 Protein of unknown function (DUF785); Region: DUF785; cl01682 998088003967 tRNA mo(5)U34 methyltransferase; Provisional; Region: PRK15068 998088003968 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cd02440 998088003969 S-adenosylmethionine binding site [chemical binding]; other site 998088003970 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cd02440 998088003971 S-adenosylmethionine binding site [chemical binding]; other site 998088003972 Protein of unknown function DUF72; Region: DUF72; cl00777 998088003973 Zinc ribbon domain; Region: CxxC_CxxC_SSSS; cl00993 998088003974 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 998088003975 EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND)...; Region: EcAspRS_like_N; cd04317 998088003976 dimer interface [polypeptide binding]; other site 998088003977 anticodon binding site; other site 998088003978 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the...; Region: AspRS_core; cd00777 998088003979 homodimer interface [polypeptide binding]; other site 998088003980 motif 1; other site 998088003981 active site 998088003982 motif 2; other site 998088003983 GAD domain; Region: GAD; pfam02938 998088003984 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 998088003985 active site 998088003986 motif 3; other site 998088003987 Domain of unknown function DUF28; Region: DUF28; cl00361 998088003988 bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional; Region: PRK13805 998088003989 Coenzyme A acylating aldehyde dehydrogenase (ACDH), ALDH family 20-like; Region: ALDH_F20_ACDH; cd07122 998088003990 putative catalytic cysteine [active] 998088003991 C-terminal alcohol dehydrogenase domain of the acetaldehyde dehydrogenase-alcohol dehydrogenase bifunctional two-domain protein (AAD); Region: AAD_C; cd08178 998088003992 putative active site [active] 998088003993 metal binding site [ion binding]; metal-binding site 998088003994 MarC family integral membrane protein; Region: MarC; cl00919 998088003995 oligopeptide ABC transporter substrate-binding protein OppA; Provisional; Region: PRK15104 998088003996 The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; Region: PBP2_OppA; cd08504 998088003997 peptide binding site [polypeptide binding]; other site 998088003998 oligopeptide transporter permease; Reviewed; Region: oppB; PRK09471 998088003999 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088004000 dimer interface [polypeptide binding]; other site 998088004001 conserved gate region; other site 998088004002 putative PBP binding loops; other site 998088004003 ABC-ATPase subunit interface; other site 998088004004 oligopeptide ABC transporter permease OppC; Provisional; Region: PRK15406 998088004005 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 998088004006 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088004007 dimer interface [polypeptide binding]; other site 998088004008 conserved gate region; other site 998088004009 putative PBP binding loops; other site 998088004010 ABC-ATPase subunit interface; other site 998088004011 oligopeptide transporter ATP-binding component; Provisional; Region: oppD; PRK09473 998088004012 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 998088004013 Walker A/P-loop; other site 998088004014 ATP binding site [chemical binding]; other site 998088004015 Q-loop/lid; other site 998088004016 ABC transporter signature motif; other site 998088004017 Walker B; other site 998088004018 D-loop; other site 998088004019 H-loop/switch region; other site 998088004020 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 998088004021 oligopeptide ABC transporter ATP-binding protein OppF; Provisional; Region: PRK15079 998088004022 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 998088004023 Walker A/P-loop; other site 998088004024 ATP binding site [chemical binding]; other site 998088004025 Q-loop/lid; other site 998088004026 ABC transporter signature motif; other site 998088004027 Walker B; other site 998088004028 D-loop; other site 998088004029 H-loop/switch region; other site 998088004030 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 998088004031 Integral membrane protein TerC family; Region: TerC; cl10468 998088004032 alanine racemase; Reviewed; Region: PRK13340 998088004033 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme, Alanine Racemase 2; Region: PLPDE_III_AR2; cd06826 998088004034 active site 998088004035 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 998088004036 dimer interface [polypeptide binding]; other site 998088004037 substrate binding site [chemical binding]; other site 998088004038 catalytic residues [active] 998088004039 Isoprenylcysteine carboxyl methyltransferase (ICMT) family; Region: ICMT; cl00763 998088004040 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 998088004041 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088004042 Walker A motif; other site 998088004043 ATP binding site [chemical binding]; other site 998088004044 Walker B motif; other site 998088004045 Protein of unknown function, DUF486; Region: DUF486; cl01236 998088004046 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088004047 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088004048 substrate binding pocket [chemical binding]; other site 998088004049 membrane-bound complex binding site; other site 998088004050 hinge residues; other site 998088004051 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist...; Region: TM_ABC_iron-siderophores_like; cd06550 998088004052 dimer interface [polypeptide binding]; other site 998088004053 putative PBP binding regions; other site 998088004054 ABC-ATPase subunit interface; other site 998088004055 vitamin B12-transporter ATPase; Provisional; Region: PRK03695 998088004056 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088004057 Walker A/P-loop; other site 998088004058 ATP binding site [chemical binding]; other site 998088004059 Q-loop/lid; other site 998088004060 ABC transporter signature motif; other site 998088004061 Walker B; other site 998088004062 D-loop; other site 998088004063 H-loop/switch region; other site 998088004064 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088004065 NeuB family; Region: NeuB; cl00496 998088004066 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 998088004067 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; cl00526 998088004068 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 998088004069 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088004070 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 998088004071 L-serine binding site [chemical binding]; other site 998088004072 ACT domain interface; other site 998088004073 RPI_A: Ribose 5-phosphate isomerase type A (RPI_A) subfamily; RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate, the first step of the non-oxidative branch of the pentose phosphate pathway. This reaction leads to the...; Region: RPI_A; cd01398 998088004074 tetramer (dimer of dimers) interface [polypeptide binding]; other site 998088004075 active site 998088004076 dimer interface [polypeptide binding]; other site 998088004077 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 998088004078 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088004079 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088004080 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 998088004081 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 998088004082 dihydrodipicolinate reductase; Provisional; Region: PRK00048 998088004083 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088004084 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 998088004085 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 998088004086 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; cl03056 998088004087 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 998088004088 catalytic site [active] 998088004089 subunit interface [polypeptide binding]; other site 998088004090 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 998088004091 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 998088004092 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 998088004093 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 998088004094 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 998088004095 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 998088004096 Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways...; Region: MGS_CPS_II; cd01424 998088004097 IMP binding site; other site 998088004098 dimer interface [polypeptide binding]; other site 998088004099 interdomain contacts; other site 998088004100 partial ornithine binding site; other site 998088004101 Protein of unknown function (DUF1615); Region: DUF1615; pfam07759 998088004102 bifunctional chorismate mutase/prephenate dehydrogenase; Provisional; Region: tyrA; PRK11199 998088004103 Chorismate mutase type II; Region: CM_2; cl00693 998088004104 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088004105 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088004106 NeuB family; Region: NeuB; cl00496 998088004107 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 998088004108 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 998088004109 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 998088004110 ligand binding site [chemical binding]; other site 998088004111 oligomer interface [polypeptide binding]; other site 998088004112 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and rate-...; Region: LbH_G1P_AT_C; cd04651 998088004113 dimer interface [polypeptide binding]; other site 998088004114 N-terminal domain interface [polypeptide binding]; other site 998088004115 sulfate 1 binding site; other site 998088004116 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13021 998088004117 Protein export membrane protein; Region: SecD_SecF; cl14618 998088004118 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK12933 998088004119 Protein export membrane protein; Region: SecD_SecF; cl14618 998088004120 Choline Kinase (ChoK). The ChoK subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and...; Region: ChoK; cd05151 998088004121 Phosphotransferase enzyme family; Region: APH; pfam01636 998088004122 active site 998088004123 ATP binding site [chemical binding]; other site 998088004124 substrate binding site [chemical binding]; other site 998088004125 dimer interface [polypeptide binding]; other site 998088004126 Curli production assembly/transport component CsgG; Region: CsgG; cl00639 998088004127 Putative periplasmic lipoprotein; Region: DUF1425; cd09030 998088004128 putative dimer interface [polypeptide binding]; other site 998088004129 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3014 998088004130 Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a...; Region: PKCI_related; cd01276 998088004131 nucleotide binding site/active site [active] 998088004132 HIT family signature motif; other site 998088004133 catalytic residue [active] 998088004134 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 998088004135 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088004136 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088004137 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088004138 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 998088004139 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 998088004140 dihydroorotase; Reviewed; Region: PRK09236 998088004141 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have...; Region: metallo-dependent_hydrolases; cl00281 998088004142 Dihydroorotase (DHOase), subgroup IIb; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This group contains the archeal members of the DHOase family; Region: DHOase_IIb; cd01318 998088004143 active site 998088004144 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 998088004145 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 998088004146 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088004147 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088004148 Bacterial protein of unknown function (DUF924); Region: DUF924; cl01561 998088004149 Protein of unknown function (DUF808); Region: DUF808; cl01002 998088004150 Protein of unknown function (DUF808); Region: DUF808; cl01002 998088004151 oligoendopeptidase, pepF/M3 family; Region: M3_fam_3; TIGR02290 998088004152 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_2; cd09607 998088004153 active site 998088004154 Zn binding site [ion binding]; other site 998088004155 Permease family; Region: Xan_ur_permease; pfam00860 998088004156 Sulfate transporter family; Region: Sulfate_transp; cl00967 998088004157 Uncharacterised protein family (UPF0227); Region: UPF0227; cl14886 998088004158 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 998088004159 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088004160 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; cl00397 998088004161 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster...; Region: Radical_SAM; cl15259 998088004162 GAF domain; Region: GAF; cl00853 998088004163 PAS fold; Region: PAS; pfam00989 998088004164 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 998088004165 putative active site [active] 998088004166 heme pocket [chemical binding]; other site 998088004167 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088004168 metal binding site [ion binding]; metal-binding site 998088004169 active site 998088004170 I-site; other site 998088004171 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 998088004172 CoA-disulfide reductase; Region: CoA_CoA_reduc; TIGR03385 998088004173 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088004174 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 998088004175 Member of the Rhodanese Homology Domain superfamily. Included in this CD are the Lactococcus lactis NADH oxidase, Bacillus cereus NADH dehydrogenase, and Bacteroides thetaiotaomicron pyridine nucleotide-disulphide oxidoreductase, and similar rhodanese-...; Region: RHOD_Pyr_redox; cd01524 998088004176 active site residue [active] 998088004177 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 998088004178 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 998088004179 MG2 domain; Region: A2M_N; pfam01835 998088004180 Alpha-2-macroglobulin family N-terminal region; Region: A2M_N_2; pfam07703 998088004181 Proteins similar to alpha2-macroglobulin (alpha (2)-M). Alpha (2)-M is a major carrier protein in serum. It is a broadly specific proteinase inhibitor. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of...; Region: A2M_like; cd02891 998088004182 surface patch; other site 998088004183 thioester region; other site 998088004184 specificity defining residues; other site 998088004185 penicillin-binding protein 1C; Provisional; Region: PRK11240 998088004186 Transglycosylase; Region: Transgly; cl07896 998088004187 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 998088004188 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 998088004189 tRNA s(4)U8 sulfurtransferase; Provisional; Region: PRK01269 998088004190 THUMP domain; Region: THUMP; cl12076 998088004191 ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. It belongs to the Adenosine Nucleotide Hydrolysis suoerfamily and predicted to bind to Adenosine nucleotide; Region: ThiI; cd01712 998088004192 Ligand Binding Site [chemical binding]; other site 998088004193 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 998088004194 active site residue [active] 998088004195 hypothetical protein; Provisional; Region: PRK10578 998088004196 UPF0126 domain; Region: UPF0126; pfam03458 998088004197 UPF0126 domain; Region: UPF0126; pfam03458 998088004198 flagellin; Provisional; Region: PRK12802 998088004199 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 998088004200 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 998088004201 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 998088004202 flagellin; Provisional; Region: PRK12802 998088004203 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 998088004204 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 998088004205 flagellin; Provisional; Region: PRK12802 998088004206 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 998088004207 flagellar capping protein; Reviewed; Region: fliD; PRK08032 998088004208 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 998088004209 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 998088004210 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 998088004211 Flagellar protein FliS; Region: FliS; cl00654 998088004212 Thiamine pyrophosphokinase; Region: TPK; cl09135 998088004213 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088004214 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 998088004215 Transposase; Region: DEDD_Tnp_IS110; pfam01548 998088004216 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 998088004217 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 998088004218 vitamin B12-transporter protein BtuF; Provisional; Region: PRK03379 998088004219 Cobalamin binding protein BtuF. These proteins have been shown to function as initial receptors in ABC transport of vitamin B12 (cobalamin) in eubacterial and some archaeal species. They belong to the TroA superfamily of helical backbone metal...; Region: BtuF; cd01144 998088004220 cobalamin binding residues [chemical binding]; other site 998088004221 putative BtuC binding residues; other site 998088004222 dimer interface [polypeptide binding]; other site 998088004223 CobD/Cbib protein; Region: CobD_Cbib; cl00561 998088004224 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 998088004225 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 998088004226 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 998088004227 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088004228 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088004229 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088004230 IMPase, inositol monophosphatase and related domains. A family of Mg++ dependent phosphatases, inhibited by lithium, many of which may act on inositol monophosphate substrate. They dephosphorylate inositol phosphate to generate inositol, which may be...; Region: IMPase; cd01639 998088004231 active site 998088004232 dimerization interface [polypeptide binding]; other site 998088004233 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 998088004234 GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen...; Region: GST_N_Ure2p_like; cd03048 998088004235 C-terminal domain interface [polypeptide binding]; other site 998088004236 GSH binding site (G-site) [chemical binding]; other site 998088004237 dimer interface [polypeptide binding]; other site 998088004238 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 998088004239 N-terminal domain interface [polypeptide binding]; other site 998088004240 dimer interface [polypeptide binding]; other site 998088004241 substrate binding pocket (H-site) [chemical binding]; other site 998088004242 multidrug resistance protein D; Provisional; Region: emrD; PRK11652 998088004243 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088004244 putative substrate translocation pore; other site 998088004245 Cell division protein ZapA; Region: ZapA; cl01146 998088004246 Uncharacterised protein family (UPF0149); Region: UPF0149; cl01173 998088004247 2-polyprenyl-6-methoxyphenol 4-hydroxylase; Region: UbiH; TIGR01984 998088004248 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088004249 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088004250 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 998088004251 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 998088004252 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 998088004253 Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and L-...; Region: GCS_H; cd06848 998088004254 lipoyl attachment site [posttranslational modification]; other site 998088004255 glycine dehydrogenase; Provisional; Region: PRK05367 998088004256 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 998088004257 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 998088004258 catalytic residue [active] 998088004259 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2...; Region: GDC-P; cd00613 998088004260 tetramer interface [polypeptide binding]; other site 998088004261 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088004262 catalytic residue [active] 998088004263 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 998088004264 PAS fold; Region: PAS_3; pfam08447 998088004265 putative active site [active] 998088004266 heme pocket [chemical binding]; other site 998088004267 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088004268 Predicted permease; Region: DUF318; cl00487 998088004269 Predicted permease; Region: DUF318; cl00487 998088004270 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 998088004271 dimerization interface [polypeptide binding]; other site 998088004272 putative DNA binding site [nucleotide binding]; other site 998088004273 putative Zn2+ binding site [ion binding]; other site 998088004274 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 998088004275 Domain of unknown function (DUF299); Region: DUF299; cl00780 998088004276 phosphoenolpyruvate synthase; Validated; Region: PRK06464 998088004277 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 998088004278 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 998088004279 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 998088004280 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 998088004281 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088004282 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 998088004283 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088004284 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 998088004285 Glycosyl hydrolase family 3 C terminal domain; Region: Glyco_hydro_3_C; pfam01915 998088004286 Peptidase S8 family domain in Protein convertases; Region: Peptidases_S8_Protein_convertases_Kexins_Furin-lik; cd04059 998088004287 calcium binding site 1 [ion binding]; other site 998088004288 active site 998088004289 catalytic triad [active] 998088004290 calcium binding site 2 [ion binding]; other site 998088004291 calcium binding site 3 [ion binding]; other site 998088004292 Proprotein convertase P-domain; Region: P_proprotein; pfam01483 998088004293 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 998088004294 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]; Region: COG3083 998088004295 Domain of unknown function (DUF3413); Region: DUF3413; pfam11893 998088004296 Sulfatase; Region: Sulfatase; cl10460 998088004297 Protein of unknown function (DUF1414); Region: DUF1414; cl01175 998088004298 Nucleoid-associated protein [General function prediction only]; Region: COG3081 998088004299 nucleoid-associated protein NdpA; Validated; Region: PRK00378 998088004300 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088004301 Maltose-binding periplasmic proteins/domains [Carbohydrate transport and metabolism]; Region: MalE; COG2182 998088004302 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088004303 dimer interface [polypeptide binding]; other site 998088004304 conserved gate region; other site 998088004305 putative PBP binding loops; other site 998088004306 ABC-ATPase subunit interface; other site 998088004307 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 998088004308 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088004309 dimer interface [polypeptide binding]; other site 998088004310 conserved gate region; other site 998088004311 putative PBP binding loops; other site 998088004312 ABC-ATPase subunit interface; other site 998088004313 maltose/maltodextrin transporter ATP-binding protein; Provisional; Region: PRK11000 998088004314 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 998088004315 Walker A/P-loop; other site 998088004316 ATP binding site [chemical binding]; other site 998088004317 Q-loop/lid; other site 998088004318 ABC transporter signature motif; other site 998088004319 Walker B; other site 998088004320 D-loop; other site 998088004321 H-loop/switch region; other site 998088004322 TOBE domain; Region: TOBE_2; cl01440 998088004323 TOBE domain; Region: TOBE_2; cl01440 998088004324 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 998088004325 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 998088004326 MltA-interacting protein MipA; Region: MipA; cl01504 998088004327 Domain of unknown function DUF20; Region: UPF0118; cl00465 998088004328 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-...; Region: SirA_YedF_YeeD; cd00291 998088004329 CPxP motif; other site 998088004330 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 998088004331 Peptidase family M48; Region: Peptidase_M48; cl12018 998088004332 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi...; Region: TPR; cd00189 998088004333 TPR motif; other site 998088004334 binding surface 998088004335 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing...; Region: TlpA_like_family; cd02966 998088004336 catalytic residues [active] 998088004337 Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the...; Region: ArsC_ArsC; cd03034 998088004338 catalytic residues [active] 998088004339 Predicted membrane protein (DUF2069); Region: DUF2069; cl01299 998088004340 Protein of unknown function, DUF479; Region: DUF479; cl01203 998088004341 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 998088004342 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088004343 substrate binding pocket [chemical binding]; other site 998088004344 membrane-bound complex binding site; other site 998088004345 hinge residues; other site 998088004346 isoaspartyl dipeptidase; Provisional; Region: PRK10657 998088004347 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have...; Region: metallo-dependent_hydrolases; cl00281 998088004348 active site 998088004349 Membrane protein of unknown function (DUF340); Region: DUF340; cl01028 998088004350 ABC-type histidine transport system, ATPase component [Amino acid transport and metabolism]; Region: HisP; COG4598 998088004351 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP; Region: ABC_HisP_GlnQ_permeases; cd03262 998088004352 Walker A/P-loop; other site 998088004353 ATP binding site [chemical binding]; other site 998088004354 Q-loop/lid; other site 998088004355 ABC transporter signature motif; other site 998088004356 Walker B; other site 998088004357 D-loop; other site 998088004358 H-loop/switch region; other site 998088004359 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 998088004360 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088004361 substrate binding pocket [chemical binding]; other site 998088004362 membrane-bound complex binding site; other site 998088004363 hinge residues; other site 998088004364 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 998088004365 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088004366 dimer interface [polypeptide binding]; other site 998088004367 conserved gate region; other site 998088004368 putative PBP binding loops; other site 998088004369 ABC-ATPase subunit interface; other site 998088004370 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 998088004371 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088004372 dimer interface [polypeptide binding]; other site 998088004373 conserved gate region; other site 998088004374 putative PBP binding loops; other site 998088004375 ABC-ATPase subunit interface; other site 998088004376 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF...; Region: PseudoU_synth_RluCD_like; cd02869 998088004377 active site 998088004378 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 998088004379 4-hydroxyphenylpyruvate dioxygenase; Region: 4HPPD; TIGR01263 998088004380 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 998088004381 dimer interface [polypeptide binding]; other site 998088004382 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 998088004383 active site 998088004384 Fe binding site [ion binding]; other site 998088004385 homogentisate 1,2-dioxygenase; Region: HgmA; cl10473 998088004386 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 998088004387 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 998088004388 GST_N family, Class Zeta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens...; Region: GST_N_Zeta; cd03042 998088004389 maleylacetoacetate isomerase; Region: maiA; TIGR01262 998088004390 C-terminal domain interface [polypeptide binding]; other site 998088004391 GSH binding site (G-site) [chemical binding]; other site 998088004392 putative dimer interface [polypeptide binding]; other site 998088004393 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 998088004394 dimer interface [polypeptide binding]; other site 998088004395 N-terminal domain interface [polypeptide binding]; other site 998088004396 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 998088004397 Peptidase family C69; Region: Peptidase_C69; cl01920 998088004398 peptidase T; Region: peptidase-T; TIGR01882 998088004399 M20 Peptidase T specifically cleaves tripeptides; Region: M20_peptT; cd03892 998088004400 metal binding site [ion binding]; metal-binding site 998088004401 dimer interface [polypeptide binding]; other site 998088004402 C4-dicarboxylate transporter DcuC; Provisional; Region: dcuC; cl15274 998088004403 C4-dicarboxylate transporter [Energy production and conversion]; Region: DcuC; COG3069 998088004404 Lipid A 3-O-deacylase (PagL); Region: PagL; pfam09411 998088004405 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 998088004406 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 998088004407 ABC-2 type transporter; Region: ABC2_membrane; cl11417 998088004408 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088004409 ABC transporter signature motif; other site 998088004410 Walker B; other site 998088004411 D-loop; other site 998088004412 H-loop/switch region; other site 998088004413 polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family; Region: BexC_CtrB_KpsE; TIGR01010 998088004414 Vi polysaccharide export inner membrane protein VexD; Provisional; Region: PRK15178 998088004415 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 998088004416 Glycosyl transferases group 1; Region: Glycos_transf_1; cl12012 998088004417 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 998088004418 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 998088004419 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088004420 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 998088004421 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088004422 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 998088004423 Glycosyl transferases group 1; Region: Glycos_transf_1; cl12012 998088004424 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 998088004425 active site 998088004426 tetramer interface [polypeptide binding]; other site 998088004427 dTDP-glucose 4,6 dehydratase; Provisional; Region: PRK10084 998088004428 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 998088004429 NAD binding site [chemical binding]; other site 998088004430 substrate binding site [chemical binding]; other site 998088004431 homodimer interface [polypeptide binding]; other site 998088004432 active site 998088004433 dTDP-4-dehydrorhamnose reductase; Provisional; Region: PRK09987 998088004434 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 998088004435 NADP binding site [chemical binding]; other site 998088004436 active site 998088004437 putative substrate binding site [chemical binding]; other site 998088004438 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 998088004439 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 998088004440 substrate binding site [chemical binding]; other site 998088004441 tetramer interface [polypeptide binding]; other site 998088004442 Cupin domain; Region: Cupin_2; cl09118 998088004443 Capsule polysaccharide export protein [Cell envelope biogenesis, outer membrane]; Region: KpsC; COG3563 998088004444 Capsule polysaccharide export protein [Cell envelope biogenesis, outer membrane]; Region: KpsS; COG3562 998088004445 asparagine synthetase B; Provisional; Region: asnB; PRK09431 998088004446 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 998088004447 active site 998088004448 dimer interface [polypeptide binding]; other site 998088004449 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes...; Region: Asn_Synthase_B_C; cd01991 998088004450 Ligand Binding Site [chemical binding]; other site 998088004451 Molecular Tunnel; other site 998088004452 Cupin domain; Region: Cupin_2; cl09118 998088004453 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 998088004454 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 998088004455 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088004456 UMP phosphatase; Provisional; Region: PRK10444 998088004457 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cd01427 998088004458 active site 998088004459 motif I; other site 998088004460 motif II; other site 998088004461 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cd01427 998088004462 Adenosine deaminase (ADA) is a monomeric zinc dependent enzyme which catalyzes the irreversible hydrolytic deamination of both adenosine, as well as desoxyadenosine, to ammonia and inosine or desoxyinosine, respectively. ADA plays an important role in...; Region: ADA; cd01320 998088004463 active site 998088004464 purine riboside binding site [chemical binding]; other site 998088004465 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR5; cd08271 998088004466 putative NAD(P) binding site [chemical binding]; other site 998088004467 substrate binding site [chemical binding]; other site 998088004468 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 998088004469 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN; cd02933 998088004470 FMN binding site [chemical binding]; other site 998088004471 active site 998088004472 substrate binding site [chemical binding]; other site 998088004473 catalytic residue [active] 998088004474 Integral membrane protein TerC family; Region: TerC; cl10468 998088004475 FOG: CBS domain [General function prediction only]; Region: COG0517 998088004476 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in...; Region: CBS_pair_CorC_HlyC_assoc; cd04590 998088004477 Transporter associated domain; Region: CorC_HlyC; cl08393 998088004478 Cation efflux family; Region: Cation_efflux; cl00316 998088004479 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 998088004480 FAD binding domain; Region: FAD_binding_4; pfam01565 998088004481 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 998088004482 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 998088004483 CoenzymeA binding site [chemical binding]; other site 998088004484 subunit interaction site [polypeptide binding]; other site 998088004485 PHB binding site; other site 998088004486 ATP-dependent RNA helicase DeaD; Provisional; Region: PRK11634 998088004487 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (...; Region: DEADc; cd00268 998088004488 ATP binding site [chemical binding]; other site 998088004489 Mg++ binding site [ion binding]; other site 998088004490 motif III; other site 998088004491 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 998088004492 nucleotide binding region [chemical binding]; other site 998088004493 ATP-binding site [chemical binding]; other site 998088004494 DbpA RNA binding domain; Region: DbpA; pfam03880 998088004495 Predicted permease [General function prediction only]; Region: COG2056 998088004496 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088004497 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 998088004498 DEDDh 3'-5' exonuclease domain of RNase T; Region: RNaseT; cd06134 998088004499 dimer interface [polypeptide binding]; other site 998088004500 putative active site [active] 998088004501 putative substrate binding site [chemical binding]; other site 998088004502 catalytic site [active] 998088004503 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cl00474 998088004504 erythronate-4-phosphate dehydrogenase; Validated; Region: PRK00257 998088004505 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088004506 Domain of unknown function (DUF3410); Region: DUF3410; pfam11890 998088004507 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 998088004508 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088004509 Semialdehyde dehydrogenase, dimerisation domain; Region: Semialdhyde_dhC; pfam02774 998088004510 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 998088004511 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 998088004512 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 998088004513 PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1)...; Region: PseudoU_synth_EcTruA; cd02570 998088004514 dimerization interface 3.5A [polypeptide binding]; other site 998088004515 active site 998088004516 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 998088004517 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 998088004518 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional; Region: PRK10846 998088004519 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 998088004520 cell division protein DedD; Provisional; Region: PRK11633 998088004521 Sporulation related domain; Region: SPOR; cl10051 998088004522 Domain of unknown function (DUF74); Region: DUF74; cl00426 998088004523 siroheme synthase; Provisional; Region: cysG; PRK10637 998088004524 precorrin-2 dehydrogenase; Validated; Region: PRK06719 998088004525 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 998088004526 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 998088004527 sulfite reductase, subunit C; Region: sulfite_red_C; TIGR02912 998088004528 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 998088004529 4Fe-4S binding domain; Region: Fer4; cl02805 998088004530 4Fe-4S binding domain; Region: Fer4; cl02805 998088004531 anaerobic sulfite reductase subunit B; Provisional; Region: PRK08221 998088004532 Anaerobic sulfite reductase contains an FAD and NADPH binding module with structural similarity to ferredoxin reductase and sequence similarity to dihydroorotate dehydrogenases. Clostridium pasteurianum inducible dissimilatory type sulfite reductase is...; Region: sulfite_reductase_like; cd06221 998088004533 FAD binding pocket [chemical binding]; other site 998088004534 FAD binding motif [chemical binding]; other site 998088004535 phosphate binding motif [ion binding]; other site 998088004536 beta-alpha-beta structure motif; other site 998088004537 NAD binding pocket [chemical binding]; other site 998088004538 Iron coordination center [ion binding]; other site 998088004539 anaerobic sulfite reductase subunit A; Provisional; Region: PRK15055 998088004540 putative encapsidation protein; Region: PHA01076 998088004541 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: COG4667 998088004542 Hypothetical patatin similar to yjju protein of Escherichia coli; Region: Pat_hypo_Ecoli_yjju_like; cd07208 998088004543 active site 998088004544 nucleophile elbow; other site 998088004545 Microcin C7 self-immunity protein determines resistance to exogenous microcin C7; Region: Peptidase_S66_mccF_like; cd07062 998088004546 putative dimer interface [polypeptide binding]; other site 998088004547 catalytic triad [active] 998088004548 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 998088004549 Sulfatase; Region: Sulfatase; cl10460 998088004550 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 998088004551 active site 998088004552 substrate binding site [chemical binding]; other site 998088004553 ATP binding site [chemical binding]; other site 998088004554 aspartate kinase III; Validated; Region: PRK09084 998088004555 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 998088004556 nucleotide binding site [chemical binding]; other site 998088004557 substrate binding site [chemical binding]; other site 998088004558 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC_1; cd04932 998088004559 lysine allosteric regulatory site; other site 998088004560 dimer interface [polypeptide binding]; other site 998088004561 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC_2; cd04917 998088004562 dimer interface [polypeptide binding]; other site 998088004563 N-acetylglutamate synthase; Validated; Region: PRK05279 998088004564 AAK_NAGS-ABP: N-acetylglutamate (NAG) kinase-like domain of the NAG Synthase (NAGS) of the arginine-biosynthesis pathway (ABP) found in gamma- and beta-proteobacteria and higher plant chloroplasts. Domain architecture of these NAGS consisted of an N-...; Region: AAK_NAGS-ABP; cd04237 998088004565 putative feedback inhibition sensing region; other site 998088004566 putative nucleotide binding site [chemical binding]; other site 998088004567 putative substrate binding site [chemical binding]; other site 998088004568 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088004569 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 998088004570 Protein of unknown function (DUF3802); Region: DUF3802; pfam12290 998088004571 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088004572 Protein of unknown function (DUF419); Region: DUF419; cl15265 998088004573 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 998088004574 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 998088004575 Hydroxyneurosporene synthase (CrtC); Region: CrtC; cl12101 998088004576 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 998088004577 FtsX-like permease family; Region: FtsX; pfam02687 998088004578 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 998088004579 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 998088004580 Walker A/P-loop; other site 998088004581 ATP binding site [chemical binding]; other site 998088004582 Q-loop/lid; other site 998088004583 ABC transporter signature motif; other site 998088004584 Walker B; other site 998088004585 D-loop; other site 998088004586 H-loop/switch region; other site 998088004587 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088004588 transmembrane helices; other site 998088004589 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 998088004590 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088004591 putative substrate translocation pore; other site 998088004592 hypothetical protein; Provisional; Region: PRK07208 998088004593 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088004594 Iron permease FTR1 family; Region: FTR1; cl00475 998088004595 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 998088004596 putative transposase OrfB; Reviewed; Region: PHA02517 998088004597 Protein of unknown function (DUF2860); Region: DUF2860; pfam11059 998088004598 putative transporter; Provisional; Region: PRK11660 998088004599 Sulfate transporter family; Region: Sulfate_transp; cl00967 998088004600 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 998088004601 recombination protein RecR; Reviewed; Region: recR; PRK00076 998088004602 RecR protein; Region: RecR; pfam02132 998088004603 TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR. RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a...; Region: TOPRIM_recR; cd01025 998088004604 putative active site [active] 998088004605 putative metal-binding site [ion binding]; other site 998088004606 tetramer interface [polypeptide binding]; other site 998088004607 heat shock protein 90; Provisional; Region: PRK05218 998088004608 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088004609 ATP binding site [chemical binding]; other site 998088004610 Mg2+ binding site [ion binding]; other site 998088004611 G-X-G motif; other site 998088004612 antimicrobial peptide ABC system ATP-binding protein SapF; Provisional; Region: PRK15112 998088004613 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 998088004614 Walker A/P-loop; other site 998088004615 ATP binding site [chemical binding]; other site 998088004616 Q-loop/lid; other site 998088004617 ABC transporter signature motif; other site 998088004618 Walker B; other site 998088004619 D-loop; other site 998088004620 H-loop/switch region; other site 998088004621 antimicrobial peptide ABC transporter ATP-binding protein; Provisional; Region: PRK15093 998088004622 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 998088004623 Walker A/P-loop; other site 998088004624 ATP binding site [chemical binding]; other site 998088004625 Q-loop/lid; other site 998088004626 ABC transporter signature motif; other site 998088004627 Walker B; other site 998088004628 D-loop; other site 998088004629 H-loop/switch region; other site 998088004630 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 998088004631 antimicrobial peptide ABC transporter permease SapC; Provisional; Region: PRK15111 998088004632 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 998088004633 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088004634 putative PBP binding loops; other site 998088004635 dimer interface [polypeptide binding]; other site 998088004636 ABC-ATPase subunit interface; other site 998088004637 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088004638 dimer interface [polypeptide binding]; other site 998088004639 conserved gate region; other site 998088004640 putative PBP binding loops; other site 998088004641 ABC-ATPase subunit interface; other site 998088004642 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 998088004643 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 998088004644 peptide binding site [polypeptide binding]; other site 998088004645 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 998088004646 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088004647 Walker A motif; other site 998088004648 ATP binding site [chemical binding]; other site 998088004649 Walker B motif; other site 998088004650 arginine finger; other site 998088004651 phage shock protein PspA; Provisional; Region: PRK10698 998088004652 phage shock protein A; Region: phageshock_pspA; TIGR02977 998088004653 Phage shock protein B; Region: PspB; cl05946 998088004654 PspC domain; Region: PspC; cl00864 998088004655 phage shock protein C; Region: phageshock_pspC; TIGR02978 998088004656 YcjX-like family, DUF463; Region: DUF463; cl01193 998088004657 hypothetical protein; Provisional; Region: PRK05415 998088004658 Domain of unknown function (DUF697); Region: DUF697; cl12064 998088004659 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088004660 DNA-binding transcriptional regulator CynR; Provisional; Region: PRK11242 998088004661 The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_PAO1_like; cd08412 998088004662 putative substrate binding pocket [chemical binding]; other site 998088004663 dimerization interface [polypeptide binding]; other site 998088004664 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088004665 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 998088004666 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088004667 Walker A/P-loop; other site 998088004668 ATP binding site [chemical binding]; other site 998088004669 Q-loop/lid; other site 998088004670 ABC transporter signature motif; other site 998088004671 Walker B; other site 998088004672 D-loop; other site 998088004673 H-loop/switch region; other site 998088004674 TOBE domain; Region: TOBE_2; cl01440 998088004675 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088004676 dimer interface [polypeptide binding]; other site 998088004677 conserved gate region; other site 998088004678 putative PBP binding loops; other site 998088004679 ABC-ATPase subunit interface; other site 998088004680 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088004681 dimer interface [polypeptide binding]; other site 998088004682 conserved gate region; other site 998088004683 putative PBP binding loops; other site 998088004684 ABC-ATPase subunit interface; other site 998088004685 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 998088004686 Escherichia coli NAD+-dependent gamma-aminobutyraldehyde dehydrogenase YdcW-like; Region: ALDH_ABALDH-YdcW; cd07092 998088004687 tetrameric interface [polypeptide binding]; other site 998088004688 NAD binding site [chemical binding]; other site 998088004689 catalytic residues [active] 998088004690 substrate binding site [chemical binding]; other site 998088004691 Prokaryotic phenylalanine-4-hydroxylase (pro_PheOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes the eukaryotic proteins, phenylalanine-4-hydroxylase (eu_PheOH)...; Region: pro_PheOH; cd03348 998088004692 cofactor binding site; other site 998088004693 metal binding site [ion binding]; metal-binding site 998088004694 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH_subfamily_a; cd00913 998088004695 aromatic arch; other site 998088004696 DCoH dimer interaction site [polypeptide binding]; other site 998088004697 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 998088004698 DCoH tetramer interaction site [polypeptide binding]; other site 998088004699 substrate binding site [chemical binding]; other site 998088004700 DNA-binding transcriptional regulator TyrR; Provisional; Region: PRK10820 998088004701 N-terminal ACT domain of the TyrR protein; Region: ACT_TyrR; cd04877 998088004702 putative aromatic amino acid binding site; other site 998088004703 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 998088004704 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088004705 Walker A motif; other site 998088004706 ATP binding site [chemical binding]; other site 998088004707 Walker B motif; other site 998088004708 arginine finger; other site 998088004709 putative inner membrane diguanylate cyclase; Provisional; Region: PRK09966 998088004710 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088004711 metal binding site [ion binding]; metal-binding site 998088004712 active site 998088004713 I-site; other site 998088004714 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088004715 ligand binding site [chemical binding]; other site 998088004716 Integral membrane protein TerC family; Region: TerC; cl10468 998088004717 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 998088004718 YfcL protein; Region: YfcL; pfam08891 998088004719 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 998088004720 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 998088004721 Cys/Met metabolism PLP-dependent enzyme; Region: Cys_Met_Meta_PP; pfam01053 998088004722 CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of...; Region: CGS_like; cd00614 998088004723 homodimer interface [polypeptide binding]; other site 998088004724 substrate-cofactor binding pocket; other site 998088004725 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088004726 catalytic residue [active] 998088004727 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 998088004728 flavanone-3-hydroxylase; Provisional; Region: PLN03176 998088004729 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl01206 998088004730 biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Region: BVR-B_like_SDR_a; cd05244 998088004731 NAD binding site [chemical binding]; other site 998088004732 substrate binding site [chemical binding]; other site 998088004733 putative active site [active] 998088004734 transcriptional regulator; Provisional; Region: PRK10632 998088004735 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088004736 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 998088004737 putative effector binding pocket; other site 998088004738 dimerization interface [polypeptide binding]; other site 998088004739 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 998088004740 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088004741 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088004742 dimerization interface [polypeptide binding]; other site 998088004743 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088004744 putative substrate translocation pore; other site 998088004745 Cupin domain; Region: Cupin_2; cl09118 998088004746 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 998088004747 Isochorismatase family; Region: Isochorismatase; pfam00857 998088004748 YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them...; Region: YcaC_related; cd01012 998088004749 catalytic triad [active] 998088004750 dimer interface [polypeptide binding]; other site 998088004751 conserved cis-peptide bond; other site 998088004752 LysR family transcriptional regulator; Provisional; Region: PRK14997 998088004753 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 998088004754 putative effector binding pocket; other site 998088004755 dimerization interface [polypeptide binding]; other site 998088004756 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088004757 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088004758 The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; Region: PBP2_MetR; cd08441 998088004759 putative dimerization interface [polypeptide binding]; other site 998088004760 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 998088004761 N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by...; Region: CIMS_N_terminal_like; cd03312 998088004762 THF binding site; other site 998088004763 C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by...; Region: CIMS_C_terminal_like; cd03311 998088004764 substrate binding site [chemical binding]; other site 998088004765 THF binding site; other site 998088004766 zinc-binding site [ion binding]; other site 998088004767 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088004768 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088004769 substrate binding pocket [chemical binding]; other site 998088004770 membrane-bound complex binding site; other site 998088004771 hinge residues; other site 998088004772 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088004773 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088004774 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 998088004775 dimerization interface [polypeptide binding]; other site 998088004776 substrate binding pocket [chemical binding]; other site 998088004777 Beta-glucosidase/6-phospho-beta-glucosidase/beta- galactosidase [Carbohydrate transport and metabolism]; Region: BglB; cl01046 998088004778 Glycosyl hydrolase family 1; Region: Glyco_hydro_1; pfam00232 998088004779 YcaO-like family; Region: YcaO; cl09146 998088004780 Formate/nitrite transporter; Region: Form_Nir_trans; cl00927 998088004781 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 998088004782 Pyruvate formate lyase 1; Region: PFL1; cd01678 998088004783 coenzyme A binding site [chemical binding]; other site 998088004784 active site 998088004785 catalytic residues [active] 998088004786 glycine loop; other site 998088004787 Flagellin N-methylase; Region: FliB; cl00497 998088004788 Cell division inhibitor SulA; Region: SulA; cl01880 998088004789 This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of...; Region: GT1_Glycogen_Phosphorylase; cd04300 998088004790 homodimer interface [polypeptide binding]; other site 998088004791 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 998088004792 active site pocket [active] 998088004793 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 998088004794 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 998088004795 transmembrane helices; other site 998088004796 thioredoxin 2; Provisional; Region: PRK10996 998088004797 TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947 998088004798 catalytic residues [active] 998088004799 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 998088004800 dimer interface [polypeptide binding]; other site 998088004801 phosphorylation site [posttranslational modification] 998088004802 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088004803 ATP binding site [chemical binding]; other site 998088004804 Mg2+ binding site [ion binding]; other site 998088004805 G-X-G motif; other site 998088004806 Response regulator receiver domain; Region: Response_reg; pfam00072 998088004807 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088004808 active site 998088004809 phosphorylation site [posttranslational modification] 998088004810 intermolecular recognition site; other site 998088004811 dimerization interface [polypeptide binding]; other site 998088004812 Response regulator receiver domain; Region: Response_reg; pfam00072 998088004813 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088004814 active site 998088004815 phosphorylation site [posttranslational modification] 998088004816 intermolecular recognition site; other site 998088004817 dimerization interface [polypeptide binding]; other site 998088004818 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 998088004819 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 998088004820 putative multidrug transporter membrane\ATP-binding components; Provisional; Region: PRK10789 998088004821 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088004822 Walker A/P-loop; other site 998088004823 ATP binding site [chemical binding]; other site 998088004824 Q-loop/lid; other site 998088004825 ABC transporter signature motif; other site 998088004826 Walker B; other site 998088004827 D-loop; other site 998088004828 H-loop/switch region; other site 998088004829 putative multidrug transporter membrane\ATP-binding components; Provisional; Region: PRK10790 998088004830 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 998088004831 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088004832 Walker A/P-loop; other site 998088004833 ATP binding site [chemical binding]; other site 998088004834 Q-loop/lid; other site 998088004835 ABC transporter signature motif; other site 998088004836 Walker B; other site 998088004837 D-loop; other site 998088004838 H-loop/switch region; other site 998088004839 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 998088004840 Pyridoxal kinase plays a key role in the synthesis of the active coenzyme pyridoxal-5'-phosphate (PLP), by catalyzing the phosphorylation of the precursor vitamin B6 in the presence of Zn2+ and ATP. Mammals are unable to synthesize PLP de novo and...; Region: pyridoxal_pyridoxamine_kinase; cd01173 998088004841 dimer interface [polypeptide binding]; other site 998088004842 pyridoxal binding site [chemical binding]; other site 998088004843 ATP binding site [chemical binding]; other site 998088004844 Glycerol dehydrogenases (GlyDH) catalyzes oxidation of glycerol to dihydroxyacetone in glycerol dissmilation; Region: GlyDH; cd08170 998088004845 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 998088004846 dimer interface [polypeptide binding]; other site 998088004847 active site 998088004848 metal binding site [ion binding]; metal-binding site 998088004849 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 998088004850 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088004851 Coenzyme A binding pocket [chemical binding]; other site 998088004852 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_31; cd04690 998088004853 nudix motif; other site 998088004854 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088004855 Escherichia coli (Ec) citrate synthase (CS) GltA_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS...; Region: EcCS_like; cd06114 998088004856 dimer interface [polypeptide binding]; other site 998088004857 Citrate synthase; Region: Citrate_synt; pfam00285 998088004858 active site 998088004859 citrylCoA binding site [chemical binding]; other site 998088004860 NADH binding [chemical binding]; other site 998088004861 cationic pore residues; other site 998088004862 oxalacetate/citrate binding site [chemical binding]; other site 998088004863 coenzyme A binding site [chemical binding]; other site 998088004864 catalytic triad [active] 998088004865 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the...; Region: SQR_TypeC_SdhC; cd03499 998088004866 Iron-sulfur protein interface; other site 998088004867 proximal quinone binding site [chemical binding]; other site 998088004868 SdhD (CybS) interface [polypeptide binding]; other site 998088004869 proximal heme binding site [chemical binding]; other site 998088004870 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. E. coli SQR, a member of this subfamily, reduces the...; Region: SQR_TypeC_SdhD; cd03494 998088004871 SdhC subunit interface [polypeptide binding]; other site 998088004872 proximal heme binding site [chemical binding]; other site 998088004873 cardiolipin binding site; other site 998088004874 Iron-sulfur protein interface; other site 998088004875 proximal quinone binding site [chemical binding]; other site 998088004876 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK08958 998088004877 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088004878 domain; Region: Succ_DH_flav_C; pfam02910 998088004879 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 998088004880 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 998088004881 TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of 2-oxoglutarate to succinyl-CoA and carbon dioxide, a key reaction of...; Region: TPP_E1_OGDC_like; cd02016 998088004882 TPP-binding site [chemical binding]; other site 998088004883 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 998088004884 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 998088004885 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 998088004886 E3 interaction surface; other site 998088004887 lipoyl attachment site [posttranslational modification]; other site 998088004888 e3 binding domain; Region: E3_binding; pfam02817 998088004889 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 998088004890 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 998088004891 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 998088004892 CoA-ligase; Region: Ligase_CoA; pfam00549 998088004893 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 998088004894 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088004895 CoA-ligase; Region: Ligase_CoA; pfam00549 998088004896 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 998088004897 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 998088004898 putative 2-aminoethylphosphonate ABC transporter, permease protein; Region: PhnU2; TIGR03262 998088004899 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088004900 dimer interface [polypeptide binding]; other site 998088004901 conserved gate region; other site 998088004902 putative PBP binding loops; other site 998088004903 ABC-ATPase subunit interface; other site 998088004904 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088004905 dimer interface [polypeptide binding]; other site 998088004906 conserved gate region; other site 998088004907 putative PBP binding loops; other site 998088004908 ABC-ATPase subunit interface; other site 998088004909 putative 2-aminoethylphosphonate ABC transporter, ATP-binding protein; Region: PhnT2; TIGR03265 998088004910 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088004911 Walker A/P-loop; other site 998088004912 ATP binding site [chemical binding]; other site 998088004913 Q-loop/lid; other site 998088004914 ABC transporter signature motif; other site 998088004915 Walker B; other site 998088004916 D-loop; other site 998088004917 H-loop/switch region; other site 998088004918 TOBE domain; Region: TOBE_2; cl01440 998088004919 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088004920 transcriptional regulator protein; Region: phnR; TIGR03337 998088004921 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 998088004922 DNA-binding site [nucleotide binding]; DNA binding site 998088004923 UTRA domain; Region: UTRA; cl01230 998088004924 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 998088004925 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 998088004926 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 998088004927 catalytic residue [active] 998088004928 4-aminobutyrate aminotransferase; Provisional; Region: PRK06082 998088004929 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase...; Region: OAT_like; cd00610 998088004930 inhibitor-cofactor binding pocket; inhibition site 998088004931 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088004932 catalytic residue [active] 998088004933 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 998088004934 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 998088004935 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_36; cd04695 998088004936 nudix motif; other site 998088004937 Predicted Zn-dependent protease (DUF2268); Region: DUF2268; cl02316 998088004938 Cytochrome C biogenesis protein; Region: CcmH; cl01179 998088004939 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi...; Region: TPR; cd00189 998088004940 binding surface 998088004941 TPR motif; other site 998088004942 TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c...; Region: TlpA_like_DsbE; cd03010 998088004943 catalytic residues [active] 998088004944 central insert; other site 998088004945 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 998088004946 Polysulphide reductase [Energy production and conversion]; Region: COG5557; cl01295 998088004947 Formate-dependent nitrite reductase, membrane component [Inorganic ion transport and metabolism]; Region: NrfD; COG3301 998088004948 cytochrome c nitrite reductase, Fe-S protein; Region: cyt_nit_nrfC; TIGR03149 998088004949 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved alpha-; Region: HCP_like; cl14655 998088004950 cytochrome c nitrite reductase pentaheme subunit; Provisional; Region: PRK11659 998088004951 cytochrome c nitrite reductase subunit c552; Provisional; Region: nrfA; cl10556 998088004952 Cytochrome c552; Region: Cytochrom_C552; pfam02335 998088004953 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 998088004954 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 998088004955 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 998088004956 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 998088004957 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 998088004958 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 998088004959 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 998088004960 type 1 secretion C-terminal target domain (VC_A0849 subclass); Region: T1SS_VCA0849; TIGR03661 998088004961 C subunit; Region: glycerol3P_GlpC; TIGR03379 998088004962 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved alpha-; Region: HCP_like; cl14655 998088004963 Cysteine-rich domain; Region: CCG; pfam02754 998088004964 anaerobic glycerol-3-phosphate dehydrogenase subunit B; Validated; Region: PRK05329 998088004965 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl10040 998088004966 sn-glycerol-3-phosphate dehydrogenase subunit A; Provisional; Region: glpA; PRK11101 998088004967 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 998088004968 SEC-C motif; Region: SEC-C; cl12132 998088004969 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4564 998088004970 Cache domain; Region: Cache_2; cl07034 998088004971 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cd06225 998088004972 dimerization interface [polypeptide binding]; other site 998088004973 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088004974 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088004975 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 998088004976 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 998088004977 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 998088004978 DTW domain; Region: DTW; cl01221 998088004979 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 998088004980 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 998088004981 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088004982 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 998088004983 dimerization interface [polypeptide binding]; other site 998088004984 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 998088004985 EamA-like transporter family; Region: EamA; cl01037 998088004986 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088004987 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 998088004988 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088004989 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]; Region: COG3593 998088004990 Protein of unknown function (DUF2813); Region: DUF2813; pfam11398 998088004991 TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as...; Region: TOPRIM_OLD; cd01026 998088004992 putative active site [active] 998088004993 putative metal-binding site [ion binding]; other site 998088004994 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 998088004995 Isoamylase N-terminus domain. Isoamylase (aka glycogen 6-glucanohydrolase) is one of the starch-debranching enzymes that catalyzes the hydrolysis of alpha-1,6-glucosidic linkages specific in alpha-glucans such as amylopectin or glycogen. Isoamylase...; Region: Isoamylase_N_term; cd02852 998088004996 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 998088004997 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein...; Region: Peptidase_M17; cd00433 998088004998 interface (dimer of trimers) [polypeptide binding]; other site 998088004999 Substrate-binding/catalytic site; other site 998088005000 Zn-binding sites [ion binding]; other site 998088005001 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 998088005002 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cd01427 998088005003 motif II; other site 998088005004 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088005005 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088005006 substrate binding pocket [chemical binding]; other site 998088005007 membrane-bound complex binding site; other site 998088005008 hinge residues; other site 998088005009 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 998088005010 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 998088005011 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and...; Region: DUS_like_FMN; cd02801 998088005012 FMN binding site [chemical binding]; other site 998088005013 active site 998088005014 catalytic residues [active] 998088005015 substrate binding site [chemical binding]; other site 998088005016 Protein of unknown function (DUF454); Region: DUF454; cl01063 998088005017 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 998088005018 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088005019 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 998088005020 Walker A motif; other site 998088005021 ATP binding site [chemical binding]; other site 998088005022 Walker B motif; other site 998088005023 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088005024 arginine finger; other site 998088005025 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 998088005026 DNA polymerase III tau subunit V interacting with alpha; Region: DNA_pol3_tau_5; pfam12170 998088005027 Uncharacterised BCR, YbaB family COG0718; Region: DUF149; cl00494 998088005028 endonuclease IV; Provisional; Region: PRK01060 998088005029 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of D-arabino-6-...; Region: AP2Ec; cd00019 998088005030 AP (apurinic/apyrimidinic) site pocket; other site 998088005031 DNA interaction; other site 998088005032 Metal-binding active site; metal-binding site 998088005033 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 998088005034 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088005035 C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; Region: PBP2_CysL_like; cd08420 998088005036 putative dimerization interface [polypeptide binding]; other site 998088005037 C4-dicarboxylate transporters of the Tellurite-resistance/Dicarboxylate Transporter (TDT) family; Region: TDT_C4-dicarb_trans; cd09325 998088005038 C4-dicarboxylate transporter/malic acid transport protein; Region: C4dic_mal_tran; pfam03595 998088005039 gating phenylalanine in ion channel; other site 998088005040 lipid A biosynthesis lauroyl acyltransferase; Provisional; Region: PRK05906 998088005041 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 998088005042 putative acyl-acceptor binding pocket; other site 998088005043 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 998088005044 putative acyl-acceptor binding pocket; other site 998088005045 RIO kinase family; RIO1, RIO3 and similar proteins, catalytic domain. The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein...; Region: RIO1_like; cd05145 998088005046 ATP binding site [chemical binding]; other site 998088005047 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088005048 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088005049 metal binding site [ion binding]; metal-binding site 998088005050 active site 998088005051 I-site; other site 998088005052 This CD includes bacterial (Agrobacterium tumefaciens and Caulobacter crescentus ProX, and Clostridium sticklandii PrdX) and eukaryotic (Plasmodium falciparum N-terminal ProRS editing domain) sequences. The C. sticklandii PrdX protein, a homolog of the...; Region: PrdX_deacylase; cd04335 998088005053 putative deacylase active site [active] 998088005054 DNA polymerase II; Reviewed; Region: PRK05762 998088005055 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases; Region: DNA_polB_II_exo; cd05784 998088005056 active site 998088005057 catalytic site [active] 998088005058 substrate binding site [chemical binding]; other site 998088005059 DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as...; Region: POLBc_Pol_II; cd05537 998088005060 active site 998088005061 metal-binding site 998088005062 DinI-like family; Region: DinI; cl11630 998088005063 Protein of unknown function (DUF2927); Region: DUF2927; pfam11150 998088005064 Protein of unknown function DUF45; Region: DUF45; cl00636 998088005065 NAD pyrophosphatase/5'-nucleotidase NadN; Region: nadN; TIGR01530 998088005066 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 998088005067 active site 998088005068 metal binding site [ion binding]; metal-binding site 998088005069 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 998088005070 C4-dicarboxylate transporter DcuC; Provisional; Region: dcuC; cl15274 998088005071 C4-dicarboxylate transporter [Energy production and conversion]; Region: DcuC; COG3069 998088005072 Bacterial protein of unknown function (DUF922); Region: DUF922; cl02415 998088005073 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 998088005074 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 998088005075 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 998088005076 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 998088005077 Beta-ketoacyl-acyl carrier protein (ACP) synthase (KAS), type I and II. KASs are responsible for the elongation steps in fatty acid biosynthesis. KASIII catalyses the initial condensation and KAS I and II catalyze further elongation steps by Claisen...; Region: KAS_I_II; cd00834 998088005078 dimer interface [polypeptide binding]; other site 998088005079 active site 998088005080 putative transporter; Provisional; Region: PRK04972 998088005081 Predicted Permease Membrane Region; Region: Asp-Al_Ex; cl06061 998088005082 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088005083 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088005084 Predicted Permease Membrane Region; Region: Asp-Al_Ex; cl06061 998088005085 excinuclease ABC subunit B; Provisional; Region: PRK05298 998088005086 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 998088005087 ATP binding site [chemical binding]; other site 998088005088 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 998088005089 nucleotide binding region [chemical binding]; other site 998088005090 ATP-binding site [chemical binding]; other site 998088005091 Ultra-violet resistance protein B; Region: UvrB; pfam12344 998088005092 UvrB/uvrC motif; Region: UVR; pfam02151 998088005093 Protein of unknown function (DUF1232); Region: DUF1232; cl01318 998088005094 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 998088005095 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 998088005096 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cd00625 998088005097 transmembrane helices; other site 998088005098 fatty acid metabolism regulator; Provisional; Region: PRK04984 998088005099 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 998088005100 DNA-binding site [nucleotide binding]; DNA binding site 998088005101 FCD domain; Region: FCD; cl11656 998088005102 Protein of unknown function (Duf2374); Region: DUF2374; cl09797 998088005103 YaeQ protein; Region: YaeQ; cl01913 998088005104 Membrane transport protein; Region: Mem_trans; cl09117 998088005105 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 998088005106 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (...; Region: S24_LexA-like; cd06529 998088005107 Catalytic site [active] 998088005108 Mu DNA-binding domain; Region: HTH_Tnp_Mu_1; pfam02316 998088005109 Integrase core domain; Region: rve; cl01316 998088005110 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088005111 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 998088005112 Protein of unknown function (DUF3164); Region: DUF3164; pfam11363 998088005113 Protein of unknown function (DUF1018); Region: DUF1018; cl01815 998088005114 Mor transcription activator family; Region: Mor; cl02360 998088005115 Predicted lysozyme (DUF847); Region: DUF847; pfam05838 998088005116 Lysozyme family protein [General function prediction only]; Region: zliS; COG3926 998088005117 Protein of unknown function (DUF2730); Region: DUF2730; pfam10805 998088005118 Protein of unknown function (DUF3486); Region: DUF3486; pfam11985 998088005119 Mu-like prophage FluMu protein gp28 [General function prediction only]; Region: COG4373 998088005120 Protein of unknown function (DUF935); Region: DUF935; pfam06074 998088005121 Mu-like prophage protein gp29 [Function unknown]; Region: COG4383 998088005122 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 998088005123 Phage virion morphogenesis family; Region: Phage_tail_S; cl02089 998088005124 Mu-like prophage I protein [General function prediction only]; Region: COG4388 998088005125 Mu-like prophage I protein; Region: Mu-like_Pro; pfam10123 998088005126 Mu-like prophage major head subunit gpT; Region: Mu-like_gpT; cl01826 998088005127 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 998088005128 Protein of unknown function (DUF1320); Region: DUF1320; cl01818 998088005129 Uncharacterised protein family (UPF0157); Region: UPF0157; cl00987 998088005130 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 998088005131 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi...; Region: TPR; cl02429 998088005132 binding surface 998088005133 TPR motif; other site 998088005134 Mu-like prophage protein [General function prediction only]; Region: COG3941; cl09192 998088005135 Membrane transport protein; Region: Mem_trans; cl09117 998088005136 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 998088005137 GAF domain; Region: GAF; cl00853 998088005138 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088005139 Walker A motif; other site 998088005140 ATP binding site [chemical binding]; other site 998088005141 Walker B motif; other site 998088005142 arginine finger; other site 998088005143 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 998088005144 multidrug efflux protein; Reviewed; Region: PRK01766 998088005145 MatE; Region: MatE; cl10513 998088005146 MatE; Region: MatE; cl10513 998088005147 Uncharacterised protein family (UPF0253); Region: UPF0253; cl11640 998088005148 EamA-like transporter family; Region: EamA; cl01037 998088005149 riboflavin synthase subunit alpha; Provisional; Region: PRK13020 998088005150 Lumazine binding domain; Region: Lum_binding; pfam00677 998088005151 Lumazine binding domain; Region: Lum_binding; pfam00677 998088005152 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 998088005153 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 998088005154 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cd01427 998088005155 motif II; other site 998088005156 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 998088005157 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088005158 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 998088005159 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 998088005160 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 998088005161 Transcriptional regulators [Transcription]; Region: MarR; COG1846 998088005162 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088005163 Uncharacterised protein family (UPF0149); Region: UPF0149; cl01173 998088005164 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 998088005165 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 998088005166 Protein of unknown function, DUF440; Region: DUF440; cl11472 998088005167 Transglycosylase; Region: Transgly; cl07896 998088005168 Protein of unknown function, DUF440; Region: DUF440; cl11472 998088005169 Septum formation topological specificity factor MinE; Region: MinE; cl00538 998088005170 cell division inhibitor MinD; Provisional; Region: PRK10818 998088005171 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a...; Region: MinD; cd02036 998088005172 Switch I; other site 998088005173 Switch II; other site 998088005174 septum formation inhibitor; Reviewed; Region: minC; PRK04804 998088005175 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 998088005176 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 998088005177 YcgL domain; Region: YcgL; cl01189 998088005178 putative transposase OrfB; Reviewed; Region: PHA02517 998088005179 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 998088005180 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 998088005181 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 998088005182 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 998088005183 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 998088005184 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 998088005185 Protein of unknown function (DUF1255); Region: DUF1255; cl01202 998088005186 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 998088005187 6-phosphofructokinase; Provisional; Region: PRK03202 998088005188 Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to a subfamily of the PFKA family (cd00363) and include bacterial ATP-dependent...; Region: Bacterial_PFK; cd00763 998088005189 active site 998088005190 ADP/pyrophosphate binding site [chemical binding]; other site 998088005191 dimerization interface [polypeptide binding]; other site 998088005192 allosteric effector site; other site 998088005193 fructose-1,6-bisphosphate binding site; other site 998088005194 Triosephosphate isomerase (TIM) is a glycolytic enzyme that catalyzes the interconversion of dihydroxyacetone phosphate and D-glyceraldehyde-3-phosphate. The reaction is very efficient and requires neither cofactors nor metal ions. TIM, usually...; Region: TIM; cd00311 998088005195 substrate binding site [chemical binding]; other site 998088005196 dimer interface [polypeptide binding]; other site 998088005197 catalytic triad [active] 998088005198 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 998088005199 putative active site [active] 998088005200 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cd02440 998088005201 S-adenosylmethionine binding site [chemical binding]; other site 998088005202 KicB killing factor; Region: KicB; cl11468 998088005203 MukE-like family; Region: MukE; cl11471 998088005204 cell division protein MukB; Provisional; Region: mukB; PRK04863 998088005205 MukB N-terminal; Region: MukB; pfam04310 998088005206 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 998088005207 nitrobindin heme-binding domain; Region: nitrobindin; cl10502 998088005208 heme-binding site [chemical binding]; other site 998088005209 Predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold [General function prediction only]; Region: LipA; COG1075 998088005210 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 998088005211 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 998088005212 aspartate/ornithine carbamoyltransferase family protein; Validated; Region: PRK07200 998088005213 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 998088005214 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088005215 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 998088005216 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD)...; Region: Trp-synth-beta_II; cd00640 998088005217 catalytic residue [active] 998088005218 peptidase; Reviewed; Region: PRK13004 998088005219 M20 Peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases; Region: M20_ArgE_DapE_like4; cd05649 998088005220 putative metal binding site [ion binding]; other site 998088005221 putative dimer interface [polypeptide binding]; other site 998088005222 phenylhydantoinase; Validated; Region: PRK08323 998088005223 D-hydantoinases (D-HYD) also called dihydropyrimidases (DHPase) and related proteins; DHPases are a family of enzymes that catalyze the reversible hydrolytic ring opening of the amide bond in five- or six-membered cyclic diamides, like...; Region: D-HYD; cd01314 998088005224 tetramer interface [polypeptide binding]; other site 998088005225 active site 998088005226 carbamate kinase; Reviewed; Region: PRK12686 998088005227 AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP. Both CK (this CD) and nonhomologous CP synthetase synthesize carbamoyl phosphate, an...; Region: AAK_CK; cd04235 998088005228 putative substrate binding site [chemical binding]; other site 998088005229 homodimer interface [polypeptide binding]; other site 998088005230 nucleotide binding site [chemical binding]; other site 998088005231 nucleotide binding site [chemical binding]; other site 998088005232 EamA-like transporter family; Region: EamA; cl01037 998088005233 EamA-like transporter family; Region: EamA; cl01037 998088005234 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 998088005235 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 998088005236 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2...; Region: Biotinyl_lipoyl_domains; cl11404 998088005237 probable selenium-dependent hydroxylase accessory protein YqeC; Region: TIGR03172 998088005238 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 998088005239 metal binding site [ion binding]; metal-binding site 998088005240 putative selenate reductase subunit YgfK; Provisional; Region: PRK09853 998088005241 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 998088005242 phosphate binding site [ion binding]; other site 998088005243 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088005244 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088005245 putative selenium metabolism protein SsnA; Region: Se_ssnA; TIGR03314 998088005246 TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are...; Region: ATZ_TRZ_like; cd01298 998088005247 active site 998088005248 putative substrate binding pocket [chemical binding]; other site 998088005249 probable selenate reductase, FAD-binding subunit; Region: Se_sel_red_FAD; TIGR03312 998088005250 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; cl08390 998088005251 putative hypoxanthine oxidase; Provisional; Region: PRK09800 998088005252 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 998088005253 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 998088005254 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 998088005255 Permease family; Region: Xan_ur_permease; pfam00860 998088005256 Sulfate transporter family; Region: Sulfate_transp; cl00967 998088005257 guanine deaminase; Provisional; Region: PRK09228 998088005258 Guanine deaminase (GDEase). Guanine deaminase is an aminohydrolase responsible for the conversion of guanine to xanthine and ammonia, the first step to utilize guanine as a nitrogen source. This reaction also removes the guanine base from the pool and...; Region: GDEase; cd01303 998088005259 active site 998088005260 Sulfate transporter family; Region: Sulfate_transp; cl00967 998088005261 Permease family; Region: Xan_ur_permease; pfam00860 998088005262 xanthine dehydrogenase subunit XdhA; Provisional; Region: PRK09970 998088005263 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 998088005264 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 998088005265 xanthine dehydrogenase subunit XdhB; Provisional; Region: PRK09971 998088005266 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; cl08390 998088005267 xanthine dehydrogenase subunit XdhC; Provisional; Region: PRK09908 998088005268 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 998088005269 catalytic loop [active] 998088005270 iron binding site [ion binding]; other site 998088005271 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 998088005272 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 998088005273 Integrase core domain; Region: rve; cl01316 998088005274 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 998088005275 acyl-CoA synthetase; Validated; Region: PRK08162 998088005276 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 998088005277 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 998088005278 PAS fold; Region: PAS_4; pfam08448 998088005279 PAS fold; Region: PAS_4; pfam08448 998088005280 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088005281 metal binding site [ion binding]; metal-binding site 998088005282 active site 998088005283 I-site; other site 998088005284 KAP family P-loop domain; Region: KAP_NTPase; pfam07693 998088005285 Predicted P-loop ATPase [General function prediction only]; Region: COG4928 998088005286 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed; Region: PRK02759 998088005287 Phosphoribosyl-AMP cyclohydrolase; Region: PRA-CH; cl00344 998088005288 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 998088005289 Imidazoleglycerol-phosphate synthase [Amino acid transport and metabolism]; Region: HisF; COG0107 998088005290 The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)-formimino-5-; Region: HisF; cd04731 998088005291 substrate binding site [chemical binding]; other site 998088005292 glutamase interaction surface [polypeptide binding]; other site 998088005293 Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase [Amino acid transport and metabolism]; Region: HisA; COG0106 998088005294 HisA. Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1'-...; Region: HisA; cd04732 998088005295 catalytic residues [active] 998088005296 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13170 998088005297 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 998088005298 putative active site [active] 998088005299 oxyanion strand; other site 998088005300 catalytic triad [active] 998088005301 imidazole glycerol-phosphate dehydratase/histidinol phosphatase; Provisional; Region: PRK05446 998088005302 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cd01427 998088005303 active site 998088005304 motif I; other site 998088005305 motif II; other site 998088005306 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 998088005307 putative active site pocket [active] 998088005308 4-fold oligomerization interface [polypeptide binding]; other site 998088005309 metal binding residues [ion binding]; metal-binding site 998088005310 3-fold/trimer interface [polypeptide binding]; other site 998088005311 histidinol-phosphate aminotransferase; Region: hisC; TIGR01141 998088005312 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 998088005313 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088005314 homodimer interface [polypeptide binding]; other site 998088005315 catalytic residue [active] 998088005316 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 998088005317 E.C 1.1.1.23. Histidinol dehydrogenase catalyzes the last two steps in the L-histidine biosynthesis pathway, which is conserved in bacteria, archaea, fungi, and plants. These last two steps are (i) the NAD-dependent oxidation of L-histidinol to L-...; Region: Histidinol_dh; cd06572 998088005318 NAD binding site [chemical binding]; other site 998088005319 dimerization interface [polypeptide binding]; other site 998088005320 product binding site; other site 998088005321 substrate binding site [chemical binding]; other site 998088005322 zinc binding site [ion binding]; other site 998088005323 catalytic residues [active] 998088005324 ATP phosphoribosyltransferase; Reviewed; Region: hisG; PRK00489 998088005325 ATP phosphoribosyltransferase; Region: HisG; cl15266 998088005326 HisG, C-terminal domain; Region: HisG_C; cl06867 998088005327 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 998088005328 DEAD_2; Region: DEAD_2; cl14887 998088005329 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088005330 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 998088005331 Outer membrane lipoprotein Slp family; Region: Slp; cl01164 998088005332 Lipase. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is 'interfacial activation', the process of becoming...; Region: Lipase; cl14883 998088005333 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 998088005334 nucleophilic elbow; other site 998088005335 catalytic triad; other site 998088005336 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08974 998088005337 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 998088005338 ribonuclease D; Provisional; Region: PRK10829 998088005339 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 998088005340 putative active site [active] 998088005341 catalytic site [active] 998088005342 putative substrate binding site [chemical binding]; other site 998088005343 HRDC domain; Region: HRDC; cl02578 998088005344 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 998088005345 tRNA 2-selenouridine synthase; Provisional; Region: PRK11784 998088005346 Member of the Rhodanese Homology Domain superfamily. This CD includes several putative ATP /GTP binding proteins including E. coli YbbB; Region: RHOD_YbbB; cd01520 998088005347 active site residue [active] 998088005348 selenophosphate synthetase; Provisional; Region: PRK00943 998088005349 Selenophosphate synthetase (SelD) catalyzes the conversion of selenium to selenophosphate which is required by a number of bacterial, archaeal and eukaryotic organisms for synthesis of Secys-tRNA, the precursor of selenocysteine in selenoenzymes. The...; Region: SelD; cd02195 998088005350 dimerization interface [polypeptide binding]; other site 998088005351 putative ATP binding site [chemical binding]; other site 998088005352 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088005353 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 998088005354 23S rRNA m(5)C1962 methyltransferase; Provisional; Region: PRK15128 998088005355 PUA domain; Region: PUA; cl00607 998088005356 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cd02440 998088005357 S-adenosylmethionine binding site [chemical binding]; other site 998088005358 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088005359 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088005360 Acylphosphatase; Region: Acylphosphatase; cl00551 998088005361 CHAD domain; Region: CHAD; cl10506 998088005362 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 998088005363 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 998088005364 active site 998088005365 HIGH motif; other site 998088005366 KMSKS motif; other site 998088005367 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 998088005368 tRNA binding surface [nucleotide binding]; other site 998088005369 anticodon binding site; other site 998088005370 tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins. This family includes EcMetRS and Aquifex aeolicus Trbp111 (AaTrbp111). This domain has general tRNA binding properties. MetRS aminoacylates methionine...; Region: tRNA_bind_EcMetRS_like; cd02800 998088005371 dimer interface [polypeptide binding]; other site 998088005372 putative tRNA-binding site [nucleotide binding]; other site 998088005373 antiporter inner membrane protein; Provisional; Region: PRK11670 998088005374 MRP (Multiple Resistance and pH adaptation) is a homologue of the Fer4_NifH superfamily. Like the other members of the superfamily, MRP contains a ATP-binding domain at the N-termini. It is found in bacteria as a membrane-spanning protein and functions...; Region: MRP-like; cd02037 998088005375 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 998088005376 Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage...; Region: UMPK; cd02023 998088005377 ATP-binding site [chemical binding]; other site 998088005378 Sugar specificity; other site 998088005379 Pyrimidine base specificity; other site 998088005380 2'-deoxycytidine 5'-triphosphate deaminase (DCD); Region: DCD; pfam06559 998088005381 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 998088005382 trimer interface [polypeptide binding]; other site 998088005383 active site 998088005384 Phosphate transporter family; Region: PHO4; cl00396 998088005385 Phosphate transporter family; Region: PHO4; cl00396 998088005386 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 998088005387 murein transglycosylase A; Provisional; Region: mltA; PRK11162 998088005388 MltA specific insert domain; Region: MltA; cl08398 998088005389 3D domain; Region: 3D; cl01439 998088005390 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 998088005391 catalytic loop [active] 998088005392 iron binding site [ion binding]; other site 998088005393 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 998088005394 dimer interface [polypeptide binding]; other site 998088005395 putative radical transfer pathway; other site 998088005396 diiron center [ion binding]; other site 998088005397 tyrosyl radical; other site 998088005398 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09103 998088005399 ATP cone domain; Region: ATP-cone; pfam03477 998088005400 Class I ribonucleotide reductase; Region: RNR_I; cd01679 998088005401 active site 998088005402 dimer interface [polypeptide binding]; other site 998088005403 catalytic residues [active] 998088005404 effector binding site; other site 998088005405 R2 peptide binding site; other site 998088005406 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 998088005407 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cd01427 998088005408 motif II; other site 998088005409 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 998088005410 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cd02440 998088005411 S-adenosylmethionine binding site [chemical binding]; other site 998088005412 DNA gyrase subunit A; Validated; Region: PRK05560 998088005413 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in...; Region: TOP4c; cd00187 998088005414 CAP-like domain; other site 998088005415 Active site [active] 998088005416 primary dimer interface [polypeptide binding]; other site 998088005417 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 998088005418 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 998088005419 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 998088005420 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 998088005421 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 998088005422 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 998088005423 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 998088005424 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 998088005425 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster...; Region: Radical_SAM; cl15259 998088005426 Sel1 repeat; Region: Sel1; cl02723 998088005427 Sel1 repeat; Region: Sel1; cl02723 998088005428 Sel1 repeat; Region: Sel1; cl02723 998088005429 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 998088005430 TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase...; Region: TGS_ThrRS_N; cd01667 998088005431 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 998088005432 Threonyl-tRNA synthetase (ThrRS) class II core catalytic domain. ThrRS is a homodimer. It is responsible for the attachment of threonine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ThrRS_core; cd00771 998088005433 active site 998088005434 dimer interface [polypeptide binding]; other site 998088005435 motif 1; other site 998088005436 motif 2; other site 998088005437 motif 3; other site 998088005438 ThrRS Threonyl-anticodon binding domain. ThrRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is...; Region: ThrRS_anticodon; cd00860 998088005439 anticodon binding site; other site 998088005440 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 998088005441 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 998088005442 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 998088005443 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 998088005444 23S rRNA binding site [nucleotide binding]; other site 998088005445 L21 binding site [polypeptide binding]; other site 998088005446 L13 binding site [polypeptide binding]; other site 998088005447 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 998088005448 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 998088005449 Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs. This domain is primarily responsible...; Region: PheRS_alpha_core; cd00496 998088005450 dimer interface [polypeptide binding]; other site 998088005451 motif 1; other site 998088005452 active site 998088005453 motif 2; other site 998088005454 motif 3; other site 998088005455 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 998088005456 tRNA-binding-domain-containing prokaryotic phenylalanly tRNA synthetase (PheRS) beta chain. PheRS aminoacylate phenylalanine transfer RNAs (tRNAphe). PheRSs belong structurally to class II aminoacyl tRNA synthetases (aaRSs) but, as they aminoacylate...; Region: tRNA_bind_bactPheRS; cd02796 998088005457 putative tRNA-binding site [nucleotide binding]; other site 998088005458 B3/4 domain; Region: B3_4; cl11458 998088005459 tRNA synthetase B5 domain; Region: B5; cl08394 998088005460 Phenylalanyl-tRNA synthetase (PheRS) beta chain core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an...; Region: PheRS_beta_core; cd00769 998088005461 dimer interface [polypeptide binding]; other site 998088005462 motif 1; other site 998088005463 motif 3; other site 998088005464 motif 2; other site 998088005465 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 998088005466 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-...; Region: HU_IHF; cd00591 998088005467 IHF dimer interface [polypeptide binding]; other site 998088005468 IHF - DNA interface [nucleotide binding]; other site 998088005469 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]; Region: HisJ; COG0834 998088005470 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088005471 substrate binding pocket [chemical binding]; other site 998088005472 membrane-bound complex binding site; other site 998088005473 hinge residues; other site 998088005474 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 998088005475 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088005476 substrate binding pocket [chemical binding]; other site 998088005477 membrane-bound complex binding site; other site 998088005478 hinge residues; other site 998088005479 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 998088005480 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 998088005481 dimer interface [polypeptide binding]; other site 998088005482 phosphorylation site [posttranslational modification] 998088005483 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088005484 ATP binding site [chemical binding]; other site 998088005485 Mg2+ binding site [ion binding]; other site 998088005486 G-X-G motif; other site 998088005487 Response regulator receiver domain; Region: Response_reg; pfam00072 998088005488 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088005489 active site 998088005490 phosphorylation site [posttranslational modification] 998088005491 intermolecular recognition site; other site 998088005492 dimerization interface [polypeptide binding]; other site 998088005493 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 998088005494 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cl09944 998088005495 Response regulator receiver domain; Region: Response_reg; pfam00072 998088005496 SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes...; Region: SIRT5_Af1_CobB; cd01412 998088005497 NAD+ binding site [chemical binding]; other site 998088005498 substrate binding site [chemical binding]; other site 998088005499 Zn binding site [ion binding]; other site 998088005500 Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the...; Region: SO_family_Moco; cl00199 998088005501 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088005502 metal binding site [ion binding]; metal-binding site 998088005503 active site 998088005504 I-site; other site 998088005505 DNA-binding transcriptional repressor PurR; Provisional; Region: PRK10703 998088005506 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 998088005507 DNA binding site [nucleotide binding] 998088005508 domain linker motif; other site 998088005509 Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli; Region: PBP1_PurR; cd06275 998088005510 dimerization interface [polypeptide binding]; other site 998088005511 ligand binding site [chemical binding]; other site 998088005512 pfkB family carbohydrate kinase; Region: PfkB; pfam00294 998088005513 Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of...; Region: ribokinase; cd01174 998088005514 substrate binding site [chemical binding]; other site 998088005515 dimer interface [polypeptide binding]; other site 998088005516 ATP binding site [chemical binding]; other site 998088005517 D-ribose transporter subunit RbsB; Provisional; Region: PRK10653 998088005518 Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs; Region: PBP1_ribose_binding; cd06323 998088005519 ligand binding site [chemical binding]; other site 998088005520 dimerization interface [polypeptide binding]; other site 998088005521 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 998088005522 TM-ABC transporter signature motif; other site 998088005523 D-ribose transporter ATP binding protein; Provisional; Region: PRK10762 998088005524 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and...; Region: ABC_Carb_Monos_I; cd03216 998088005525 Walker A/P-loop; other site 998088005526 ATP binding site [chemical binding]; other site 998088005527 Q-loop/lid; other site 998088005528 ABC transporter signature motif; other site 998088005529 Walker B; other site 998088005530 D-loop; other site 998088005531 H-loop/switch region; other site 998088005532 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (; Region: ABC_Carb_Monos_II; cd03215 998088005533 RbsD / FucU transport protein family; Region: RbsD_FucU; cl00809 998088005534 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 998088005535 GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens...; Region: GST_N_Beta; cd03057 998088005536 C-terminal domain interface [polypeptide binding]; other site 998088005537 GSH binding site (G-site) [chemical binding]; other site 998088005538 dimer interface [polypeptide binding]; other site 998088005539 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 998088005540 dimer interface [polypeptide binding]; other site 998088005541 substrate binding pocket (H-site) [chemical binding]; other site 998088005542 N-terminal domain interface [polypeptide binding]; other site 998088005543 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 998088005544 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088005545 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cl00427 998088005546 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 998088005547 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088005548 dimer interface [polypeptide binding]; other site 998088005549 conserved gate region; other site 998088005550 putative PBP binding loops; other site 998088005551 ABC-ATPase subunit interface; other site 998088005552 putrescine/spermidine ABC transporter ATPase protein; Reviewed; Region: potA; PRK09452 998088005553 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088005554 Walker A/P-loop; other site 998088005555 ATP binding site [chemical binding]; other site 998088005556 Q-loop/lid; other site 998088005557 ABC transporter signature motif; other site 998088005558 Walker B; other site 998088005559 D-loop; other site 998088005560 H-loop/switch region; other site 998088005561 TOBE domain; Region: TOBE_2; cl01440 998088005562 Protein of unknown function (DUF2987); Region: DUF2987; pfam11205 998088005563 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 998088005564 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This...; Region: Alpha_ANH_like_II; cd01993 998088005565 Ligand Binding Site [chemical binding]; other site 998088005566 universal stress protein UspE; Provisional; Region: PRK11175 998088005567 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 998088005568 Ligand Binding Site [chemical binding]; other site 998088005569 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 998088005570 Ligand Binding Site [chemical binding]; other site 998088005571 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 998088005572 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 998088005573 ligand binding site [chemical binding]; other site 998088005574 flexible hinge region; other site 998088005575 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 998088005576 putative switch regulator; other site 998088005577 non-specific DNA interactions [nucleotide binding]; other site 998088005578 DNA binding site [nucleotide binding] 998088005579 sequence specific DNA binding site [nucleotide binding]; other site 998088005580 putative cAMP binding site [chemical binding]; other site 998088005581 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl00515 998088005582 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; cl01253 998088005583 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor...; Region: Ribosomal_L24e_L24; cl00909 998088005584 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 998088005585 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 998088005586 metal-binding site [ion binding] 998088005587 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 998088005588 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 998088005589 FixH; Region: FixH; cl01254 998088005590 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 998088005591 Cytochrome c; Region: Cytochrom_C; cl11414 998088005592 Cytochrome c; Region: Cytochrom_C; cl11414 998088005593 Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of...; Region: cbb3_Oxidase_CcoQ; cl00282 998088005594 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 998088005595 Cytochrome cbb3 oxidase subunit I. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the...; Region: cbb3_Oxidase_I; cd01661 998088005596 Low-spin heme binding site [chemical binding]; other site 998088005597 Putative water exit pathway; other site 998088005598 Binuclear center (active site) [active] 998088005599 Putative proton exit pathway; other site 998088005600 GAF domain; Region: GAF; cl00853 998088005601 ProP expression regulator; Provisional; Region: PRK04950 998088005602 FinO bacterial conjugation repressor domain; the basic protein FinO is part of the the two component FinOP system which is responsible for repressing bacterial conjugation; the FinOP system represses the transfer (tra) operon of the F-plasmid which...; Region: FinO_conjug_rep; cl15270 998088005603 carboxy-terminal protease; Provisional; Region: PRK11186 998088005604 PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for...; Region: PDZ_CTP_protease; cd00988 998088005605 protein binding site [polypeptide binding]; other site 998088005606 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 998088005607 Catalytic dyad [active] 998088005608 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 998088005609 aminopeptidase N; Provisional; Region: pepN; PRK14015 998088005610 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 998088005611 active site 998088005612 Zn binding site [ion binding]; other site 998088005613 Protein of unknown function (DUF2835); Region: DUF2835; pfam11197 998088005614 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 998088005615 ATP P2X receptor; Region: P2X_receptor; cl02993 998088005616 Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD...; Region: DHOD_2_like; cd04738 998088005617 quinone interaction residues [chemical binding]; other site 998088005618 Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Region: PyrD; COG0167 998088005619 active site 998088005620 catalytic residues [active] 998088005621 FMN binding site [chemical binding]; other site 998088005622 substrate binding site [chemical binding]; other site 998088005623 Protein of unknown function (DUF1379); Region: DUF1379; pfam07126 998088005624 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 998088005625 23S rRNA m(2)G2445 methyltransferase; Provisional; Region: rlmL; PRK11783 998088005626 THUMP domain; Region: THUMP; cl12076 998088005627 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 998088005628 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 998088005629 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 998088005630 ABC transporter ATPase component; Reviewed; Region: PRK11147 998088005631 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 998088005632 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088005633 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 998088005634 ABC transporter; Region: ABC_tran_2; pfam12848 998088005635 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 998088005636 Ribosome modulation factor; Region: RMF; cl01207 998088005637 FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA...; Region: FabA; cd01287 998088005638 active site 1 [active] 998088005639 dimer interface [polypeptide binding]; other site 998088005640 active site 2 [active] 998088005641 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 998088005642 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 998088005643 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 998088005644 INT_SG1, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 1, C-terminal catalytic domain. The CD contains mainly predicted integrase/recombinase and site-specific XerD recombinases. The members of this CD are found predominantly in...; Region: INT_SG1_C; cd01183 998088005645 Phage integrase family; Region: Phage_integrase; pfam00589 998088005646 Int/Topo IB signature motif; other site 998088005647 YebG protein; Region: YebG; cl01217 998088005648 Predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold [General function prediction only]; Region: LipA; COG1075 998088005649 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 998088005650 short chain dehydrogenase; Provisional; Region: PRK07201 998088005651 Pseudomonas fluorescens MupV-like, extended (e) SDRs; Region: MupV_like_SDR_e; cd05263 998088005652 putative NAD(P) binding site [chemical binding]; other site 998088005653 active site 998088005654 putative substrate binding site [chemical binding]; other site 998088005655 classical (c) SDRs; Region: SDR_c; cd05233 998088005656 NAD(P) binding site [chemical binding]; other site 998088005657 active site 998088005658 Poly(hydroxyalcanoate) granule associated protein (phasin); Region: Phasin; cl07863 998088005659 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 998088005660 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 998088005661 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088005662 acyltransferase, WS/DGAT/MGAT; Region: acyl_WS_DGAT; TIGR02946 998088005663 Condensation domain; Region: Condensation; cl09290 998088005664 Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn); Region: PHA_gran_rgn; cl09865 998088005665 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 998088005666 2-methylcitrate dehydratase; Region: prpD; TIGR02330 998088005667 Citrate synthase (CS), citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CS catalyzes the condensation of acetyl coenzyme A (...; Region: CS_ACL-C_CCL; cl00416 998088005668 Citrate synthase; Region: Citrate_synt; pfam00285 998088005669 oxalacetate binding site [chemical binding]; other site 998088005670 citrylCoA binding site [chemical binding]; other site 998088005671 coenzyme A binding site [chemical binding]; other site 998088005672 catalytic triad [active] 998088005673 PEP phosphonomutase and related enzymes [Carbohydrate transport and metabolism]; Region: PrpB; COG2513 998088005674 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 998088005675 tetramer interface [polypeptide binding]; other site 998088005676 active site 998088005677 Mg2+/Mn2+ binding site [ion binding]; other site 998088005678 Paraquat-inducible protein A; Region: PqiA; pfam04403 998088005679 Paraquat-inducible protein A; Region: PqiA; pfam04403 998088005680 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 998088005681 mce related protein; Region: MCE; pfam02470 998088005682 mce related protein; Region: MCE; pfam02470 998088005683 mce related protein; Region: MCE; pfam02470 998088005684 paraquat-inducible protein B; Provisional; Region: PRK10807 998088005685 mce related protein; Region: MCE; pfam02470 998088005686 mce related protein; Region: MCE; pfam02470 998088005687 mce related protein; Region: MCE; pfam02470 998088005688 rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed; Region: yebU; PRK11933 998088005689 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 998088005690 Uncharacterized conserved protein [Function unknown]; Region: COG3270 998088005691 Replication regulatory protein RepB; Region: RepB-RCR_reg; cl11673 998088005692 Cre recombinase, C-terminal catalytic domain. Cre-like recombinases belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The bacteriophage P1 Cre...; Region: INT_Cre; cd00799 998088005693 DNA binding site [nucleotide binding] 998088005694 dimer interface [polypeptide binding]; other site 998088005695 Int/Topo IB signature motif; other site 998088005696 active site 998088005697 putative deoxyribonuclease YjjV; Provisional; Region: PRK11449 998088005698 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 998088005699 active site 998088005700 DNA polymerase III, delta' subunit; Region: holB; TIGR00678 998088005701 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088005702 Walker A motif; other site 998088005703 ATP binding site [chemical binding]; other site 998088005704 Walker B motif; other site 998088005705 arginine finger; other site 998088005706 C terminal; Region: DNApol3-delta_C; pfam09115 998088005707 thymidylate kinase; Validated; Region: tmk; PRK00698 998088005708 Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting...; Region: TMPK; cd01672 998088005709 TMP-binding site; other site 998088005710 ATP-binding site [chemical binding]; other site 998088005711 YceG-like family; Region: YceG; pfam02618 998088005712 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 998088005713 dimerization interface [polypeptide binding]; other site 998088005714 ADCL_like: 4-Amino-4-deoxychorismate lyase: is a member of the fold-type IV of PLP dependent enzymes that converts 4-amino-4-deoxychorismate (ADC) to p-aminobenzoate and pyruvate. Based on the information available from the crystal structure, most...; Region: ADCL_like; cd01559 998088005715 Aminotransferase class IV; Region: Aminotran_4; pfam01063 998088005716 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088005717 catalytic residue [active] 998088005718 Beta-ketoacyl-acyl carrier protein (ACP) synthase (KAS), type I and II. KASs are responsible for the elongation steps in fatty acid biosynthesis. KASIII catalyses the initial condensation and KAS I and II catalyze further elongation steps by Claisen...; Region: KAS_I_II; cd00834 998088005719 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 998088005720 dimer interface [polypeptide binding]; other site 998088005721 active site 998088005722 Phosphopantetheine attachment site; Region: PP-binding; cl09936 998088005723 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 998088005724 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 998088005725 NAD(P) binding site [chemical binding]; other site 998088005726 homotetramer interface [polypeptide binding]; other site 998088005727 homodimer interface [polypeptide binding]; other site 998088005728 active site 998088005729 Acyl transferase domain; Region: Acyl_transf_1; cl08282 998088005730 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 998088005731 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 998088005732 Ketoacyl-acyl carrier protein synthase III (KASIII) initiates the elongation in type II fatty acid synthase systems. It is found in bacteria and plants. Elongation of fatty acids in the type II systems occurs by Claisen condensation of malonyl-acyl...; Region: KAS_III; cd00830 998088005733 dimer interface [polypeptide binding]; other site 998088005734 active site 998088005735 CoA binding pocket [chemical binding]; other site 998088005736 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 998088005737 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 998088005738 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 998088005739 Nucleotide binding protein Maf. Maf has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea, but homologs in B.subtilis and S.cerevisiae are nonessential for cell division. Maf has been predicted to be a nucleotide- or...; Region: Maf; cd00555 998088005740 active site 998088005741 dimer interface [polypeptide binding]; other site 998088005742 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 998088005743 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cd01427 998088005744 motif II; other site 998088005745 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 998088005746 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 998088005747 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF...; Region: PseudoU_synth_RluCD_like; cd02869 998088005748 active site 998088005749 ribonuclease E; Reviewed; Region: rne; PRK10811 998088005750 S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and...; Region: S1_RNase_E; cd04453 998088005751 homodimer interface [polypeptide binding]; other site 998088005752 oligonucleotide binding site [chemical binding]; other site 998088005753 PTS system fructose-specific transporter subunits IIBC; Provisional; Region: PRK10712 998088005754 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA...; Region: PTS_IIB_fructose; cd05569 998088005755 P-loop; other site 998088005756 active site 998088005757 phosphorylation site [posttranslational modification] 998088005758 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA...; Region: PTS_IIB_fructose; cd05569 998088005759 P-loop; other site 998088005760 active site 998088005761 phosphorylation site [posttranslational modification] 998088005762 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 998088005763 Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]; Region: FruK; COG1105 998088005764 1-phosphofructokinase (FruK), minor 6-phosphofructokinase (pfkB) and related sugar kinases. FruK plays an important role in the predominant pathway for fructose utilisation.This group also contains tagatose-6-phophate kinase, an enzyme of the tagatose...; Region: FruK_PfkB_like; cd01164 998088005765 putative substrate binding site [chemical binding]; other site 998088005766 putative ATP binding site [chemical binding]; other site 998088005767 bifunctional PTS system fructose-specific transporter subunit IIA/HPr protein; Provisional; Region: PRK11109 998088005768 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 998088005769 active site 998088005770 phosphorylation site [posttranslational modification] 998088005771 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 998088005772 dimerization domain swap beta strand [polypeptide binding]; other site 998088005773 regulatory protein interface [polypeptide binding]; other site 998088005774 active site 998088005775 regulatory phosphorylation site [posttranslational modification]; other site 998088005776 DNA-binding transcriptional regulator FruR; Provisional; Region: PRK11303 998088005777 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 998088005778 DNA binding site [nucleotide binding] 998088005779 domain linker motif; other site 998088005780 Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs; Region: PBP1_FruR; cd06274 998088005781 dimerization interface [polypeptide binding]; other site 998088005782 ligand binding site [chemical binding]; other site 998088005783 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 998088005784 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4337 998088005785 MAPEG family; Region: MAPEG; cl09190 998088005786 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (...; Region: DEADc; cd00268 998088005787 DEAD-like helicases superfamily; Region: DEXDc; smart00487 998088005788 ATP binding site [chemical binding]; other site 998088005789 Mg++ binding site [ion binding]; other site 998088005790 motif III; other site 998088005791 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 998088005792 nucleotide binding region [chemical binding]; other site 998088005793 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088005794 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088005795 substrate binding pocket [chemical binding]; other site 998088005796 membrane-bound complex binding site; other site 998088005797 hinge residues; other site 998088005798 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 998088005799 Tetramer interface [polypeptide binding]; other site 998088005800 Active site [active] 998088005801 FMN-binding site [chemical binding]; other site 998088005802 HemK family putative methylases; Region: hemK_fam; TIGR00536 998088005803 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cd02440 998088005804 S-adenosylmethionine binding site [chemical binding]; other site 998088005805 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 998088005806 Smr domain; Region: Smr; cl02619 998088005807 PAS fold; Region: PAS_4; pfam08448 998088005808 PAS domain S-box; Region: sensory_box; TIGR00229 998088005809 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 998088005810 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088005811 metal binding site [ion binding]; metal-binding site 998088005812 active site 998088005813 I-site; other site 998088005814 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 998088005815 Histidine phosphatase superfamily (branch 1); Region: His_Phos_1; pfam00300 998088005816 catalytic core [active] 998088005817 Uncharacterized protein contain chitin-binding domain type 3 [General function prediction only]; Region: COG3979 998088005818 Glycoside hydrolase family 19 chitinase domain. Chitinases are enzymes that catalyze the hydrolysis of the beta-1,4-N-acetyl-D-glucosamine linkages in chitin polymers. Family 19 chitinases are found primarily in plants (classes I, III, and IV), but...; Region: chitinase_glyco_hydro_19; cd00325 998088005819 putative sugar binding site [chemical binding]; other site 998088005820 catalytic residues [active] 998088005821 Chitin/cellulose binding domain. Putative carbohydrate binding domain found in many different glycosyl hydrolase enzymes. May occur in tandem arrangements; Region: ChtBD3; cd00036 998088005822 chitin/cellulose binding site [chemical binding]; other site 998088005823 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; smart00782 998088005824 PhnA protein; Region: PhnA; pfam03831 998088005825 Fumarate hydratase (Fumerase); Region: Fumerase; cl00851 998088005826 Fumarase C-terminus; Region: Fumerase_C; cl00795 998088005827 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 998088005828 aminodeoxychorismate synthase subunit I; Provisional; Region: pabB; PRK15465 998088005829 chorismate binding enzyme; Region: Chorismate_bind; cl10555 998088005830 Coenzyme A pyrophosphatase (CoAse), a member of the Nudix hydrolase superfamily, functions to catalyze the elimination of oxidized inactive CoA, which can inhibit CoA-utilizing enzymes. The need of CoAses mainly arises under conditions of oxidative...; Region: CoAse; cd03426 998088005831 putative active site [active] 998088005832 putative CoA binding site [chemical binding]; other site 998088005833 nudix motif; other site 998088005834 metal binding site [ion binding]; metal-binding site 998088005835 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 998088005836 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 998088005837 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 998088005838 DEAD-like helicases superfamily; Region: DEXDc; smart00487 998088005839 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 998088005840 ATP binding site [chemical binding]; other site 998088005841 putative Mg++ binding site [ion binding]; other site 998088005842 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 998088005843 nucleotide binding region [chemical binding]; other site 998088005844 Superfamily II RNA helicase [DNA replication, recombination, and repair]; Region: COG4581 998088005845 ATP-binding site [chemical binding]; other site 998088005846 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 998088005847 PrkA family serine protein kinase; Provisional; Region: PRK15455 998088005848 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088005849 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 998088005850 Protein of unknown function (DUF444); Region: DUF444; pfam04285 998088005851 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 998088005852 SpoVR family protein; Provisional; Region: PRK11767 998088005853 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 998088005854 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 998088005855 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase...; Region: crotonase-like; cd06558 998088005856 substrate binding site [chemical binding]; other site 998088005857 oxyanion hole (OAH) forming residues; other site 998088005858 trimer interface [polypeptide binding]; other site 998088005859 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 998088005860 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 998088005861 3-ketoacyl-CoA thiolase; Reviewed; Region: fadI; PRK08963 998088005862 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 998088005863 dimer interface [polypeptide binding]; other site 998088005864 active site 998088005865 MoxR-like ATPases [General function prediction only]; Region: COG0714 998088005866 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088005867 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 998088005868 Protein of unknown function DUF58; Region: DUF58; pfam01882 998088005869 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 998088005870 metal ion-dependent adhesion site (MIDAS); other site 998088005871 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 998088005872 metal ion-dependent adhesion site (MIDAS); other site 998088005873 RNA polymerase sigma factor; Provisional; Region: PRK12517 998088005874 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 998088005875 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 998088005876 Protein of unknown function (DUF3379); Region: DUF3379; pfam11859 998088005877 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 998088005878 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl09488 998088005879 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 998088005880 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl09488 998088005881 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 998088005882 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cl00290 998088005883 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 998088005884 putative acyltransferase; Provisional; Region: PRK05790 998088005885 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 998088005886 dimer interface [polypeptide binding]; other site 998088005887 active site 998088005888 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 998088005889 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 998088005890 DNA binding residues [nucleotide binding] 998088005891 putative dimer interface [polypeptide binding]; other site 998088005892 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 998088005893 CTC domain interface [polypeptide binding]; other site 998088005894 L16 interface [polypeptide binding]; other site 998088005895 ATP-dependent RNA helicase HrpA; Provisional; Region: PRK11131 998088005896 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 998088005897 ATP binding site [chemical binding]; other site 998088005898 putative Mg++ binding site [ion binding]; other site 998088005899 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 998088005900 nucleotide binding region [chemical binding]; other site 998088005901 ATP-binding site [chemical binding]; other site 998088005902 Helicase associated domain (HA2); Region: HA2; cl04503 998088005903 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 998088005904 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 998088005905 FOG: CBS domain [General function prediction only]; Region: COG0517 998088005906 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-...; Region: CBS_pair_16; cd04629 998088005907 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088005908 Zn2+ binding site [ion binding]; other site 998088005909 Mg2+ binding site [ion binding]; other site 998088005910 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088005911 Zn2+ binding site [ion binding]; other site 998088005912 Mg2+ binding site [ion binding]; other site 998088005913 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 998088005914 Sulfatase; Region: Sulfatase; cl10460 998088005915 MoxR-like ATPases [General function prediction only]; Region: COG0714 998088005916 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088005917 Walker A motif; other site 998088005918 ATP binding site [chemical binding]; other site 998088005919 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088005920 Walker B motif; other site 998088005921 arginine finger; other site 998088005922 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 998088005923 Protein of unknown function DUF58; Region: DUF58; pfam01882 998088005924 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 998088005925 metal ion-dependent adhesion site (MIDAS); other site 998088005926 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 998088005927 metal ion-dependent adhesion site (MIDAS); other site 998088005928 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi...; Region: TPR; cd00189 998088005929 binding surface 998088005930 TPR motif; other site 998088005931 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 998088005932 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088005933 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088005934 dimerization interface [polypeptide binding]; other site 998088005935 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; cl00556 998088005936 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi...; Region: TPR; cd00189 998088005937 TPR motif; other site 998088005938 binding surface 998088005939 anaerobic sulfatase-maturating enzyme; Region: sulfatase_rSAM; TIGR03942 998088005940 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster...; Region: Radical_SAM; cd01335 998088005941 FeS/SAM binding site; other site 998088005942 radical SAM additional 4Fe4S-binding domain; Region: rSAM_more_4Fe4S; TIGR04085 998088005943 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088005944 metal binding site [ion binding]; metal-binding site 998088005945 active site 998088005946 I-site; other site 998088005947 uncharacterized phage protein; Region: phage_xxxx; TIGR02642 998088005948 Protein of unknown function (DUF1364); Region: DUF1364; pfam07102 998088005949 Protein of unknown function (DUF1367); Region: DUF1367; pfam07105 998088005950 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 998088005951 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088005952 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088005953 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088005954 nitrobindin heme-binding domain; Region: nitrobindin; cl10502 998088005955 heme-binding site [chemical binding]; other site 998088005956 N-glycosyltransferase; Provisional; Region: PRK11204 998088005957 CESA_like is the cellulose synthase superfamily; Region: CESA_like; cd06423 998088005958 DXD motif; other site 998088005959 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 998088005960 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2...; Region: Biotinyl_lipoyl_domains; cl11404 998088005961 lipoyl-biotinyl attachment site [posttranslational modification]; other site 998088005962 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 998088005963 Transposase; Region: DEDD_Tnp_IS110; pfam01548 998088005964 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 998088005965 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 998088005966 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 998088005967 Int/Topo IB signature motif; other site 998088005968 active site 998088005969 DNA binding site [nucleotide binding] 998088005970 exonuclease I; Provisional; Region: sbcB; PRK11779 998088005971 N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; Region: ExoI_N; cd06138 998088005972 active site 998088005973 substrate binding site [chemical binding]; other site 998088005974 catalytic site [active] 998088005975 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 998088005976 Alpha-galactosidase [Carbohydrate transport and metabolism]; Region: GalA; COG3345 998088005977 The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-...; Region: GH31; cl11402 998088005978 catalytic site [active] 998088005979 LrgA family; Region: LrgA; cl00608 998088005980 LrgB-like family; Region: LrgB; cl00596 998088005981 cytidine deaminase; Provisional; Region: PRK09027 998088005982 Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on...; Region: cytidine_deaminase; cd01283 998088005983 active site 998088005984 catalytic motif [active] 998088005985 Zn binding site [ion binding]; other site 998088005986 Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes. All members...; Region: cytidine_deaminase-like; cl00269 998088005987 tryptophanase/L-cysteine desulfhydrase, PLP-dependent; Provisional; Region: tnaA; PRK13238 998088005988 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 998088005989 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 998088005990 catalytic residue [active] 998088005991 Uncharacterized protein conserved in bacteria (DUF2256); Region: DUF2256; cl01792 998088005992 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]; Region: COG3046 998088005993 Deoxyribodipyrimidine photo-lyase-related protein; Region: DPRP; pfam04244 998088005994 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 998088005995 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 998088005996 D-amino acid dehydrogenase small subunit; Provisional; Region: PRK12409 998088005997 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 998088005998 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088005999 Semialdehyde dehydrogenase, dimerisation domain; Region: Semialdhyde_dhC; pfam02774 998088006000 FdhD/NarQ family; Region: FdhD-NarQ; cl00659 998088006001 Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]; Region: FhlA; COG3604 998088006002 GAF domain; Region: GAF; cl00853 998088006003 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088006004 Walker A motif; other site 998088006005 ATP binding site [chemical binding]; other site 998088006006 Walker B motif; other site 998088006007 arginine finger; other site 998088006008 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 998088006009 putative oxidoreductase Fe-S binding subunit; Reviewed; Region: PRK12769 998088006010 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 998088006011 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 998088006012 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088006013 Coenzyme A binding pocket [chemical binding]; other site 998088006014 K+ potassium transporter; Region: K_trans; cl01227 998088006015 potassium uptake protein; Region: kup; TIGR00794 998088006016 Alginate Lyase A1-III; enzymatically depolymerizes alginate, a complex copolymer of beta-D-mannuronate and alpha-L-guluronate, by cleaving the beta-(1,4) glycosidic bond; Region: AlgLyase; cl00179 998088006017 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 998088006018 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 998088006019 active site 998088006020 intersubunit interface [polypeptide binding]; other site 998088006021 catalytic residue [active] 998088006022 pfkB family carbohydrate kinase; Region: PfkB; pfam00294 998088006023 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the...; Region: KdgK; cd01166 998088006024 substrate binding site [chemical binding]; other site 998088006025 ATP binding site [chemical binding]; other site 998088006026 Bacterial inner membrane protein; Region: Imp-YgjV; pfam10688 998088006027 2-deoxy-D-gluconate 3-dehydrogenase; Validated; Region: PRK08993 998088006028 gluconate 5-dehydrogenase (Ga5DH)-like, classical (c) SDRs; Region: Ga5DH-like_SDR_c; cd05347 998088006029 NADP binding site [chemical binding]; other site 998088006030 homodimer interface [polypeptide binding]; other site 998088006031 active site 998088006032 KduI/IolB family; Region: KduI; cl01508 998088006033 putative outer membrane porin protein; Provisional; Region: PRK11379 998088006034 outer membrane porin, OprD family; Region: OprD; pfam03573 998088006035 SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars; Region: SIS; cl00389 998088006036 LanC-like proteins. LanC is the cyclase enzyme of the lanthionine synthetase. Lanthionine is a lantibiotic, a unique class of peptide antibiotics. They are ribosomally synthesized as a precursor peptide and then post-translationally modified to contain...; Region: LanC_like; cl04955 998088006037 hypothetical protein; Provisional; Region: PRK02947 998088006038 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose...; Region: SIS_RpiR; cd05013 998088006039 putative active site [active] 998088006040 Mannose/sorbose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four...; Region: PTS_IIB_man; cl00021 998088006041 PTS system mannose/fructose/sorbose family IID component; Region: EIID-AGA; cl01507 998088006042 PTS system sorbose-specific iic component; Region: EII-Sor; cl01506 998088006043 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 998088006044 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 998088006045 DNA-binding site [nucleotide binding]; DNA binding site 998088006046 UTRA domain; Region: UTRA; cl01230 998088006047 putative oxidoreductase Fe-S binding subunit; Reviewed; Region: PRK12769 998088006048 hydrogenase 4 subunit B; Validated; Region: PRK06521 998088006049 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 998088006050 NADH dehydrogenase; Region: NADHdh; cl00469 998088006051 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl00539 998088006052 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; cl00417 998088006053 hydrogenase 4 subunit H; Validated; Region: PRK08222 998088006054 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved alpha-; Region: HCP_like; cl14655 998088006055 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl00419 998088006056 Formate hydrogenlyase maturation protein HycH; Region: HycH; cl06472 998088006057 Endopeptidases belonging to membrane-bound hydrogen evolving hydrogenase group. In hydrogenase 3 from E coli, the maturation of the large subunit (HycE) requires the cleavage of a C-terminal peptide by the endopeptidase HycI, before the final formation...; Region: H2MP_MemB-H2evol; cd06067 998088006058 nickel binding site [ion binding]; other site 998088006059 seryl-tRNA(sec) selenium transferase; Region: selA; TIGR00474 998088006060 Selenocysteine synthase N terminal; Region: Se-cys_synth_N; pfam12390 998088006061 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 998088006062 SelB subfamily. SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of...; Region: SelB; cd04171 998088006063 Elongation factor Tu GTP binding domain; Region: GTP_EFTU; pfam00009 998088006064 G1 box; other site 998088006065 putative GEF interaction site [polypeptide binding]; other site 998088006066 GTP/Mg2+ binding site [chemical binding]; other site 998088006067 Switch I region; other site 998088006068 G2 box; other site 998088006069 G3 box; other site 998088006070 Switch II region; other site 998088006071 G4 box; other site 998088006072 G5 box; other site 998088006073 selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires...; Region: selB_II; cd03696 998088006074 Elongation factor SelB, winged helix; Region: SelB-wing_3; pfam09107 998088006075 Acylphosphatase; Region: Acylphosphatase; cl00551 998088006076 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 998088006077 HypF finger; Region: zf-HYPF; pfam07503 998088006078 HypF finger; Region: zf-HYPF; pfam07503 998088006079 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 998088006080 HupF/HypC family; Region: HupF_HypC; cl00394 998088006081 Hydrogenase formation hypA family; Region: HypD; cl12072 998088006082 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 998088006083 HypE (Hydrogenase expression/formation protein). HypE is involved in Ni-Fe hydrogenase biosynthesis. HypE dehydrates its own carbamoyl moiety in an ATP-dependent process to yield the enzyme thiocyanate. The N-terminal domain of HypE is related to the...; Region: HypE; cd02197 998088006084 dimerization interface [polypeptide binding]; other site 998088006085 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 998088006086 ATP binding site [chemical binding]; other site 998088006087 Hydrogenase expression/synthesis hypA family; Region: HypA; cl00418 998088006088 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 998088006089 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 998088006090 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 998088006091 Walker A/P-loop; other site 998088006092 ATP binding site [chemical binding]; other site 998088006093 Q-loop/lid; other site 998088006094 ABC transporter signature motif; other site 998088006095 Walker B; other site 998088006096 D-loop; other site 998088006097 H-loop/switch region; other site 998088006098 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 998088006099 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 998088006100 Walker A/P-loop; other site 998088006101 ATP binding site [chemical binding]; other site 998088006102 Q-loop/lid; other site 998088006103 ABC transporter signature motif; other site 998088006104 Walker B; other site 998088006105 D-loop; other site 998088006106 H-loop/switch region; other site 998088006107 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 998088006108 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cl00427 998088006109 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 998088006110 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088006111 dimer interface [polypeptide binding]; other site 998088006112 conserved gate region; other site 998088006113 putative PBP binding loops; other site 998088006114 ABC-ATPase subunit interface; other site 998088006115 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_19; cd08518 998088006116 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 998088006117 Protein of unknown function (DUF3457); Region: DUF3457; cl08122 998088006118 Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase...; Region: H2MP_MemB-H2up; cd06062 998088006119 coenzyme F420-reducing hydrogenase delta subunit (putative coenzyme F420 hydrogenase processing subunit); Region: frhD; TIGR00130 998088006120 putative substrate-binding site; other site 998088006121 nickel binding site [ion binding]; other site 998088006122 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; cl00417 998088006123 Polysulphide reductase [Energy production and conversion]; Region: COG5557; cl01295 998088006124 hydrogenase 2 protein HybA; Provisional; Region: PRK10882 998088006125 Tat (twin-arginine translocation) pathway signal sequence; Region: TAT_signal_seq; TIGR01409 998088006126 hydrogenase 2 small subunit; Provisional; Region: PRK10468 998088006127 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl00419 998088006128 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088006129 metal binding site [ion binding]; metal-binding site 998088006130 active site 998088006131 I-site; other site 998088006132 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 998088006133 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 998088006134 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 998088006135 O-Antigen ligase; Region: Wzy_C; cl04850 998088006136 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 998088006137 Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins. MAT and GAT catalyze the CoA-dependent acetylation of the 6-...; Region: LbH_MAT_like; cd04647 998088006138 trimer interface [polypeptide binding]; other site 998088006139 active site 998088006140 substrate binding site [chemical binding]; other site 998088006141 CoA binding site [chemical binding]; other site 998088006142 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: GT1_like_1; cd04950 998088006143 putative homodimer interface [polypeptide binding]; other site 998088006144 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 998088006145 polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Region: pepcterm_ChnLen; TIGR03007 998088006146 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 998088006147 CESA_like_1 is a member of the cellulose synthase (CESA) superfamily; Region: CESA_like_1; cd06439 998088006148 DXD motif; other site 998088006149 Bacterial sugar transferase; Region: Bac_transf; cl00939 998088006150 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 998088006151 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 998088006152 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 998088006153 Response regulator receiver domain; Region: Response_reg; pfam00072 998088006154 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088006155 active site 998088006156 phosphorylation site [posttranslational modification] 998088006157 intermolecular recognition site; other site 998088006158 dimerization interface [polypeptide binding]; other site 998088006159 Sigma factor PP2C-like phosphatases; Region: PP2C_SIG; smart00331 998088006160 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 998088006161 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Mrp; COG0489 998088006162 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 998088006163 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 998088006164 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 998088006165 SLBB domain; Region: SLBB; pfam10531 998088006166 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 998088006167 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 998088006168 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 998088006169 SLBB domain; Region: SLBB; pfam10531 998088006170 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 998088006171 anti sigma factor interaction site; other site 998088006172 regulatory phosphorylation site [posttranslational modification]; other site 998088006173 Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the...; Region: SO_family_Moco; cl00199 998088006174 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 998088006175 dimer interface [polypeptide binding]; other site 998088006176 phosphorylation site [posttranslational modification] 998088006177 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088006178 ATP binding site [chemical binding]; other site 998088006179 Mg2+ binding site [ion binding]; other site 998088006180 G-X-G motif; other site 998088006181 Response regulator receiver domain; Region: Response_reg; pfam00072 998088006182 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088006183 active site 998088006184 phosphorylation site [posttranslational modification] 998088006185 intermolecular recognition site; other site 998088006186 dimerization interface [polypeptide binding]; other site 998088006187 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088006188 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088006189 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_5; cd08474 998088006190 putative effector binding pocket; other site 998088006191 putative dimerization interface [polypeptide binding]; other site 998088006192 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 998088006193 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 998088006194 Domain of unknown function (DUF369); Region: DUF369; cl00950 998088006195 ribonucleoside transporter; Reviewed; Region: nepI; PRK10213 998088006196 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088006197 putative substrate translocation pore; other site 998088006198 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 998088006199 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 998088006200 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 998088006201 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088006202 NAD(P) binding site [chemical binding]; other site 998088006203 active site 998088006204 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088006205 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 998088006206 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase...; Region: crotonase-like; cd06558 998088006207 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 998088006208 substrate binding site [chemical binding]; other site 998088006209 oxyanion hole (OAH) forming residues; other site 998088006210 trimer interface [polypeptide binding]; other site 998088006211 enoyl-CoA hydratase; Provisional; Region: PRK09076 998088006212 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase...; Region: crotonase-like; cd06558 998088006213 substrate binding site [chemical binding]; other site 998088006214 oxyanion hole (OAH) forming residues; other site 998088006215 trimer interface [polypeptide binding]; other site 998088006216 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 998088006217 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 998088006218 active site 998088006219 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 998088006220 isovaleryl-CoA dehydrogenase; Region: PLN02519 998088006221 substrate binding site [chemical binding]; other site 998088006222 FAD binding site [chemical binding]; other site 998088006223 catalytic base [active] 998088006224 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 998088006225 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 998088006226 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 998088006227 enoyl-CoA hydratase; Provisional; Region: PRK05995 998088006228 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase...; Region: crotonase-like; cd06558 998088006229 substrate binding site [chemical binding]; other site 998088006230 oxyanion hole (OAH) forming residues; other site 998088006231 trimer interface [polypeptide binding]; other site 998088006232 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 998088006233 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 998088006234 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 998088006235 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 998088006236 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase...; Region: biotinyl_domain; cd06850 998088006237 carboxyltransferase (CT) interaction site; other site 998088006238 biotinylation site [posttranslational modification]; other site 998088006239 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 998088006240 active site 998088006241 catalytic residues [active] 998088006242 metal binding site [ion binding]; metal-binding site 998088006243 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 998088006244 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 998088006245 DNA binding residues [nucleotide binding] 998088006246 putative dimer interface [polypeptide binding]; other site 998088006247 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088006248 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 998088006249 substrate binding pocket [chemical binding]; other site 998088006250 membrane-bound complex binding site; other site 998088006251 hinge residues; other site 998088006252 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 998088006253 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 998088006254 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 998088006255 GPR1/FUN34/yaaH family; Region: Grp1_Fun34_YaaH; cl00685 998088006256 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; cl01267 998088006257 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088006258 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 998088006259 Insertion element 4 transposase N-terminal; Region: Nterm_IS4; pfam13006 998088006260 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 998088006261 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 998088006262 Transposase; Region: DEDD_Tnp_IS110; pfam01548 998088006263 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 998088006264 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 998088006265 Phage-related protein [Function unknown]; Region: COG4695; cl01923 998088006266 putative transposase OrfB; Reviewed; Region: PHA02517 998088006267 putative transposase OrfB; Reviewed; Region: PHA02517 998088006268 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 998088006269 IS2 transposase TnpB; Reviewed; Region: PRK09409 998088006270 Integrase core domain; Region: rve; cl01316 998088006271 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cl01116 998088006272 Phage-related protein [Function unknown]; Region: COG4695; cl01923 998088006273 enoyl-CoA hydratase; Provisional; Region: PRK07509 998088006274 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase...; Region: crotonase-like; cd06558 998088006275 substrate binding site [chemical binding]; other site 998088006276 oxyanion hole (OAH) forming residues; other site 998088006277 trimer interface [polypeptide binding]; other site 998088006278 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 998088006279 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 998088006280 ligand binding site [chemical binding]; other site 998088006281 flexible hinge region; other site 998088006282 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-...; Region: CBS_pair; cl09141 998088006283 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 998088006284 metal binding triad; other site 998088006285 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 998088006286 active site 998088006287 substrate binding site [chemical binding]; other site 998088006288 catalytic site [active] 998088006289 Protein of unknown function, DUF485; Region: DUF485; cl01231 998088006290 Sodium:solute symporter family; Region: SSF; cl00456 998088006291 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 998088006292 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 998088006293 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088006294 Walker A/P-loop; other site 998088006295 ATP binding site [chemical binding]; other site 998088006296 Q-loop/lid; other site 998088006297 ABC transporter signature motif; other site 998088006298 Walker B; other site 998088006299 D-loop; other site 998088006300 H-loop/switch region; other site 998088006301 ABC transporter; Region: ABC_tran_2; pfam12848 998088006302 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 998088006303 periplasmic folding chaperone; Provisional; Region: PRK10788 998088006304 SurA N-terminal domain; Region: SurA_N; pfam09312 998088006305 PPIC-type PPIASE domain; Region: Rotamase; cl08278 998088006306 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-...; Region: HU_IHF; cd00591 998088006307 IHF dimer interface [polypeptide binding]; other site 998088006308 IHF - DNA interface [nucleotide binding]; other site 998088006309 DNA-binding ATP-dependent protease La; Provisional; Region: PRK10787 998088006310 Found in ATP-dependent protease La (LON); Region: LON; smart00464 998088006311 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088006312 Walker A motif; other site 998088006313 ATP binding site [chemical binding]; other site 998088006314 Walker B motif; other site 998088006315 arginine finger; other site 998088006316 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 998088006317 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 998088006318 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 998088006319 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088006320 Walker A motif; other site 998088006321 ATP binding site [chemical binding]; other site 998088006322 Walker B motif; other site 998088006323 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 998088006324 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 998088006325 oligomer interface [polypeptide binding]; other site 998088006326 active site residues [active] 998088006327 trigger factor; Provisional; Region: tig; PRK01490 998088006328 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 998088006329 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 998088006330 hypothetical protein; Provisional; Region: PRK11770 998088006331 Domain of unknown function (DUF307); Region: DUF307; pfam03733 998088006332 Domain of unknown function (DUF307); Region: DUF307; pfam03733 998088006333 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 998088006334 outer membrane-specific lipoprotein transporter subunit LolE; Provisional; Region: PRK11146 998088006335 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 998088006336 FtsX-like permease family; Region: FtsX; pfam02687 998088006337 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 998088006338 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 998088006339 Walker A/P-loop; other site 998088006340 ATP binding site [chemical binding]; other site 998088006341 Q-loop/lid; other site 998088006342 ABC transporter signature motif; other site 998088006343 Walker B; other site 998088006344 D-loop; other site 998088006345 H-loop/switch region; other site 998088006346 LolC/E family; Region: lolCE; TIGR02212 998088006347 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 998088006348 FtsX-like permease family; Region: FtsX; pfam02687 998088006349 transcription-repair coupling factor; Provisional; Region: PRK10689 998088006350 CarD-like/TRCF domain; Region: CarD_TRCF; cl00588 998088006351 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 998088006352 ATP binding site [chemical binding]; other site 998088006353 putative Mg++ binding site [ion binding]; other site 998088006354 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 998088006355 nucleotide binding region [chemical binding]; other site 998088006356 ATP-binding site [chemical binding]; other site 998088006357 TRCF domain; Region: TRCF; cl04088 998088006358 fructose-1,6-bisphosphatase family protein; Region: PLN02628 998088006359 Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1,7-...; Region: FBPase; cd00354 998088006360 AMP binding site [chemical binding]; other site 998088006361 metal binding site [ion binding]; metal-binding site 998088006362 active site 998088006363 oligopeptide ABC transporter substrate-binding protein OppA; Provisional; Region: PRK15104 998088006364 The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; Region: PBP2_OppA; cd08504 998088006365 peptide binding site [polypeptide binding]; other site 998088006366 EamA-like transporter family; Region: EamA; cl01037 998088006367 Protein of unknown function (DUF1107); Region: DUF1107; pfam06526 998088006368 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 998088006369 catalytic core [active] 998088006370 Secreted/periplasmic Zn-dependent peptidases, insulinase-like [Posttranslational modification, protein turnover, chaperones]; Region: Ptr; COG1025 998088006371 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 998088006372 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 998088006373 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 998088006374 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 998088006375 Leucine-rich repeat (LRR) protein [Function unknown]; Region: COG4886 998088006376 Protein tyrosine kinase; Region: Pkinase_Tyr; pfam07714 998088006377 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 998088006378 active site 998088006379 ATP binding site [chemical binding]; other site 998088006380 substrate binding site [chemical binding]; other site 998088006381 activation loop (A-loop); other site 998088006382 GMP synthase; Reviewed; Region: guaA; PRK00074 998088006383 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 998088006384 AMP/PPi binding site [chemical binding]; other site 998088006385 candidate oxyanion hole; other site 998088006386 catalytic triad [active] 998088006387 potential glutamine specificity residues [chemical binding]; other site 998088006388 The C-terminal domain of GMP synthetase. It contains two subdomains; the ATP pyrophosphatase domain which closes to the N-termial and the dimerization domain at C-terminal end. The ATP-PPase is a twisted, five-stranded parallel beta-sheet sandwiched...; Region: GMP_synthase_C; cd01997 998088006389 ATP Binding subdomain [chemical binding]; other site 998088006390 Ligand Binding sites [chemical binding]; other site 998088006391 Dimerization subdomain; other site 998088006392 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 998088006393 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 998088006394 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a key...; Region: CBS_pair_IMPDH; cd04601 998088006395 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of the...; Region: IMPDH; cd00381 998088006396 active site 998088006397 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria...; Region: Cytochrome_b_N; cl00859 998088006398 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 998088006399 ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-...; Region: ExoVII_LU_OBF; cd04489 998088006400 generic binding surface II; other site 998088006401 generic binding surface I; other site 998088006402 DNA-binding transcriptional repressor MngR; Provisional; Region: PRK09764 998088006403 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 998088006404 DNA-binding site [nucleotide binding]; DNA binding site 998088006405 UTRA domain; Region: UTRA; cl01230 998088006406 PTS system 2-O-a-mannosyl-D-glycerate specific transporter subunit IIABC; Provisional; Region: PRK09765 998088006407 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 998088006408 active site 998088006409 phosphorylation site [posttranslational modification] 998088006410 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA...; Region: PTS_IIB_fructose; cd05569 998088006411 P-loop; other site 998088006412 active site 998088006413 phosphorylation site [posttranslational modification] 998088006414 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 998088006415 alpha-mannosidase; Provisional; Region: PRK09819 998088006416 Glycosyl hydrolases family 38 N-terminal domain; Region: Glyco_hydro_38; pfam01074 998088006417 Alpha mannosidase, middle domain; Region: Alpha-mann_mid; cl08536 998088006418 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 998088006419 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 998088006420 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 998088006421 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl01206 998088006422 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue...; Region: GSH_Peroxidase; cd00340 998088006423 catalytic residues [active] 998088006424 dimer interface [polypeptide binding]; other site 998088006425 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088006426 ATP binding site [chemical binding]; other site 998088006427 putative Mg++ binding site [ion binding]; other site 998088006428 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 998088006429 nucleotide binding region [chemical binding]; other site 998088006430 ATP-binding site [chemical binding]; other site 998088006431 coproporphyrinogen III oxidase; Provisional; Region: PRK09058 998088006432 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster...; Region: Radical_SAM; cl15259 998088006433 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088006434 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088006435 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088006436 NeuB family; Region: NeuB; cl00496 998088006437 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 998088006438 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 998088006439 EPSP synthase domain. 3-phosphoshikimate 1-carboxyvinyltransferase (5-enolpyruvylshikimate-3-phosphate synthase) (EC 2.5.1.19) catalyses the reaction between shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP) to form 5-enolpyruvylshkimate-3-...; Region: EPSP_synthase; cd01556 998088006440 hinge; other site 998088006441 active site 998088006442 Phosphoserine aminotransferase (PSAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major group in this CD corresponds to phosphoserine aminotransferase (PSAT). PSAT is active...; Region: PSAT_like; cd00611 998088006443 homodimer interface [polypeptide binding]; other site 998088006444 substrate-cofactor binding pocket; other site 998088006445 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088006446 catalytic residue [active] 998088006447 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 998088006448 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_alpha; cd01715 998088006449 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 998088006450 Electron transfer flavoprotein, beta subunit [Energy production and conversion]; Region: FixA; COG2086 998088006451 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_beta; cd01714 998088006452 Ligand binding site [chemical binding]; other site 998088006453 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 998088006454 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088006455 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 998088006456 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 998088006457 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 998088006458 Protein of unknown function (DUF2919); Region: DUF2919; pfam11143 998088006459 Protein of unknown function (DUF1439); Region: DUF1439; cl06345 998088006460 Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones]; Region: COG1331 998088006461 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 998088006462 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 998088006463 ligand binding site [chemical binding]; other site 998088006464 oligomer interface [polypeptide binding]; other site 998088006465 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and rate-...; Region: LbH_G1P_AT_C; cd04651 998088006466 dimer interface [polypeptide binding]; other site 998088006467 N-terminal domain interface [polypeptide binding]; other site 998088006468 sulfate 1 binding site; other site 998088006469 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088006470 metal binding site [ion binding]; metal-binding site 998088006471 active site 998088006472 I-site; other site 998088006473 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 998088006474 Protein of unknown function (DUF2750); Region: DUF2750; pfam11042 998088006475 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, 2-...; Region: ribokinase_pfkB_like; cl00192 998088006476 pfkB family carbohydrate kinase; Region: PfkB; pfam00294 998088006477 substrate binding site [chemical binding]; other site 998088006478 ATP binding site [chemical binding]; other site 998088006479 MAPEG family; Region: MAPEG; cl09190 998088006480 ferrochelatase; Reviewed; Region: hemH; PRK00035 998088006481 Ferrochelatase, N-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_N; cd03411 998088006482 C-terminal domain interface [polypeptide binding]; other site 998088006483 active site 998088006484 Ferrochelatase, C-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_C; cd00419 998088006485 active site 998088006486 N-terminal domain interface [polypeptide binding]; other site 998088006487 adenylate kinase; Reviewed; Region: adk; PRK00279 998088006488 Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP). This enzyme is required for the biosynthesis of ADP and is essential for...; Region: ADK; cd01428 998088006489 AMP-binding site [chemical binding]; other site 998088006490 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 998088006491 MiaE tRNA-modifying nonheme diiron monooxygenase, ferritin-like diiron-binding domain; Region: MiaE; cd07910 998088006492 active site 998088006493 dinuclear metal binding site [ion binding]; other site 998088006494 dimerization interface [polypeptide binding]; other site 998088006495 amidophosphoribosyltransferase; Provisional; Region: PRK09246 998088006496 Glutamine amidotransferases class-II (GN-AT)_GPAT- type. This domain is found at the N-terminus of glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase) . The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the...; Region: GPATase_N; cd00715 998088006497 active site 998088006498 tetramer interface [polypeptide binding]; other site 998088006499 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 998088006500 Colicin V production protein; Region: Colicin_V; cl00567 998088006501 seryl-tRNA synthetase; Provisional; Region: PRK05431 998088006502 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 998088006503 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme...; Region: SerRS_core; cd00770 998088006504 dimer interface [polypeptide binding]; other site 998088006505 active site 998088006506 motif 1; other site 998088006507 motif 2; other site 998088006508 motif 3; other site 998088006509 recombination factor protein RarA; Reviewed; Region: PRK13342 998088006510 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088006511 Walker A motif; other site 998088006512 ATP binding site [chemical binding]; other site 998088006513 Walker B motif; other site 998088006514 arginine finger; other site 998088006515 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 998088006516 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 998088006517 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 998088006518 DNA translocase FtsK; Provisional; Region: PRK10263 998088006519 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088006520 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 998088006521 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 998088006522 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088006523 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 998088006524 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; pfam05222 998088006525 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088006526 thioredoxin reductase; Provisional; Region: PRK10262 998088006527 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088006528 Response regulator receiver domain; Region: Response_reg; pfam00072 998088006529 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088006530 active site 998088006531 phosphorylation site [posttranslational modification] 998088006532 intermolecular recognition site; other site 998088006533 dimerization interface [polypeptide binding]; other site 998088006534 Response regulator receiver domain; Region: Response_reg; pfam00072 998088006535 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088006536 active site 998088006537 phosphorylation site [posttranslational modification] 998088006538 intermolecular recognition site; other site 998088006539 dimerization interface [polypeptide binding]; other site 998088006540 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088006541 metal binding site [ion binding]; metal-binding site 998088006542 active site 998088006543 I-site; other site 998088006544 Leucyl/phenylalanyl-tRNA protein transferase; Region: Leu_Phe_trans; cl01006 998088006545 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 998088006546 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 998088006547 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 998088006548 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the...; Region: S1_IF1; cd04451 998088006549 rRNA binding site [nucleotide binding]; other site 998088006550 predicted 30S ribosome binding site; other site 998088006551 ATP-dependent Clp protease ATP-binding subunit; Provisional; Region: clpA; PRK11034 998088006552 Clp amino terminal domain; Region: Clp_N; pfam02861 998088006553 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088006554 Walker A motif; other site 998088006555 ATP binding site [chemical binding]; other site 998088006556 Walker B motif; other site 998088006557 arginine finger; other site 998088006558 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088006559 Walker A motif; other site 998088006560 ATP binding site [chemical binding]; other site 998088006561 Walker B motif; other site 998088006562 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 998088006563 ATP-dependent Clp protease adaptor protein ClpS; Region: ClpS; cl00933 998088006564 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein...; Region: CSP_CDS; cd04458 998088006565 DNA-binding site [nucleotide binding]; DNA binding site 998088006566 RNA-binding motif; other site 998088006567 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 998088006568 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 998088006569 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 998088006570 homodimer interface [polypeptide binding]; other site 998088006571 NADP binding site [chemical binding]; other site 998088006572 substrate binding site [chemical binding]; other site 998088006573 DNA-binding transcriptional regulator RstA; Provisional; Region: PRK10701 998088006574 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088006575 active site 998088006576 phosphorylation site [posttranslational modification] 998088006577 intermolecular recognition site; other site 998088006578 dimerization interface [polypeptide binding]; other site 998088006579 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 998088006580 DNA binding site [nucleotide binding] 998088006581 sensor protein RstB; Provisional; Region: PRK10604 998088006582 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088006583 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cl00080 998088006584 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088006585 ATP binding site [chemical binding]; other site 998088006586 Mg2+ binding site [ion binding]; other site 998088006587 G-X-G motif; other site 998088006588 Predicted integral membrane protein [Function unknown]; Region: COG0392 998088006589 Uncharacterised protein family (UPF0104); Region: UPF0104; cl04219 998088006590 Uncharacterized conserved protein [Function unknown]; Region: COG2898 998088006591 Uncharacterized conserved protein (DUF2156); Region: DUF2156; cl12090 998088006592 Bacterial virulence protein (VirJ); Region: VirJ; pfam06057 998088006593 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 998088006594 Putative bacterial sensory transduction regulator; Region: YbjN; pfam10722 998088006595 conserved hypothetical protein; Region: QEGLA; TIGR02421 998088006596 Domain of unknown function (DUF1704); Region: DUF1704; cl06858 998088006597 Thymidine kinase; Region: TK; cl00631 998088006598 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 998088006599 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088006600 Domain in histone-like proteins of HNS family; Region: HNS; cl09251 998088006601 DNA binding protein, nucleoid-associated; Provisional; Region: PRK10328 998088006602 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; cl00920 998088006603 Protein of unknown function (DUF3820); Region: DUF3820; cl01411 998088006604 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 998088006605 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster...; Region: Radical_SAM; cl15259 998088006606 ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In...; Region: ExsB; cd01995 998088006607 Ligand Binding Site [chemical binding]; other site 998088006608 DTW domain; Region: DTW; cl01221 998088006609 Rhomboid family; Region: Rhomboid; cl11446 998088006610 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase contains two...; Region: OMP_decarboxylase_like; cd04725 998088006611 active site 998088006612 dimer interface [polypeptide binding]; other site 998088006613 tetratricopeptide repeat protein; Provisional; Region: PRK11788 998088006614 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi...; Region: TPR; cd00189 998088006615 binding surface 998088006616 TPR motif; other site 998088006617 Protein of unknown function (DUF1049); Region: DUF1049; cl01539 998088006618 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-...; Region: HU_IHF; cd00591 998088006619 IHF dimer interface [polypeptide binding]; other site 998088006620 IHF - DNA interface [nucleotide binding]; other site 998088006621 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 998088006622 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 998088006623 RNA binding site [nucleotide binding]; other site 998088006624 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 998088006625 RNA binding site [nucleotide binding]; other site 998088006626 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec3; cd05688 998088006627 RNA binding site [nucleotide binding]; other site 998088006628 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain...; Region: S1_like; cl09927 998088006629 RNA binding site [nucleotide binding]; other site 998088006630 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain...; Region: S1_like; cl09927 998088006631 RNA binding site [nucleotide binding]; other site 998088006632 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec6; cd05691 998088006633 RNA binding site [nucleotide binding]; other site 998088006634 cytidylate kinase; Provisional; Region: cmk; PRK00023 998088006635 Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor; Region: CMPK; cd02020 998088006636 CMP-binding site; other site 998088006637 The sites determining sugar specificity; other site 998088006638 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cd00641 998088006639 GTP cyclohydrolase II [Coenzyme metabolism]; Region: RibA; COG0807 998088006640 dimerization interface [polypeptide binding]; other site 998088006641 active site 998088006642 transcriptional regulator CysB; Reviewed; Region: cysB; PRK12681 998088006643 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088006644 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088006645 dimerization interface [polypeptide binding]; other site 998088006646 DNA-binding transcriptional regulator CynR; Provisional; Region: PRK11242 998088006647 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088006648 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 998088006649 dimerization interface [polypeptide binding]; other site 998088006650 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088006651 putative substrate translocation pore; other site 998088006652 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 998088006653 active site 998088006654 metal binding site [ion binding]; metal-binding site 998088006655 This family contains NADPH-dependent flavin reductase and oxygen-insensitive nitroreductase. These enzymes are homodimeric flavoproteins that contain one FMN per monomer as a cofactor. Flavin reductase catalyzes the reduction of flavin by using NADPH...; Region: NfsA_FRP; cd02146 998088006656 dimer interface [polypeptide binding]; other site 998088006657 FMN binding site [chemical binding]; other site 998088006658 NADPH bind site [chemical binding]; other site 998088006659 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 998088006660 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088006661 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088006662 metal binding site [ion binding]; metal-binding site 998088006663 active site 998088006664 I-site; other site 998088006665 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 998088006666 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088006667 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088006668 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 998088006669 putative effector binding pocket; other site 998088006670 dimerization interface [polypeptide binding]; other site 998088006671 Response regulator receiver domain; Region: Response_reg; pfam00072 998088006672 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088006673 active site 998088006674 phosphorylation site [posttranslational modification] 998088006675 intermolecular recognition site; other site 998088006676 dimerization interface [polypeptide binding]; other site 998088006677 Chemotaxis protein CheC, inhibitor of MCP methylation [Cell motility and secretion / Signal transduction mechanisms]; Region: CheC; COG1776 998088006678 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 998088006679 PAS fold; Region: PAS_4; pfam08448 998088006680 Low-specificity threonine aldolase (TA). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). TA catalyzes the conversion of L-threonine or L-allo-threonine to glycine and acetaldehyde in a...; Region: TA_like; cd06502 998088006681 Beta-eliminating lyase; Region: Beta_elim_lyase; pfam01212 998088006682 tetramer interface [polypeptide binding]; other site 998088006683 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088006684 catalytic residue [active] 998088006685 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088006686 NAD(P) binding site [chemical binding]; other site 998088006687 active site 998088006688 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 998088006689 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and...; Region: Aldo_ket_red; cd06660 998088006690 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 998088006691 active site 998088006692 catalytic tetrad [active] 998088006693 RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA...; Region: RRM; cd00590 998088006694 RNA/DNA binding site [nucleotide binding]; other site 998088006695 RRM dimerization site [polypeptide binding]; other site 998088006696 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 998088006697 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP; Region: ABC_HisP_GlnQ_permeases; cd03262 998088006698 Walker A/P-loop; other site 998088006699 ATP binding site [chemical binding]; other site 998088006700 Q-loop/lid; other site 998088006701 ABC transporter signature motif; other site 998088006702 Walker B; other site 998088006703 D-loop; other site 998088006704 H-loop/switch region; other site 998088006705 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088006706 dimer interface [polypeptide binding]; other site 998088006707 conserved gate region; other site 998088006708 putative PBP binding loops; other site 998088006709 ABC-ATPase subunit interface; other site 998088006710 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088006711 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088006712 substrate binding pocket [chemical binding]; other site 998088006713 membrane-bound complex binding site; other site 998088006714 hinge residues; other site 998088006715 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 998088006716 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088006717 dimer interface [polypeptide binding]; other site 998088006718 conserved gate region; other site 998088006719 putative PBP binding loops; other site 998088006720 ABC-ATPase subunit interface; other site 998088006721 Penicillin-insensitive murein endopeptidase; Region: Peptidase_M74; cl01538 998088006722 LemA family; Region: LemA; cl00742 998088006723 Domain of unknown function (DUF477); Region: DUF477; cl01535 998088006724 Domain of unknown function (DUF477); Region: DUF477; cl01535 998088006725 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 998088006726 flagellar motor protein MotB; Reviewed; Region: motB; PRK08944 998088006727 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088006728 ligand binding site [chemical binding]; other site 998088006729 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 998088006730 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 998088006731 N-terminal plug; other site 998088006732 ligand-binding site [chemical binding]; other site 998088006733 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 998088006734 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 998088006735 Peptidase M36 family also known as fungalysin family; Region: M36; cd09596 998088006736 Zn binding site [ion binding]; other site 998088006737 Proprotein convertase P-domain; Region: P_proprotein; pfam01483 998088006738 Protein of unknown function (DUF1566); Region: DUF1566; pfam07603 998088006739 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 998088006740 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl00419 998088006741 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl00539 998088006742 bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional; Region: PRK11742 998088006743 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; cl00417 998088006744 NADH-quinone oxidoreductase, E subunit; Region: nuoE_fam; TIGR01958 998088006745 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of...; Region: TRX_Fd_NuoE; cd03064 998088006746 putative dimer interface [polypeptide binding]; other site 998088006747 [2Fe-2S] cluster binding site [ion binding]; other site 998088006748 NADH dehydrogenase I subunit F; Provisional; Region: PRK11278 998088006749 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 998088006750 SLBB domain; Region: SLBB; pfam10531 998088006751 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; cl11211 998088006752 NADH dehydrogenase subunit G; Validated; Region: PRK08166 998088006753 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 998088006754 catalytic loop [active] 998088006755 iron binding site [ion binding]; other site 998088006756 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; cl11210 998088006757 MopB_NDH-1_NuoG2-N7: The second domain of the NuoG subunit (with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory...; Region: MopB_NDH-1_NuoG2-N7; cd02771 998088006758 [4Fe-4S] binding site [ion binding]; other site 998088006759 MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting...; Region: MopB_CT_NDH-1_NuoG2-N7; cd02788 998088006760 NADH dehydrogenase; Region: NADHdh; cl00469 998088006761 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 998088006762 4Fe-4S binding domain; Region: Fer4; cl02805 998088006763 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 998088006764 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 998088006765 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 998088006766 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 998088006767 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 998088006768 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 998088006769 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 998088006770 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 998088006771 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 998088006772 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 998088006773 FIST N domain; Region: FIST; cl10701 998088006774 FIST C domain; Region: FIST_C; pfam10442 998088006775 PAS fold; Region: PAS_4; pfam08448 998088006776 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 998088006777 putative active site [active] 998088006778 heme pocket [chemical binding]; other site 998088006779 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088006780 Zn2+ binding site [ion binding]; other site 998088006781 Mg2+ binding site [ion binding]; other site 998088006782 PAS fold; Region: PAS_4; pfam08448 998088006783 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 998088006784 putative active site [active] 998088006785 heme pocket [chemical binding]; other site 998088006786 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088006787 Zn2+ binding site [ion binding]; other site 998088006788 Mg2+ binding site [ion binding]; other site 998088006789 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 998088006790 PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), first repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP...; Region: PurL_repeat1; cd02203 998088006791 dimerization interface [polypeptide binding]; other site 998088006792 ATP binding site [chemical binding]; other site 998088006793 PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), second repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP...; Region: PurL_repeat2; cd02204 998088006794 dimerization interface [polypeptide binding]; other site 998088006795 ATP binding site [chemical binding]; other site 998088006796 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 998088006797 putative active site [active] 998088006798 catalytic triad [active] 998088006799 membrane-bound lytic transglycosylase F; Provisional; Region: PRK10859 998088006800 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088006801 substrate binding pocket [chemical binding]; other site 998088006802 membrane-bound complex binding site; other site 998088006803 hinge residues; other site 998088006804 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 998088006805 N-acetyl-D-glucosamine binding site [chemical binding]; other site 998088006806 catalytic residue [active] 998088006807 Protein of unknown function (DUF1407); Region: DUF1407; pfam07191 998088006808 GTP-binding protein Der; Reviewed; Region: PRK00093 998088006809 EngA1 subfamily. This CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that...; Region: EngA1; cd01894 998088006810 G1 box; other site 998088006811 GTP/Mg2+ binding site [chemical binding]; other site 998088006812 Switch I region; other site 998088006813 G2 box; other site 998088006814 Switch II region; other site 998088006815 G3 box; other site 998088006816 G4 box; other site 998088006817 G5 box; other site 998088006818 EngA2 subfamily. This CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that...; Region: EngA2; cd01895 998088006819 G1 box; other site 998088006820 GTP/Mg2+ binding site [chemical binding]; other site 998088006821 Switch I region; other site 998088006822 G2 box; other site 998088006823 G3 box; other site 998088006824 Switch II region; other site 998088006825 G4 box; other site 998088006826 G5 box; other site 998088006827 outer membrane biogenesis protein BamB; Provisional; Region: PRK11138 998088006828 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 998088006829 Trp docking motif; other site 998088006830 active site 998088006831 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 998088006832 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 998088006833 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 998088006834 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: HisRS-like_core; cd00773 998088006835 dimer interface [polypeptide binding]; other site 998088006836 motif 1; other site 998088006837 active site 998088006838 motif 2; other site 998088006839 motif 3; other site 998088006840 HisRS Histidyl-anticodon binding domain. HisRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is...; Region: HisRS_anticodon; cd00859 998088006841 anticodon binding site; other site 998088006842 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 998088006843 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase; Region: ispG_gcpE; TIGR00612 998088006844 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 998088006845 cytoskeletal protein RodZ; Provisional; Region: PRK10856 998088006846 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi...; Region: TPR; cd00189 998088006847 binding surface 998088006848 TPR motif; other site 998088006849 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi...; Region: TPR; cd00189 998088006850 binding surface 998088006851 TPR motif; other site 998088006852 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 998088006853 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster...; Region: Radical_SAM; cd01335 998088006854 FeS/SAM binding site; other site 998088006855 Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside...; Region: NDPk_I; cd04413 998088006856 active site 998088006857 multimer interface [polypeptide binding]; other site 998088006858 aminopeptidase B; Provisional; Region: PRK05015 998088006859 Peptidase; Region: DUF3663; pfam12404 998088006860 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein...; Region: Peptidase_M17; cd00433 998088006861 interface (dimer of trimers) [polypeptide binding]; other site 998088006862 Substrate-binding/catalytic site; other site 998088006863 Zn-binding sites [ion binding]; other site 998088006864 aminopeptidase B; Provisional; Region: PRK05015 998088006865 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein...; Region: Peptidase_M17; cd00433 998088006866 interface (dimer of trimers) [polypeptide binding]; other site 998088006867 Substrate-binding/catalytic site; other site 998088006868 Zn-binding sites [ion binding]; other site 998088006869 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 998088006870 catalytic loop [active] 998088006871 iron binding site [ion binding]; other site 998088006872 chaperone protein HscA; Provisional; Region: hscA; PRK05183 998088006873 co-chaperone HscB; Provisional; Region: hscB; PRK05014 998088006874 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of...; Region: DnaJ; cl02542 998088006875 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 998088006876 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 998088006877 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 998088006878 trimerization site [polypeptide binding]; other site 998088006879 active site 998088006880 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 998088006881 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 998088006882 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 998088006883 catalytic residue [active] 998088006884 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088006885 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 998088006886 SCP-2 sterol transfer family; Region: SCP2; cl01225 998088006887 Peptidase family U32; Region: Peptidase_U32; cl03113 998088006888 Peptidase family U32; Region: Peptidase_U32; cl03113 998088006889 lipoprotein NlpI; Provisional; Region: PRK11189 998088006890 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi...; Region: TPR; cd00189 998088006891 binding surface 998088006892 TPR motif; other site 998088006893 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 998088006894 active site residue [active] 998088006895 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 998088006896 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 998088006897 Protein export membrane protein; Region: SecD_SecF; cl14618 998088006898 EnvZ/OmpR regulon moderator; Provisional; Region: PRK10629 998088006899 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 998088006900 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 998088006901 Protein export membrane protein; Region: SecD_SecF; cl14618 998088006902 Preprotein translocase subunit; Region: YajC; cl00806 998088006903 Queuine tRNA-ribosyltransferase; Region: TGT; cl00409 998088006904 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 998088006905 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 998088006906 FOG: CBS domain [General function prediction only]; Region: COG0517 998088006907 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-...; Region: CBS_pair; cl09141 998088006908 peroxiredoxin; Region: AhpC; TIGR03137 998088006909 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic...; Region: PRX_Typ2cys; cd03015 998088006910 dimer interface [polypeptide binding]; other site 998088006911 decamer (pentamer of dimers) interface [polypeptide binding]; other site 998088006912 catalytic triad [active] 998088006913 peroxidatic and resolving cysteines [active] 998088006914 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 998088006915 Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) family, N-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which in turn catalyzes the...; Region: AhpF_NTD_N; cd02974 998088006916 catalytic residue [active] 998088006917 TRX-GRX-like family, Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) subfamily, C-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which then...; Region: AhpF_NTD_C; cd03026 998088006918 catalytic residues [active] 998088006919 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088006920 Protein of unknown function (DUF541); Region: SIMPL; cl01077 998088006921 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 998088006922 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA_subfamily_ECM; cd01450 998088006923 integrin inhibitor binding pocket; other site 998088006924 metal ion-dependent adhesion site (MIDAS); other site 998088006925 integrin-collagen binding site; other site 998088006926 putative vWF-collagen binding site; other site 998088006927 glycoprotein Ib (GpIb) binding site [polypeptide binding]; other site 998088006928 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 998088006929 metal ion-dependent adhesion site (MIDAS); other site 998088006930 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 998088006931 type 1 secretion C-terminal target domain (VC_A0849 subclass); Region: T1SS_VCA0849; TIGR03661 998088006932 putative inner membrane diguanylate cyclase; Provisional; Region: PRK09966 998088006933 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088006934 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088006935 metal binding site [ion binding]; metal-binding site 998088006936 active site 998088006937 I-site; other site 998088006938 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 998088006939 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 998088006940 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 998088006941 Outer membrane efflux protein; Region: OEP; pfam02321 998088006942 Outer membrane efflux protein; Region: OEP; pfam02321 998088006943 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 998088006944 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2...; Region: Biotinyl_lipoyl_domains; cl11404 998088006945 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the 'double-glycine' leader peptides from the precursors of various...; Region: Peptidase_C39_likeD; cd02421 998088006946 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 998088006947 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 998088006948 ABC-type bacteriocin exporters. Many non-lantibiotic bacteriocins of lactic acid bacteria are produced as precursors which have N-terminal leader peptides that share similarities in amino acid sequence and contain a conserved processing site of two...; Region: ABCC_bacteriocin_exporters; cd03245 998088006949 Walker A/P-loop; other site 998088006950 ATP binding site [chemical binding]; other site 998088006951 Q-loop/lid; other site 998088006952 ABC transporter signature motif; other site 998088006953 Walker B; other site 998088006954 D-loop; other site 998088006955 H-loop/switch region; other site 998088006956 radical SAM protein, TIGR01212 family; Region: TIGR01212 998088006957 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster...; Region: Radical_SAM; cl15259 998088006958 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 998088006959 Glutamine amidotransferases class-II (Gn-AT), glutamate synthase (GltS)-type. GltS is a homodimer that synthesizes L-glutamate from 2-oxoglutarate and L-glutamine, an important step in ammonia assimilation in bacteria, cyanobacteria and plants. The N-...; Region: GltS; cd00713 998088006960 active site 998088006961 dimer interface [polypeptide binding]; other site 998088006962 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 998088006963 Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant...; Region: GltS_FMN; cd02808 998088006964 active site 998088006965 FMN binding site [chemical binding]; other site 998088006966 substrate binding site [chemical binding]; other site 998088006967 3Fe-4S cluster binding site [ion binding]; other site 998088006968 gltb_C. This domain is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS). GltS encodes a complex iron-sulfur flavoprotein that catalyzes the synthesis of L-glutamate from L-glutamine and 2-oxoglutarate. It requires the...; Region: gltB_C; cd00982 998088006969 domain interface; other site 998088006970 glutamate synthase small subunit family protein, proteobacterial; Region: gltD_gamma_fam; TIGR01318 998088006971 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved alpha-; Region: HCP_like; cl14655 998088006972 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088006973 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088006974 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cd02440 998088006975 S-adenosylmethionine binding site [chemical binding]; other site 998088006976 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 998088006977 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (...; Region: DEADc; cd00268 998088006978 ATP binding site [chemical binding]; other site 998088006979 Mg++ binding site [ion binding]; other site 998088006980 motif III; other site 998088006981 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 998088006982 nucleotide binding region [chemical binding]; other site 998088006983 ATP-binding site [chemical binding]; other site 998088006984 Protein of unknown function (DUF2913); Region: DUF2913; pfam11140 998088006985 FeoC like transcriptional regulator; Region: FeoC; cl07573 998088006986 ferrous iron transport protein B; Reviewed; Region: feoB; PRK09554 998088006987 Ferrous iron transport protein B (FeoB) subfamily. E. coli has an iron(II) transport system, known as feo, which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this...; Region: FeoB; cd01879 998088006988 G1 box; other site 998088006989 GTP/Mg2+ binding site [chemical binding]; other site 998088006990 Switch I region; other site 998088006991 G2 box; other site 998088006992 G3 box; other site 998088006993 Switch II region; other site 998088006994 G4 box; other site 998088006995 G5 box; other site 998088006996 Nucleoside recognition; Region: Gate; cl00486 998088006997 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 998088006998 Nucleoside recognition; Region: Gate; cl00486 998088006999 translation initiation factor Sui1; Validated; Region: PRK06824 998088007000 The SUI1/eIF1 (eukaryotic initiation factor 1) fold is found in eukaryotes, archaea, and some bacteria and is thought to play an important role in accurate initiator codon recognition during translation initiation. This fold, which includes two...; Region: SUI1_eIF1; cl00229 998088007001 Predicted membrane protein [Function unknown]; Region: COG2119 998088007002 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 998088007003 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 998088007004 Predicted membrane protein (DUF2157); Region: DUF2157; cl10480 998088007005 Uncharacterized membrane-anchored protein [Function unknown]; Region: COG4929 998088007006 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088007007 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088007008 substrate binding pocket [chemical binding]; other site 998088007009 membrane-bound complex binding site; other site 998088007010 hinge residues; other site 998088007011 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088007012 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088007013 substrate binding pocket [chemical binding]; other site 998088007014 membrane-bound complex binding site; other site 998088007015 hinge residues; other site 998088007016 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088007017 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088007018 substrate binding pocket [chemical binding]; other site 998088007019 membrane-bound complex binding site; other site 998088007020 hinge residues; other site 998088007021 Predicted ATP-binding protein involved in virulence [General function prediction only]; Region: COG3950 998088007022 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 998088007023 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 998088007024 active site 998088007025 HIGH motif; other site 998088007026 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 998088007027 KMSKS motif; other site 998088007028 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 998088007029 tRNA binding surface [nucleotide binding]; other site 998088007030 anticodon binding site; other site 998088007031 cyclophilin_EcCYP_like: cyclophilin-type A-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to the cytosolic E. coli cyclophilin A and Streptomyces antibioticus SanCyp18. Compared to the archetypal cyclophilin Human cyclophilin A, these...; Region: cyclophilin_EcCYP_like; cd01920 998088007032 substrate binding site [chemical binding]; other site 998088007033 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 998088007034 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 998088007035 putative active site [active] 998088007036 putative metal binding site [ion binding]; other site 998088007037 Protein of unknown function (DUF3606); Region: DUF3606; pfam12244 998088007038 Transglycosylase associated protein; Region: Transgly_assoc; cl00978 998088007039 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 998088007040 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cl00080 998088007041 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088007042 ATP binding site [chemical binding]; other site 998088007043 Mg2+ binding site [ion binding]; other site 998088007044 G-X-G motif; other site 998088007045 transcriptional regulatory protein TctD; Provisional; Region: PRK15479 998088007046 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088007047 active site 998088007048 phosphorylation site [posttranslational modification] 998088007049 intermolecular recognition site; other site 998088007050 dimerization interface [polypeptide binding]; other site 998088007051 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 998088007052 DNA binding site [nucleotide binding] 998088007053 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 998088007054 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 998088007055 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 998088007056 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 998088007057 integrase; Provisional; Region: int; PHA02601 998088007058 Phage HP1 integrase, C-terminal catalytic domain. Bacteriophage HP1 and related integrases are found in eubacteria, plasmids and temperate bacteriophages of the P2 family. They belong to the DNA breaking-rejoining enzyme superfamily, which includes...; Region: HP1_INT_C; cd00797 998088007059 dimer interface [polypeptide binding]; other site 998088007060 Int/Topo IB signature motif; other site 998088007061 active site 998088007062 catalytic residues [active] 998088007063 NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]; Region: Lig; COG0272 998088007064 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (...; Region: S24_LexA-like; cd06529 998088007065 Catalytic site [active] 998088007066 Phage regulatory protein CII (CP76); Region: Phage_CP76; pfam06892 998088007067 Ogr/Delta-like zinc finger; Region: Ogr_Delta; cl04623 998088007068 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 998088007069 Bacteriophage replication gene A protein (GPA); Region: Phage_GPA; cl15276 998088007070 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 998088007071 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 998088007072 active site 998088007073 DNA binding site [nucleotide binding] 998088007074 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (...; Region: S24_LexA-like; cd06529 998088007075 Catalytic site [active] 998088007076 Phage-related protein [Function unknown]; Region: COG4695; cl01923 998088007077 phage portal protein, PBSX family; Region: portal_PBSX; TIGR01540 998088007078 terminase ATPase subunit; Provisional; Region: P; PHA02535 998088007079 Putative ATPase subunit of terminase (gpP-like); Region: Terminase_5; pfam06056 998088007080 Mu-like prophage FluMu protein gp28 [General function prediction only]; Region: COG4373 998088007081 capsid-scaffolding protein; Provisional; Region: O; PHA02529 998088007082 Phage capsid scaffolding protein (GPO) serine peptidase; Region: Phage_GPO; pfam05929 998088007083 Phage major capsid protein, P2 family; Region: Phage_cap_P2; cl04947 998088007084 terminase endonuclease subunit; Provisional; Region: M; PHA02537 998088007085 Phage small terminase subunit; Region: Phage_term_smal; pfam05944 998088007086 Phage head completion protein (GPL); Region: Phage_GPL; pfam05926 998088007087 Phage Tail Protein X; Region: Phage_tail_X; cl02088 998088007088 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 998088007089 Protein of unknown function (DUF754); Region: DUF754; pfam05449 998088007090 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 998088007091 Protein of unknown function (DUF3380); Region: DUF3380; pfam11860 998088007092 phage lysis regulatory protein, LysB family; Region: phage_LysB; TIGR03495 998088007093 P2 phage tail completion protein R (GpR); Region: P2_Phage_GpR; pfam06891 998088007094 Phage virion morphogenesis family; Region: Phage_tail_S; cl02089 998088007095 Phage-related baseplate assembly protein; Region: Phage_base_V; cl11432 998088007096 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 998088007097 Baseplate J-like protein; Region: Baseplate_J; cl01294 998088007098 Phage tail protein (Tail_P2_I); Region: Tail_P2_I; cl01817 998088007099 Phage-related tail fibre protein [General function prediction only]; Region: COG5301 998088007100 long tail fiber, proximal subunit; Provisional; Region: 34; PHA02584 998088007101 Caudovirales tail fibre assembly protein; Region: Caudo_TAP; cl05448 998088007102 Phage tail sheath protein; Region: Phage_sheath_1; cl01389 998088007103 Phage tail tube protein FII; Region: Phage_tube; cl01390 998088007104 Phage tail protein E; Region: Phage_E; pfam06158 998088007105 Phage-related tail protein [Function unknown]; Region: COG5283 998088007106 phage tail tape measure protein, TP901 family, core region; Region: tape_meas_TP901; TIGR01760 998088007107 Phage P2 GpU; Region: Phage_P2_GpU; cl01391 998088007108 Phage protein D [General function prediction only]; Region: COG3500; cl12180 998088007109 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 998088007110 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 998088007111 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 998088007112 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 998088007113 GIY-YIG motif/motif A; other site 998088007114 active site 998088007115 catalytic site [active] 998088007116 putative DNA binding site [nucleotide binding]; other site 998088007117 metal binding site [ion binding]; metal-binding site 998088007118 UvrB/uvrC motif; Region: UVR; pfam02151 998088007119 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 998088007120 response regulator; Provisional; Region: PRK09483 998088007121 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088007122 active site 998088007123 phosphorylation site [posttranslational modification] 998088007124 intermolecular recognition site; other site 998088007125 dimerization interface [polypeptide binding]; other site 998088007126 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors...; Region: LuxR_C_like; cd06170 998088007127 DNA binding residues [nucleotide binding] 998088007128 dimerization interface [polypeptide binding]; other site 998088007129 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 998088007130 Ligand binding site [chemical binding]; other site 998088007131 oligomer interface [polypeptide binding]; other site 998088007132 Trm112p-like protein; Region: Trm112p; cl01066 998088007133 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 998088007134 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 998088007135 lipid transporter ATP-binding/permease protein; Provisional; Region: PRK11176 998088007136 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 998088007137 MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic...; Region: ABCC_MsbA; cd03251 998088007138 Walker A/P-loop; other site 998088007139 ATP binding site [chemical binding]; other site 998088007140 Q-loop/lid; other site 998088007141 ABC transporter signature motif; other site 998088007142 Walker B; other site 998088007143 D-loop; other site 998088007144 H-loop/switch region; other site 998088007145 DNA internalization-related competence protein ComEC/Rec2; Region: ComEC_Rec2; TIGR00361 998088007146 Competence protein; Region: Competence; cl00471 998088007147 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 998088007148 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; cl01261 998088007149 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; cl01261 998088007150 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 998088007151 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088007152 homodimer interface [polypeptide binding]; other site 998088007153 catalytic residue [active] 998088007154 transcriptional regulator HdfR; Provisional; Region: PRK03601 998088007155 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088007156 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088007157 Protein of unknown function, DUF; Region: DUF413; cl10479 998088007158 Protease Inhibitor Ecotin; homodimeric protease inhibitor; Region: Ecotin; cl00178 998088007159 secondary substrate binding site; other site 998088007160 primary substrate binding site; other site 998088007161 inhibition loop; other site 998088007162 dimerization interface [polypeptide binding]; other site 998088007163 Glycerophosphodiester phosphodiesterase domain of Escherichia coli (GlpQ) and similar proteins; Region: GDPD_EcGlpQ_like; cd08600 998088007164 Glycerophosphoryl diester phosphodiesterase family; Region: GDPD; pfam03009 998088007165 active site 998088007166 catalytic site [active] 998088007167 metal binding site [ion binding]; metal-binding site 998088007168 glycerol-3-phosphate dehydrogenase; Reviewed; Region: glpD; PRK12266 998088007169 DNA-binding transcriptional repressor GlpR; Provisional; Region: PRK10906 998088007170 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088007171 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 998088007172 sn-glycerol-3-phosphate transporter; Provisional; Region: glpT; PRK11273 998088007173 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088007174 putative substrate translocation pore; other site 998088007175 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088007176 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-...; Region: MIP; cd00333 998088007177 amphipathic channel; other site 998088007178 Asn-Pro-Ala signature motifs; other site 998088007179 glycerol kinase; Provisional; Region: glpK; PRK00047 998088007180 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 998088007181 N- and C-terminal domain interface [polypeptide binding]; other site 998088007182 active site 998088007183 MgATP binding site [chemical binding]; other site 998088007184 catalytic site [active] 998088007185 metal binding site [ion binding]; metal-binding site 998088007186 glycerol binding site [chemical binding]; other site 998088007187 homotetramer interface [polypeptide binding]; other site 998088007188 homodimer interface [polypeptide binding]; other site 998088007189 FBP binding site [chemical binding]; other site 998088007190 protein IIAGlc interface [polypeptide binding]; other site 998088007191 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088007192 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088007193 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088007194 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088007195 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088007196 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088007197 dimerization interface [polypeptide binding]; other site 998088007198 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 998088007199 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and...; Region: Aldo_ket_red; cd06660 998088007200 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 998088007201 active site 998088007202 catalytic tetrad [active] 998088007203 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 998088007204 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 998088007205 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 998088007206 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088007207 putative substrate translocation pore; other site 998088007208 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 998088007209 DoxX; Region: DoxX; cl00976 998088007210 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 998088007211 hypothetical protein; Provisional; Region: PRK05409 998088007212 Protein of unknown function (DUF692); Region: DUF692; cl01263 998088007213 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 998088007214 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 998088007215 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 998088007216 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 998088007217 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 998088007218 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 998088007219 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 998088007220 DNA-binding site [nucleotide binding]; DNA binding site 998088007221 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 998088007222 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088007223 homodimer interface [polypeptide binding]; other site 998088007224 catalytic residue [active] 998088007225 tellurium resistance terB-like protein, subgroup 3; Region: terB_like_YebE; cd07178 998088007226 putative metal binding site [ion binding]; other site 998088007227 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain...; Region: BFIT_BACH; cd03442 998088007228 Protein of unknown function (DUF2496); Region: DUF2496; cl11670 998088007229 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088007230 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088007231 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088007232 dimerization interface [polypeptide binding]; other site 998088007233 putative cyanate transporter; Provisional; Region: cynX; PRK09705 998088007234 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088007235 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 998088007236 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 998088007237 RNA binding surface [nucleotide binding]; other site 998088007238 PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like. This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to...; Region: PseudoU_synth_RluF; cd02554 998088007239 probable active site [active] 998088007240 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 998088007241 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_2; cd07253 998088007242 dimer interface [polypeptide binding]; other site 998088007243 metal binding site [ion binding]; metal-binding site 998088007244 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 998088007245 DNA binding site [nucleotide binding] 998088007246 substrate interaction site [chemical binding]; other site 998088007247 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 998088007248 Very Short Patch Repair (Vsr) Endonuclease. Endonucleases in DNA repair that recognize damaged DNA and cleave the phosphodiester backbone. Vsr endonucleases have a common endonuclease topology that has been tailored for recognition of TG mismatches; Region: Vsr; cd00221 998088007249 additional DNA contacts [nucleotide binding]; other site 998088007250 mismatch recognition site; other site 998088007251 active site 998088007252 zinc binding site [ion binding]; other site 998088007253 DNA intercalation site [nucleotide binding]; other site 998088007254 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 998088007255 ferredoxin; Provisional; Region: PRK08764 998088007256 Putative Fe-S cluster; Region: FeS; pfam04060 998088007257 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 998088007258 electron transport complex protein RnfC; Provisional; Region: PRK05035 998088007259 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 998088007260 SLBB domain; Region: SLBB; pfam10531 998088007261 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved alpha-; Region: HCP_like; cl14655 998088007262 RnfE family; Region: NQR2_RnfD_RnfE; cl00779 998088007263 FMN-binding domain; Region: FMN_bind; cl01081 998088007264 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 998088007265 endonuclease III; Provisional; Region: PRK10702 998088007266 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 998088007267 minor groove reading motif; other site 998088007268 helix-hairpin-helix signature motif; other site 998088007269 substrate binding pocket [chemical binding]; other site 998088007270 active site 998088007271 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 998088007272 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 998088007273 dimer interface [polypeptide binding]; other site 998088007274 active site 998088007275 glutathione binding site [chemical binding]; other site 998088007276 metal binding site [ion binding]; metal-binding site 998088007277 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088007278 ligand binding site [chemical binding]; other site 998088007279 Integrase core domain; Region: rve; cl01316 998088007280 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface...; Region: gram_neg_porins; cd00342 998088007281 trimer interface [polypeptide binding]; other site 998088007282 eyelet of channel; other site 998088007283 ATP-dependent DNA helicase DinG; Provisional; Region: dinG; PRK11747 998088007284 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088007285 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088007286 Uncharacterized protein conserved in bacteria (DUF2057); Region: DUF2057; cl11437 998088007287 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 998088007288 GTPase YlqF; Reviewed; Region: rbgA; PRK09563 998088007289 YlqF. Proteins of the YlqF family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases...; Region: YlqF; cd01856 998088007290 GTP/Mg2+ binding site [chemical binding]; other site 998088007291 G4 box; other site 998088007292 G5 box; other site 998088007293 G1 box; other site 998088007294 Switch I region; other site 998088007295 G2 box; other site 998088007296 G3 box; other site 998088007297 Switch II region; other site 998088007298 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH...; Region: alkPPc; cd00016 998088007299 dimer interface [polypeptide binding]; other site 998088007300 Alkaline phosphatase homologues; Region: alkPPc; smart00098 998088007301 active site 998088007302 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH...; Region: alkPPc; cd00016 998088007303 dimer interface [polypeptide binding]; other site 998088007304 Alkaline phosphatase homologues; Region: alkPPc; smart00098 998088007305 active site 998088007306 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088007307 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088007308 substrate binding pocket [chemical binding]; other site 998088007309 membrane-bound complex binding site; other site 998088007310 hinge residues; other site 998088007311 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 998088007312 C-term; Region: GreA_GreB; pfam01272 998088007313 DNA-binding transcriptional activator UhpA; Provisional; Region: PRK10360 998088007314 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088007315 active site 998088007316 phosphorylation site [posttranslational modification] 998088007317 intermolecular recognition site; other site 998088007318 dimerization interface [polypeptide binding]; other site 998088007319 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors...; Region: LuxR_C_like; cd06170 998088007320 DNA binding residues [nucleotide binding] 998088007321 dimerization interface [polypeptide binding]; other site 998088007322 sensory histidine kinase UhpB; Provisional; Region: PRK11644 998088007323 MASE1; Region: MASE1; pfam05231 998088007324 Histidine kinase; Region: HisKA_3; pfam07730 998088007325 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088007326 ATP binding site [chemical binding]; other site 998088007327 Mg2+ binding site [ion binding]; other site 998088007328 G-X-G motif; other site 998088007329 regulatory protein UhpC; Provisional; Region: PRK11663 998088007330 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088007331 putative substrate translocation pore; other site 998088007332 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088007333 metal binding site [ion binding]; metal-binding site 998088007334 active site 998088007335 I-site; other site 998088007336 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 998088007337 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088007338 substrate binding pocket [chemical binding]; other site 998088007339 membrane-bound complex binding site; other site 998088007340 hinge residues; other site 998088007341 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 998088007342 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088007343 dimer interface [polypeptide binding]; other site 998088007344 conserved gate region; other site 998088007345 putative PBP binding loops; other site 998088007346 ABC-ATPase subunit interface; other site 998088007347 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 998088007348 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP; Region: ABC_HisP_GlnQ_permeases; cd03262 998088007349 Walker A/P-loop; other site 998088007350 ATP binding site [chemical binding]; other site 998088007351 Q-loop/lid; other site 998088007352 ABC transporter signature motif; other site 998088007353 Walker B; other site 998088007354 D-loop; other site 998088007355 H-loop/switch region; other site 998088007356 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088007357 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088007358 substrate binding pocket [chemical binding]; other site 998088007359 membrane-bound complex binding site; other site 998088007360 hinge residues; other site 998088007361 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; cl01132 998088007362 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 998088007363 Homocysteine/selenocysteine methylase (S-methylmethionine-dependent) [Amino acid transport and metabolism]; Region: MHT1; cl14105 998088007364 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 998088007365 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 998088007366 Domain of unknown function DUF21; Region: DUF21; pfam01595 998088007367 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in...; Region: CBS_pair_CorC_HlyC_assoc; cd04590 998088007368 Transporter associated domain; Region: CorC_HlyC; cl08393 998088007369 transcriptional regulator PhoU; Provisional; Region: PRK11115 998088007370 PhoU domain; Region: PhoU; pfam01895 998088007371 PhoU domain; Region: PhoU; pfam01895 998088007372 phosphate transporter ATP-binding protein; Provisional; Region: PRK14236 998088007373 Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient. The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein...; Region: ABC_PstB_phosphate_transporter; cd03260 998088007374 Walker A/P-loop; other site 998088007375 ATP binding site [chemical binding]; other site 998088007376 Q-loop/lid; other site 998088007377 ABC transporter signature motif; other site 998088007378 Walker B; other site 998088007379 D-loop; other site 998088007380 H-loop/switch region; other site 998088007381 ABC-type phosphate transport system, auxiliary component [Inorganic ion transport and metabolism]; Region: COG4985 998088007382 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088007383 dimer interface [polypeptide binding]; other site 998088007384 conserved gate region; other site 998088007385 putative PBP binding loops; other site 998088007386 ABC-ATPase subunit interface; other site 998088007387 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4590 998088007388 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088007389 conserved gate region; other site 998088007390 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088007391 ABC-ATPase subunit interface; other site 998088007392 Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a...; Region: nucleoside_deaminase; cd01285 998088007393 nucleoside/Zn binding site; other site 998088007394 dimer interface [polypeptide binding]; other site 998088007395 catalytic motif [active] 998088007396 malate synthase A; Region: malate_syn_A; TIGR01344 998088007397 Malate synthase A (MSA), present in some bacteria, plants and fungi. Prokaryotic MSAs tend to be monomeric, whereas eukaryotic enzymes are homomultimers. In general, malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to...; Region: malate_synt_A; cd00727 998088007398 active site 998088007399 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 998088007400 tetramer interface [polypeptide binding]; other site 998088007401 active site 998088007402 Mg2+/Mn2+ binding site [ion binding]; other site 998088007403 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088007404 Uncharacterized protein conserved in bacteria (DUF2066); Region: DUF2066; cl01278 998088007405 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 998088007406 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 998088007407 PurM (Aminoimidazole Ribonucleotide [AIR] synthetase), one of eleven enzymes required for purine biosynthesis, catalyzes the conversion of formylglycinamide ribonucleotide (FGAM) and ATP to AIR, ADP, and Pi, the fifth step in de novo purine...; Region: PurM; cd02196 998088007408 dimerization interface [polypeptide binding]; other site 998088007409 putative ATP binding site [chemical binding]; other site 998088007410 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 998088007411 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 998088007412 active site 998088007413 substrate binding site [chemical binding]; other site 998088007414 cosubstrate binding site; other site 998088007415 catalytic site [active] 998088007416 Uncharacterized conserved protein [Function unknown]; Region: COG0327 998088007417 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl00412 998088007418 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 998088007419 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088007420 active site 998088007421 phosphorylation site [posttranslational modification] 998088007422 intermolecular recognition site; other site 998088007423 dimerization interface [polypeptide binding]; other site 998088007424 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088007425 Walker A motif; other site 998088007426 ATP binding site [chemical binding]; other site 998088007427 Walker B motif; other site 998088007428 arginine finger; other site 998088007429 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 998088007430 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 998088007431 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 998088007432 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 998088007433 dimer interface [polypeptide binding]; other site 998088007434 phosphorylation site [posttranslational modification] 998088007435 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088007436 ATP binding site [chemical binding]; other site 998088007437 G-X-G motif; other site 998088007438 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 998088007439 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cl09944 998088007440 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088007441 Walker A motif; other site 998088007442 ATP binding site [chemical binding]; other site 998088007443 Walker B motif; other site 998088007444 arginine finger; other site 998088007445 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 998088007446 Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and...; Region: Restriction_endonuclease_like; cl00277 998088007447 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 998088007448 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 998088007449 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-...; Region: CBS_pair; cl09141 998088007450 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains; Region: ACT_GcvR_2; cd04869 998088007451 polyphosphate kinase 1; Region: poly_P_kin; TIGR03705 998088007452 Catalytic C-terminal domain, first repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Region: PLDc_EcPPK1_C1_like; cd09164 998088007453 domain interface [polypeptide binding]; other site 998088007454 active site 998088007455 catalytic site [active] 998088007456 Catalytic C-terminal domain, second repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Region: PLDc_EcPPK1_C2_like; cd09167 998088007457 domain interface [polypeptide binding]; other site 998088007458 active site 998088007459 catalytic site [active] 998088007460 exopolyphosphatase; Provisional; Region: PRK10854 998088007461 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 998088007462 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 998088007463 MgtE intracellular N domain; Region: MgtE_N; cl15244 998088007464 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 998088007465 Divalent cation transporter; Region: MgtE; cl00786 998088007466 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 998088007467 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 998088007468 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK05683 998088007469 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 998088007470 flagellar rod assembly protein/muramidase FlgJ; Validated; Region: flgJ; PRK05684 998088007471 Rod binding protein; Region: Rod-binding; cl01626 998088007472 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; cl00743 998088007473 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 998088007474 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 998088007475 Flagellar L-ring protein; Region: FlgH; cl00905 998088007476 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 998088007477 Flagella basal body rod protein; Region: Flg_bb_rod; cl15245 998088007478 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 998088007479 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 998088007480 Flagella basal body rod protein; Region: Flg_bb_rod; cl15245 998088007481 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 998088007482 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 998088007483 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 998088007484 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 998088007485 Flagellar hook capping protein; Region: FlgD; cl04347 998088007486 flagellar basal body rod protein FlgC; Provisional; Region: flgC; PRK12631 998088007487 Flagella basal body rod protein; Region: Flg_bb_rod; cl15245 998088007488 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 998088007489 Flagella basal body rod protein; Region: Flg_bb_rod; cl15245 998088007490 flagellar basal body rod protein FlgB; Provisional; Region: flgB; PRK12625 998088007491 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 998088007492 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 998088007493 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 998088007494 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 998088007495 Response regulator receiver domain; Region: Response_reg; pfam00072 998088007496 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088007497 active site 998088007498 phosphorylation site [posttranslational modification] 998088007499 intermolecular recognition site; other site 998088007500 dimerization interface [polypeptide binding]; other site 998088007501 SAF domain; Region: SAF; cl00555 998088007502 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 998088007503 FlgN protein; Region: FlgN; cl09176 998088007504 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 998088007505 active site 998088007506 metal binding site [ion binding]; metal-binding site 998088007507 homotetramer interface [polypeptide binding]; other site 998088007508 oligopeptide ABC transporter substrate-binding protein OppA; Provisional; Region: PRK15104 998088007509 The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; Region: PBP2_OppA; cd08504 998088007510 peptide binding site [polypeptide binding]; other site 998088007511 EamA-like transporter family; Region: EamA; cl01037 998088007512 16S rRNA pseudouridylate synthase A; Provisional; Region: PRK10839 998088007513 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 998088007514 RNA binding surface [nucleotide binding]; other site 998088007515 PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA...; Region: PseudoU_synth_RsuA; cd02553 998088007516 active site 998088007517 uracil binding [chemical binding]; other site 998088007518 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 998088007519 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088007520 Zn2+ binding site [ion binding]; other site 998088007521 Mg2+ binding site [ion binding]; other site 998088007522 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea; Region: Transaldolase_FSA; cd00956 998088007523 active site 998088007524 intersubunit interactions; other site 998088007525 catalytic residue [active] 998088007526 glycyl-radical enzyme activating protein family; Region: PFLE_PFLC; TIGR02494 998088007527 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster...; Region: Radical_SAM; cl15259 998088007528 pyruvate formate-lyase; Region: PFL2-3; TIGR01774 998088007529 Pyruvate formate lyase 2 and related enzymes; Region: PFL2_DhaB_BssA; cd01677 998088007530 dimer interface [polypeptide binding]; other site 998088007531 active site 998088007532 glycine loop; other site 998088007533 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 998088007534 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088007535 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 998088007536 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 998088007537 EamA-like transporter family; Region: EamA; cl01037 998088007538 EamA-like transporter family; Region: EamA; cl01037 998088007539 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_14; cd08497 998088007540 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 998088007541 Protein of unknown function (DUF2750); Region: DUF2750; pfam11042 998088007542 Phosphate-starvation-inducible E; Region: PsiE; cl01264 998088007543 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein...; Region: CSP_CDS; cd04458 998088007544 DNA-binding site [nucleotide binding]; DNA binding site 998088007545 RNA-binding motif; other site 998088007546 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 998088007547 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 998088007548 E3 interaction surface; other site 998088007549 lipoyl attachment site [posttranslational modification]; other site 998088007550 e3 binding domain; Region: E3_binding; pfam02817 998088007551 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 998088007552 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 998088007553 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 998088007554 alpha subunit interface [polypeptide binding]; other site 998088007555 TPP binding site [chemical binding]; other site 998088007556 heterodimer interface [polypeptide binding]; other site 998088007557 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 998088007558 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]; Region: AcoA; COG1071 998088007559 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 998088007560 tetramer interface [polypeptide binding]; other site 998088007561 TPP-binding site [chemical binding]; other site 998088007562 heterodimer interface [polypeptide binding]; other site 998088007563 phosphorylation loop region [posttranslational modification] 998088007564 enterobactin synthase subunit F; Provisional; Region: entF; PRK10252 998088007565 Condensation domain; Region: Condensation; cl09290 998088007566 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 998088007567 Phosphopantetheine attachment site; Region: PP-binding; cl09936 998088007568 2,3-dihydroxybenzoate-2,3-dehydrogenase; Validated; Region: PRK08220 998088007569 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088007570 NAD(P) binding site [chemical binding]; other site 998088007571 active site 998088007572 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cl00220 998088007573 Isochorismatase family; Region: Isochorismatase; pfam00857 998088007574 catalytic triad [active] 998088007575 conserved cis-peptide bond; other site 998088007576 Phosphopantetheine attachment site; Region: PP-binding; cl09936 998088007577 enterobactin synthase subunit E; Provisional; Region: entE; PRK10946 998088007578 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 998088007579 isochorismate synthase DhbC; Validated; Region: PRK06923 998088007580 chorismate binding enzyme; Region: Chorismate_bind; cl10555 998088007581 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 998088007582 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 998088007583 N-terminal plug; other site 998088007584 ligand-binding site [chemical binding]; other site 998088007585 NeuB family; Region: NeuB; cl00496 998088007586 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 998088007587 Transcriptional regulators [Transcription]; Region: PurR; COG1609 998088007588 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 998088007589 DNA binding site [nucleotide binding] 998088007590 domain linker motif; other site 998088007591 Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism; Region: PBP1_GalS_like; cd06270 998088007592 dimerization interface (closed form) [polypeptide binding]; other site 998088007593 ligand binding site [chemical binding]; other site 998088007594 lytic murein transglycosylase; Provisional; Region: PRK11619 998088007595 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 998088007596 N-acetyl-D-glucosamine binding site [chemical binding]; other site 998088007597 catalytic residue [active] 998088007598 PAS domain S-box; Region: sensory_box; TIGR00229 998088007599 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 998088007600 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088007601 metal binding site [ion binding]; metal-binding site 998088007602 active site 998088007603 I-site; other site 998088007604 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 998088007605 RaiA ('ribosome-associated inhibitor A', also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site...; Region: RaiA; cd00552 998088007606 30S subunit binding site; other site 998088007607 Ribosomal S4P (gammaproteobacterial); Region: Ribosomal_S4Pg; pfam11993 998088007608 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 998088007609 Family of unknown function (DUF490); Region: DUF490; pfam04357 998088007610 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 998088007611 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 998088007612 Surface antigen; Region: Bac_surface_Ag; cl03097 998088007613 PPIC-type PPIASE domain; Region: Rotamase; cl08278 998088007614 Protein of unknown function (DUF1499); Region: DUF1499; cl01841 998088007615 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 998088007616 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 998088007617 mercuric reductase; Validated; Region: PRK06370 998088007618 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088007619 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 998088007620 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088007621 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG4134 998088007622 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4135 998088007623 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: COG4136 998088007624 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088007625 Walker A/P-loop; other site 998088007626 ATP binding site [chemical binding]; other site 998088007627 Q-loop/lid; other site 998088007628 ABC transporter signature motif; other site 998088007629 Walker B; other site 998088007630 D-loop; other site 998088007631 H-loop/switch region; other site 998088007632 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 998088007633 lytic murein transglycosylase; Region: MltB_2; TIGR02283 998088007634 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 998088007635 N-acetyl-D-glucosamine binding site [chemical binding]; other site 998088007636 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088007637 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 998088007638 EamA-like transporter family; Region: EamA; cl01037 998088007639 phosphoglucomutase; Validated; Region: PRK07564 998088007640 This bacterial PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl...; Region: PGM_like3; cd05801 998088007641 active site 998088007642 substrate binding site [chemical binding]; other site 998088007643 metal binding site [ion binding]; metal-binding site 998088007644 SeqA protein; Region: SeqA; cl11470 998088007645 acyl-CoA esterase; Provisional; Region: PRK10673 998088007646 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 998088007647 Protein of unknown function (DUF2788); Region: DUF2788; pfam10981 998088007648 LexA regulated protein; Provisional; Region: PRK11675 998088007649 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 998088007650 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 998088007651 CoenzymeA binding site [chemical binding]; other site 998088007652 subunit interaction site [polypeptide binding]; other site 998088007653 PHB binding site; other site 998088007654 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 998088007655 metal binding site 2 [ion binding]; metal-binding site 998088007656 putative DNA binding helix; other site 998088007657 metal binding site 1 [ion binding]; metal-binding site 998088007658 dimer interface [polypeptide binding]; other site 998088007659 structural Zn2+ binding site [ion binding]; other site 998088007660 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 998088007661 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 998088007662 active site 998088007663 HIGH motif; other site 998088007664 nucleotide binding site [chemical binding]; other site 998088007665 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 998088007666 KMSKS motif; other site 998088007667 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 998088007668 Putative carbohydrate binding domain; Region: CHB_HEX; cl03918 998088007669 N-acetyl-beta-hexosaminidase [Carbohydrate transport and metabolism]; Region: Chb; COG3525 998088007670 The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i)...; Region: GH20_Sm-chitobiase-like; cd06569 998088007671 active site 998088007672 E or 'early' set of sugar utilizing enzymes which may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end; Region: E_set; cl09101 998088007673 PTS system, N-acetylglucosamine-specific IIBC component; Region: PTS-II-BC-nag; TIGR01998 998088007674 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 998088007675 PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIB_glc; cd00212 998088007676 active site turn [active] 998088007677 phosphorylation site [posttranslational modification] 998088007678 GlcN6P_deaminase: Glucosamine-6-phosphate (GlcN6P) deaminase subfamily; GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium. The reaction is an aldo-keto isomerization coupled with an amination...; Region: GlcN6P_deaminase; cd01399 998088007679 active site 998088007680 trimer interface [polypeptide binding]; other site 998088007681 allosteric site; other site 998088007682 active site lid [active] 998088007683 hexamer (dimer of trimers) interface [polypeptide binding]; other site 998088007684 N-acetylglucosamine-6-phosphate deacetylase; Region: nagA; TIGR00221 998088007685 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of N-acetyl-glucosamine-6-phosphate (GlcNAc-6-P) to glucosamine 6-phosphate and acetate. This is the first committed step in the biosynthetic pathway to...; Region: NagA; cd00854 998088007686 active site 998088007687 dimer interface [polypeptide binding]; other site 998088007688 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088007689 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 998088007690 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 998088007691 putative metal dependent hydrolase; Provisional; Region: PRK11598 998088007692 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 998088007693 Sulfatase; Region: Sulfatase; cl10460 998088007694 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 998088007695 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088007696 Zn2+ binding site [ion binding]; other site 998088007697 Mg2+ binding site [ion binding]; other site 998088007698 Putative regulator of cell autolysis [Signal transduction mechanisms]; Region: LytS; COG3275 998088007699 Protein of unknown function (DUF1393); Region: DUF1393; cl01942 998088007700 GAF domain; Region: GAF; cl00853 998088007701 Histidine kinase; Region: His_kinase; pfam06580 998088007702 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 998088007703 putative two-component response-regulatory protein YehT; Provisional; Region: PRK11697 998088007704 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088007705 active site 998088007706 phosphorylation site [posttranslational modification] 998088007707 intermolecular recognition site; other site 998088007708 dimerization interface [polypeptide binding]; other site 998088007709 LytTr DNA-binding domain; Region: LytTR; cl04498 998088007710 Carbon starvation protein CstA; Region: CstA; cl00856 998088007711 Protein of unknown function (DUF3302); Region: DUF3302; pfam11742 998088007712 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 998088007713 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 998088007714 ATP binding site [chemical binding]; other site 998088007715 putative Mg++ binding site [ion binding]; other site 998088007716 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 998088007717 nucleotide binding region [chemical binding]; other site 998088007718 ATP-binding site [chemical binding]; other site 998088007719 D-Ala-D-Ala carboxypeptidase 3 (S13) family; Region: Peptidase_S13; cl15297 998088007720 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 4) [Cell envelope biogenesis, outer membrane]; Region: DacB; COG2027 998088007721 Glutaredoxin (GRX) family; composed of GRX, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide...; Region: GRX_family; cd02066 998088007722 GSH binding site [chemical binding]; other site 998088007723 catalytic residues [active] 998088007724 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 998088007725 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain...; Region: BFIT_BACH; cd03442 998088007726 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088007727 NAD(P) binding site [chemical binding]; other site 998088007728 active site 998088007729 pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric; Region: pyruv_ox_red; TIGR02176 998088007730 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 998088007731 dimer interface [polypeptide binding]; other site 998088007732 PYR/PP interface [polypeptide binding]; other site 998088007733 TPP binding site [chemical binding]; other site 998088007734 substrate binding site [chemical binding]; other site 998088007735 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 998088007736 Domain of unknown function; Region: EKR; cl11037 998088007737 4Fe-4S binding domain; Region: Fer4; cl02805 998088007738 4Fe-4S binding domain; Region: Fer4; cl02805 998088007739 TPP-binding module; composed of proteins similar to the single subunit pyruvate ferredoxin oxidoreductase (PFOR) of Desulfovibrio Africanus, present in bacteria and amitochondriate eukaryotes. This subfamily also includes proteins characterized as...; Region: TPP_PFOR_PNO; cd03377 998088007740 TPP-binding site [chemical binding]; other site 998088007741 dimer interface [polypeptide binding]; other site 998088007742 putative glutamate synthase (NADPH) small subunit; Provisional; Region: PRK12771 998088007743 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088007744 4Fe-4S binding domain; Region: Fer4; cl02805 998088007745 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088007746 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088007747 substrate binding pocket [chemical binding]; other site 998088007748 membrane-bound complex binding site; other site 998088007749 hinge residues; other site 998088007750 Uncharacterized Fe-S protein [General function prediction only]; Region: COG3217 998088007751 MOSC N-terminal beta barrel domain; Region: MOSC_N; pfam03476 998088007752 MOSC domain; Region: MOSC; pfam03473 998088007753 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 998088007754 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron...; Region: FNR_iron_sulfur_binding_1; cd06215 998088007755 FAD binding pocket [chemical binding]; other site 998088007756 FAD binding motif [chemical binding]; other site 998088007757 phosphate binding motif [ion binding]; other site 998088007758 beta-alpha-beta structure motif; other site 998088007759 NAD binding pocket [chemical binding]; other site 998088007760 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 998088007761 catalytic loop [active] 998088007762 iron binding site [ion binding]; other site 998088007763 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088007764 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088007765 Peptidase family M48; Region: Peptidase_M48; cl12018 998088007766 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 998088007767 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 998088007768 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 998088007769 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 998088007770 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cd02440 998088007771 S-adenosylmethionine binding site [chemical binding]; other site 998088007772 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 998088007773 KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS), 8-amino-7-...; Region: KBL_like; cd06454 998088007774 substrate-cofactor binding pocket; other site 998088007775 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088007776 catalytic residue [active] 998088007777 biotin synthase; Provisional; Region: PRK15108 998088007778 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster...; Region: Radical_SAM; cd01335 998088007779 FeS/SAM binding site; other site 998088007780 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 998088007781 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase...; Region: OAT_like; cd00610 998088007782 adenosylmethionine--8-amino-7-oxononanoate transaminase; Validated; Region: PRK07986 998088007783 inhibitor-cofactor binding pocket; inhibition site 998088007784 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088007785 catalytic residue [active] 998088007786 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cd06225 998088007787 dimerization interface [polypeptide binding]; other site 998088007788 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 998088007789 EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (...; Region: EcAsnRS_like_N; cd04318 998088007790 putative dimer interface [polypeptide binding]; other site 998088007791 putative anticodon binding site; other site 998088007792 Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well...; Region: AsxRS_core; cd00776 998088007793 homodimer interface [polypeptide binding]; other site 998088007794 motif 1; other site 998088007795 motif 2; other site 998088007796 active site 998088007797 motif 3; other site 998088007798 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088007799 Anaerobic c4-dicarboxylate membrane transporter; Region: DcuA_DcuB; cl01040 998088007800 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This...; Region: Alpha_ANH_like_IV; cd01994 998088007801 Ligand Binding Site [chemical binding]; other site 998088007802 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 998088007803 hypothetical protein; Provisional; Region: PRK07338 998088007804 metal binding site [ion binding]; metal-binding site 998088007805 dimer interface [polypeptide binding]; other site 998088007806 C4-dicarboxylate transporter [Energy production and conversion]; Region: DcuC; COG3069 998088007807 C4-dicarboxylate transporter DcuC; Provisional; Region: dcuC; cl15274 998088007808 Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine...; Region: ArsC_Yffb; cd03035 998088007809 putative catalytic residues [active] 998088007810 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 998088007811 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 998088007812 metal binding site [ion binding]; metal-binding site 998088007813 dimer interface [polypeptide binding]; other site 998088007814 D-alanyl-D-alanine carboxypeptidase; Region: VanY; cl00813 998088007815 potassium/proton antiporter; Reviewed; Region: PRK05326 998088007816 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088007817 Transporter associated domain; Region: CorC_HlyC; cl08393 998088007818 beta-N-acetylglucosaminidase; Region: NAGidase; pfam07555 998088007819 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 998088007820 LysE type translocator; Region: LysE; cl00565 998088007821 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088007822 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088007823 Protein of unknown function (DUF1523); Region: DUF1523; pfam07509 998088007824 Uncharacterized protein conserved in bacteria (DUF2131); Region: DUF2131; cl11547 998088007825 nuc_hydro_IU_UC_XIUA: inosine-uridine preferring, xanthosine-inosine-uridine-adenosine-preferring and, uridine-cytidine preferring nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the...; Region: nuc_hydro_IU_UC_XIUA; cd02651 998088007826 active site 998088007827 tetramer interface [polypeptide binding]; other site 998088007828 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF...; Region: PseudoU_synth_RluCD_like; cd02869 998088007829 active site 998088007830 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 998088007831 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 998088007832 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 998088007833 Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria; Region: LPO; cd08176 998088007834 dimer interface [polypeptide binding]; other site 998088007835 active site 998088007836 metal binding site [ion binding]; metal-binding site 998088007837 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 998088007838 Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]; Region: TadD; COG5010 998088007839 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 998088007840 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 998088007841 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 998088007842 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial...; Region: VirB11-like_ATPase; cd01130 998088007843 ATP binding site [chemical binding]; other site 998088007844 Walker A motif; other site 998088007845 hexamer interface [polypeptide binding]; other site 998088007846 Walker B motif; other site 998088007847 Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]; Region: CpaE; COG4963 998088007848 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 998088007849 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 998088007850 SAF domain; Region: SAF; cl00555 998088007851 Protein of unknown function (DUF1566); Region: DUF1566; pfam07603 998088007852 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 998088007853 CC3(TIP30)-like, atypical (a) SDRs; Region: CC3_like_SDR_a; cd05250 998088007854 NAD binding site [chemical binding]; other site 998088007855 active site 998088007856 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 998088007857 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 998088007858 catalytic residue [active] 998088007859 lipoate-protein ligase A; Provisional; Region: lplA; PRK03822 998088007860 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 998088007861 Bacterial lipoate protein ligase C-terminus; Region: Lip_prot_lig_C; pfam10437 998088007862 NMT1/THI5 like; Region: NMT1; pfam09084 998088007863 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088007864 substrate binding pocket [chemical binding]; other site 998088007865 membrane-bound complex binding site; other site 998088007866 PAS domain S-box; Region: sensory_box; TIGR00229 998088007867 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 998088007868 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088007869 metal binding site [ion binding]; metal-binding site 998088007870 active site 998088007871 I-site; other site 998088007872 hemerythrin-like metal-binding domain; Region: hemeryth_dom; TIGR02481 998088007873 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl11605 998088007874 octamerization interface [polypeptide binding]; other site 998088007875 diferric-oxygen binding site [ion binding]; other site 998088007876 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 998088007877 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 998088007878 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 998088007879 FtsX-like permease family; Region: FtsX; pfam02687 998088007880 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 998088007881 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 998088007882 Walker A/P-loop; other site 998088007883 ATP binding site [chemical binding]; other site 998088007884 Q-loop/lid; other site 998088007885 ABC transporter signature motif; other site 998088007886 Walker B; other site 998088007887 D-loop; other site 998088007888 H-loop/switch region; other site 998088007889 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 998088007890 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 998088007891 Protein export membrane protein; Region: SecD_SecF; cl14618 998088007892 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 998088007893 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2...; Region: Biotinyl_lipoyl_domains; cl11404 998088007894 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 998088007895 YeeE/YedE family (DUF395); Region: DUF395; cl01018 998088007896 YeeE/YedE family (DUF395); Region: DUF395; cl01018 998088007897 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 998088007898 putative DNA binding site [nucleotide binding]; other site 998088007899 putative Zn2+ binding site [ion binding]; other site 998088007900 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 998088007901 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 998088007902 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088007903 MgtC family; Region: MgtC; cl12207 998088007904 D-fructose-responsive transcription factor; Region: fruct_sucro_rep; TIGR02417 998088007905 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 998088007906 DNA binding site [nucleotide binding] 998088007907 domain linker motif; other site 998088007908 Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs; Region: PBP1_FruR; cd06274 998088007909 dimerization interface [polypeptide binding]; other site 998088007910 ligand binding site [chemical binding]; other site 998088007911 sucrose-6-phosphate hydrolase; Region: scrB_fam; TIGR01322 998088007912 Glycosyl hydrolase family 32, beta-fructosidases; Region: GH32_B_Fructosidase; cd08996 998088007913 substrate binding [chemical binding]; other site 998088007914 active site 998088007915 PTS system, sucrose-specific IIBC component; Region: PTS-II-BC-sucr; TIGR01996 998088007916 PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIB_glc; cd00212 998088007917 active site turn [active] 998088007918 phosphorylation site [posttranslational modification] 998088007919 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 998088007920 pfkB family carbohydrate kinase; Region: PfkB; pfam00294 998088007921 Fructokinases (FRKs) mainly from bacteria and plants are enzymes with high specificity for fructose, as are all FRKs, but they catalyzes the conversion of fructose to fructose-6-phosphate, which is an entry point into glycolysis via conversion into...; Region: bac_FRK; cd01167 998088007922 putative substrate binding site [chemical binding]; other site 998088007923 putative ATP binding site [chemical binding]; other site 998088007924 The Maltoporin-like channels (LamB porin) form a trimeric structure which facilitate the diffusion of maltodextrins and other sugars across the outer membrane of Gram-negative bacteria. The membrane channel is formed by an 18-strand antiparallel beta-...; Region: Maltoporin-like; cd01346 998088007925 trimer interface; other site 998088007926 sugar binding site [chemical binding]; other site 998088007927 chaperone protein DnaJ; Provisional; Region: PRK10767 998088007928 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of...; Region: DnaJ; cd06257 998088007929 HSP70 interaction site [polypeptide binding]; other site 998088007930 DnaJ central domain; Region: DnaJ_CXXCXGXG; cl14908 998088007931 DnaJ C terminal domain; Region: DnaJ_C; pfam01556 998088007932 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 998088007933 FGGY family of carbohydrate kinases; Region: FGGY; cl08364 998088007934 Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: GrpE; COG0576 998088007935 GrpE is the adenine nucleotide exchange factor of DnaK (Hsp70)-type ATPases. The GrpE dimer binds to the ATPase domain of Hsp70 catalyzing the dissociation of ADP, which enables rebinding of ATP, one step in the Hsp70 reaction cycle in protein folding...; Region: GrpE; cd00446 998088007936 dimer interface [polypeptide binding]; other site 998088007937 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 998088007938 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 998088007939 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 998088007940 recombination and repair protein; Provisional; Region: PRK10869 998088007941 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides...; Region: ABC_RecN; cd03241 998088007942 Walker A/P-loop; other site 998088007943 ATP binding site [chemical binding]; other site 998088007944 Q-loop/lid; other site 998088007945 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides...; Region: ABC_RecN; cd03241 998088007946 Q-loop/lid; other site 998088007947 ABC transporter signature motif; other site 998088007948 Walker B; other site 998088007949 D-loop; other site 998088007950 H-loop/switch region; other site 998088007951 putative manganese-dependent inorganic pyrophosphatase; Provisional; Region: PRK05427 998088007952 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-...; Region: CBS_pair; cl09141 998088007953 DHHA2 domain; Region: DHHA2; pfam02833 998088007954 macrolide transporter subunit MacA; Provisional; Region: PRK11578 998088007955 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 998088007956 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 998088007957 Walker A/P-loop; other site 998088007958 ATP binding site [chemical binding]; other site 998088007959 Q-loop/lid; other site 998088007960 ABC transporter signature motif; other site 998088007961 Walker B; other site 998088007962 D-loop; other site 998088007963 H-loop/switch region; other site 998088007964 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 998088007965 FtsX-like permease family; Region: FtsX; pfam02687 998088007966 NodT family; Region: outer_NodT; TIGR01845 998088007967 Outer membrane efflux protein; Region: OEP; pfam02321 998088007968 Outer membrane efflux protein; Region: OEP; pfam02321 998088007969 Domain in histone-like proteins of HNS family; Region: HNS; cl09251 998088007970 DNA binding protein, nucleoid-associated; Provisional; Region: PRK10328 998088007971 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 998088007972 O-Antigen ligase; Region: Wzy_C; cl04850 998088007973 Domain of unknown function (DUF3366); Region: DUF3366; pfam11846 998088007974 Chain length determinant protein; Region: Wzz; cl01623 998088007975 putative transposase OrfB; Reviewed; Region: PHA02517 998088007976 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 998088007977 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 998088007978 Polysaccharide biosynthesis protein; Region: Polysacc_synt_2; pfam02719 998088007979 NAD(P) binding site [chemical binding]; other site 998088007980 homodimer interface [polypeptide binding]; other site 998088007981 substrate binding site [chemical binding]; other site 998088007982 active site 998088007983 Bacterial sugar transferase; Region: Bac_transf; cl00939 998088007984 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 998088007985 UDP-glucose 4 epimerase, subgroup 4, extended (e) SDRs; Region: UDP_G4E_4_SDR_e; cd05232 998088007986 putative NAD(P) binding site [chemical binding]; other site 998088007987 active site 998088007988 putative substrate binding site [chemical binding]; other site 998088007989 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 998088007990 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 998088007991 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 998088007992 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues...; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 998088007993 active site 998088007994 homodimer interface [polypeptide binding]; other site 998088007995 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088007996 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 998088007997 NAD(P) binding site [chemical binding]; other site 998088007998 active site 998088007999 Cupin domain; Region: Cupin_2; cl09118 998088008000 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 998088008001 Polysaccharide biosynthesis protein; Region: Polysacc_synt_2; pfam02719 998088008002 NAD(P) binding site [chemical binding]; other site 998088008003 homodimer interface [polypeptide binding]; other site 998088008004 substrate binding site [chemical binding]; other site 998088008005 active site 998088008006 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 998088008007 Imidazoleglycerol-phosphate synthase [Amino acid transport and metabolism]; Region: HisF; COG0107 998088008008 The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)-formimino-5-; Region: HisF; cd04731 998088008009 substrate binding site [chemical binding]; other site 998088008010 glutamase interaction surface [polypeptide binding]; other site 998088008011 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 998088008012 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This...; Region: Alpha_ANH_like_III; cd01996 998088008013 Ligand Binding Site [chemical binding]; other site 998088008014 flagellin modification protein A; Provisional; Region: PRK09186 998088008015 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088008016 NAD(P) binding site [chemical binding]; other site 998088008017 active site 998088008018 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 998088008019 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 998088008020 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088008021 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 998088008022 FOG: CBS domain [General function prediction only]; Region: COG0517 998088008023 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain associated with the NTP (Nucleotidyl transferase) domain downstream. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently...; Region: CBS_pair_NTP_transferase_assoc; cd04607 998088008024 NTP_trnasferase_like_2 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_2; cd06426 998088008025 Substrate binding site [chemical binding]; other site 998088008026 metal binding site [ion binding]; metal-binding site 998088008027 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 998088008028 Putative Acyltransferase (AT), Left-handed parallel beta-Helix (LbH) domain; This group is composed of mostly uncharacterized proteins containing an N-terminal helical subdomain followed by a LbH domain. The alignment contains 6 turns, each containing...; Region: LbH_AT_putative; cd03360 998088008029 putative trimer interface [polypeptide binding]; other site 998088008030 putative CoA binding site [chemical binding]; other site 998088008031 N-acetylneuraminate synthase; Region: NeuB_NnaB; TIGR03569 998088008032 NeuB family; Region: NeuB; cl00496 998088008033 SAF domain; Region: SAF; cl00555 998088008034 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues...; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 998088008035 UDP-N-acetyl-D-glucosamine 2-epimerase, UDP-hydrolysing; Region: NeuC_NnaA; TIGR03568 998088008036 active site 998088008037 homodimer interface [polypeptide binding]; other site 998088008038 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 998088008039 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 998088008040 inhibitor-cofactor binding pocket; inhibition site 998088008041 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088008042 catalytic residue [active] 998088008043 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088008044 NAD(P) binding site [chemical binding]; other site 998088008045 active site 998088008046 MatE; Region: MatE; cl10513 998088008047 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 998088008048 Protein export membrane protein; Region: SecD_SecF; cl14618 998088008049 Protein export membrane protein; Region: SecD_SecF; cl14618 998088008050 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 998088008051 DNA-binding transcriptional repressor AcrR; Provisional; Region: PRK10668 998088008052 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088008053 MAATS-type transcriptional repressor, C-terminal region; Region: TetR_C_2; pfam08361 998088008054 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 998088008055 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 998088008056 This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme; Region: NifX_NifB; cl00252 998088008057 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088008058 Zn2+ binding site [ion binding]; other site 998088008059 Mg2+ binding site [ion binding]; other site 998088008060 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 998088008061 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 998088008062 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster...; Region: Radical_SAM; cd01335 998088008063 FeS/SAM binding site; other site 998088008064 Protein of unknown function (DUF1349); Region: DUF1349; cl01397 998088008065 Uncharacterized conserved protein [Function unknown]; Region: COG4938 998088008066 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088008067 Walker A/P-loop; other site 998088008068 ATP binding site [chemical binding]; other site 998088008069 Uncharacterized conserved protein [Function unknown]; Region: COG4938 998088008070 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 998088008071 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD)...; Region: Trp-synth-beta_II; cl00342 998088008072 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 998088008073 catalytic residue [active] 998088008074 homoserine kinase; Provisional; Region: PRK01212 998088008075 GHMP kinases N terminal domain; Region: GHMP_kinases_N; cl08256 998088008076 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 998088008077 bifunctional aspartokinase I/homoserine dehydrogenase I; Provisional; Region: thrA; PRK09436 998088008078 AAK_AK-HSDH: Amino Acid Kinase Superfamily (AAK), AK-HSDH; this CD includes the N-terminal catalytic domain of aspartokinase (AK) of the bifunctional enzyme AK - homoserine dehydrogenase (HSDH). These aspartokinases are found in bacteria (E. coli AKI-...; Region: AAK_AK-HSDH; cd04257 998088008079 putative catalytic residues [active] 998088008080 putative nucleotide binding site [chemical binding]; other site 998088008081 putative aspartate binding site [chemical binding]; other site 998088008082 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA-like_1; cd04921 998088008083 dimer interface [polypeptide binding]; other site 998088008084 putative threonine allosteric regulatory site; other site 998088008085 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA_2; cd04922 998088008086 putative threonine allosteric regulatory site; other site 998088008087 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088008088 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 998088008089 putative RNA methyltransferase; Provisional; Region: PRK10433 998088008090 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 998088008091 Isocitrate dehydrogenase kinase/phosphatase (AceK); Region: AceK; cl01891 998088008092 acyl-CoA thioesterase II; Provisional; Region: PRK10526 998088008093 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP)...; Region: Thioesterase_II_repeat2; cd03445 998088008094 active site 998088008095 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP)...; Region: Thioesterase_II_repeat1; cd03444 998088008096 catalytic triad [active] 998088008097 dimer interface [polypeptide binding]; other site 998088008098 23S rRNA pseudouridylate synthase B; Provisional; Region: PRK10700 998088008099 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 998088008100 PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like. This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to...; Region: PseudoU_synth_RluB; cd02556 998088008101 probable active site [active] 998088008102 Putative transcriptional regulators (Ypuh-like); Region: DUF387; cl00612 998088008103 ScpA/B protein; Region: ScpA_ScpB; cl00598 998088008104 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 998088008105 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 998088008106 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 998088008107 anthranilate synthase component I; Provisional; Region: PRK13564 998088008108 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 998088008109 chorismate binding enzyme; Region: Chorismate_bind; cl10555 998088008110 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 998088008111 Glutamine amidotransferase class-I; Region: GATase; pfam00117 998088008112 glutamine binding [chemical binding]; other site 998088008113 catalytic triad [active] 998088008114 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 998088008115 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 998088008116 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 998088008117 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase; Provisional; Region: PRK09427 998088008118 Indole-3-glycerol phosphate synthase (IGPS); an enzyme in the tryptophan biosynthetic pathway, catalyzing the ring closure reaction of 1-(o-carboxyphenylamino)-1-deoxyribulose-5-phosphate (CdRP) to indole-3-glycerol phosphate (IGP), accompanied by the...; Region: IGPS; cd00331 998088008119 active site 998088008120 ribulose/triose binding site [chemical binding]; other site 998088008121 phosphate binding site [ion binding]; other site 998088008122 substrate (anthranilate) binding pocket [chemical binding]; other site 998088008123 product (indole) binding pocket [chemical binding]; other site 998088008124 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are monomeric...; Region: PRAI; cd00405 998088008125 active site 998088008126 tryptophan synthase, beta chain; Region: PLN02618 998088008127 Tryptophan synthase-beta: Trptophan synthase is a bifunctional enzyme that catalyses the last two steps in the biosynthesis of L-tryptophan via its alpha and beta reactions. In the alpha reaction, indole 3-glycerol phosphate is cleaved reversibly to...; Region: Trp-synth_B; cd06446 998088008128 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088008129 catalytic residue [active] 998088008130 tryptophan synthase; Region: PLN02591 998088008131 Ttryptophan synthase (TRPS) alpha subunit (TSA). TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are...; Region: Tryptophan_synthase_alpha; cd04724 998088008132 substrate binding site [chemical binding]; other site 998088008133 active site 998088008134 catalytic residues [active] 998088008135 heterodimer interface [polypeptide binding]; other site 998088008136 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; cl00868 998088008137 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 998088008138 Biotin-protein ligase, N terminal; Region: BPL_N; pfam09825 998088008139 conserved cys residue [active] 998088008140 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 998088008141 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 998088008142 Nucleoside recognition; Region: Gate; cl00486 998088008143 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 998088008144 Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the...; Region: ArsC_ArsC; cd03034 998088008145 catalytic residues [active] 998088008146 Membrane transport protein; Region: Mem_trans; cl09117 998088008147 Anion-transporting ATPase; Region: ArsA_ATPase; pfam02374 998088008148 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 998088008149 ATP binding site [chemical binding]; other site 998088008150 dimerization interface [polypeptide binding]; other site 998088008151 Metal binding site [ion binding]; metal-binding site 998088008152 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 998088008153 Anion-transporting ATPase; Region: ArsA_ATPase; pfam02374 998088008154 ATP binding site [chemical binding]; other site 998088008155 dimerization interface [polypeptide binding]; other site 998088008156 Metal binding site [ion binding]; metal-binding site 998088008157 Arsenical resistance operon trans-acting repressor ArsD; Region: ArsD; pfam06953 998088008158 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 998088008159 dimerization interface [polypeptide binding]; other site 998088008160 putative DNA binding site [nucleotide binding]; other site 998088008161 putative Zn2+ binding site [ion binding]; other site 998088008162 META domain; Region: META; cl01245 998088008163 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 998088008164 Protein of unknown function (DUF3293); Region: DUF3293; pfam11697 998088008165 two-component response regulator; Provisional; Region: PRK11173 998088008166 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088008167 active site 998088008168 phosphorylation site [posttranslational modification] 998088008169 intermolecular recognition site; other site 998088008170 dimerization interface [polypeptide binding]; other site 998088008171 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 998088008172 DNA binding site [nucleotide binding] 998088008173 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11174 998088008174 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 998088008175 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088008176 Walker A/P-loop; other site 998088008177 ATP binding site [chemical binding]; other site 998088008178 Q-loop/lid; other site 998088008179 ABC transporter signature motif; other site 998088008180 Walker B; other site 998088008181 D-loop; other site 998088008182 H-loop/switch region; other site 998088008183 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11160 998088008184 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088008185 Walker A/P-loop; other site 998088008186 ATP binding site [chemical binding]; other site 998088008187 Q-loop/lid; other site 998088008188 ABC transporter signature motif; other site 998088008189 Walker B; other site 998088008190 D-loop; other site 998088008191 H-loop/switch region; other site 998088008192 outer membrane lipoprotein; Reviewed; Region: rcsF; PRK10781 998088008193 Protein of unknown function, DUF488; Region: DUF488; cl01246 998088008194 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088008195 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 998088008196 NAD(P) binding site [chemical binding]; other site 998088008197 active site 998088008198 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 998088008199 homodimer interaction site [polypeptide binding]; other site 998088008200 cofactor binding site; other site 998088008201 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria...; Region: Cytochrome_b_N; cl00859 998088008202 Polymer-forming cytoskeletal; Region: Bactofilin; cl09137 998088008203 DNA-binding transcriptional regulator PhoP; Provisional; Region: PRK10816 998088008204 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088008205 active site 998088008206 phosphorylation site [posttranslational modification] 998088008207 intermolecular recognition site; other site 998088008208 dimerization interface [polypeptide binding]; other site 998088008209 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 998088008210 DNA binding site [nucleotide binding] 998088008211 sensor protein PhoQ; Provisional; Region: PRK10815 998088008212 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088008213 ATP binding site [chemical binding]; other site 998088008214 Mg2+ binding site [ion binding]; other site 998088008215 G-X-G motif; other site 998088008216 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 998088008217 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088008218 Protein of unknown function (DUF3297); Region: DUF3297; pfam11730 998088008219 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 998088008220 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 998088008221 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 998088008222 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 998088008223 non-specific DNA binding site [nucleotide binding]; other site 998088008224 salt bridge; other site 998088008225 sequence-specific DNA binding site [nucleotide binding]; other site 998088008226 Cupin domain; Region: Cupin_2; cl09118 998088008227 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 998088008228 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 998088008229 tetramerization interface [polypeptide binding]; other site 998088008230 NAD(P) binding site [chemical binding]; other site 998088008231 catalytic residues [active] 998088008232 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase...; Region: OAT_like; cd00610 998088008233 4-aminobutyrate aminotransferase; Provisional; Region: PRK07495 998088008234 inhibitor-cofactor binding pocket; inhibition site 998088008235 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088008236 catalytic residue [active] 998088008237 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 998088008238 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 998088008239 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 998088008240 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 998088008241 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 998088008242 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 998088008243 peptidyl-prolyl isomerase, gliding motility-associated; Region: ppisom_GldI; TIGR03516 998088008244 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 998088008245 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 998088008246 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 998088008247 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 998088008248 Putative exonuclease, RdgC; Region: RdgC; cl01122 998088008249 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 998088008250 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088008251 Coenzyme A binding pocket [chemical binding]; other site 998088008252 exonuclease subunit SbcD; Provisional; Region: PRK10966 998088008253 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 998088008254 active site 998088008255 metal binding site [ion binding]; metal-binding site 998088008256 DNA binding site [nucleotide binding] 998088008257 Type 5 capsule protein repressor C-terminal domain; Region: SbcD_C; pfam12320 998088008258 exonuclease SbcC; Region: sbcc; TIGR00618 998088008259 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088008260 Walker A/P-loop; other site 998088008261 ATP binding site [chemical binding]; other site 998088008262 Q-loop/lid; other site 998088008263 exonuclease subunit SbcC; Provisional; Region: PRK10246 998088008264 exonuclease subunit SbcC; Provisional; Region: PRK10246 998088008265 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088008266 Q-loop/lid; other site 998088008267 ABC transporter signature motif; other site 998088008268 Walker B; other site 998088008269 D-loop; other site 998088008270 H-loop/switch region; other site 998088008271 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 998088008272 The Class III extradiol dioxygenase, 4,5-DOPA Dioxygenase, catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine; Region: 45_DOPA_Dioxygenase; cd07363 998088008273 putative active site [active] 998088008274 metal binding site [ion binding]; metal-binding site 998088008275 pyruvate kinase; Provisional; Region: PRK09206 998088008276 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cd00288 998088008277 domain interfaces; other site 998088008278 active site 998088008279 hypothetical protein; Provisional; Region: PRK11281 998088008280 Mechanosensitive ion channel inner membrane domain 1; Region: MscS_TM; pfam12794 998088008281 Mechanosensitive ion channel; Region: MS_channel; pfam00924 998088008282 putative transposase OrfB; Reviewed; Region: PHA02517 998088008283 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 998088008284 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 998088008285 active site 998088008286 Zn binding site [ion binding]; other site 998088008287 PAS domain S-box; Region: sensory_box; TIGR00229 998088008288 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088008289 metal binding site [ion binding]; metal-binding site 998088008290 active site 998088008291 I-site; other site 998088008292 PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_glc; cd00210 998088008293 HPr interaction site; other site 998088008294 glycerol kinase (GK) interaction site [polypeptide binding]; other site 998088008295 active site 998088008296 phosphorylation site [posttranslational modification] 998088008297 phosphoenolpyruvate-protein phosphotransferase; Provisional; Region: PRK11177 998088008298 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 998088008299 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 998088008300 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 998088008301 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 998088008302 dimerization domain swap beta strand [polypeptide binding]; other site 998088008303 regulatory protein interface [polypeptide binding]; other site 998088008304 active site 998088008305 regulatory phosphorylation site [posttranslational modification]; other site 998088008306 cysteine synthases; Region: cysKM; TIGR01136 998088008307 CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS is a unique heme-containing enzyme that catalyzes a pyridoxal 5'-phosphate (PLP)-dependent condensation of serine and homocysteine to give cystathionine...; Region: CBS_like; cd01561 998088008308 dimer interface [polypeptide binding]; other site 998088008309 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088008310 catalytic residue [active] 998088008311 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 998088008312 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088008313 Walker A motif; other site 998088008314 ATP binding site [chemical binding]; other site 998088008315 Walker B motif; other site 998088008316 arginine finger; other site 998088008317 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 998088008318 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK07515 998088008319 Ketoacyl-acyl carrier protein synthase III (KASIII) initiates the elongation in type II fatty acid synthase systems. It is found in bacteria and plants. Elongation of fatty acids in the type II systems occurs by Claisen condensation of malonyl-acyl...; Region: KAS_III; cd00830 998088008320 dimer interface [polypeptide binding]; other site 998088008321 active site 998088008322 CoA binding pocket [chemical binding]; other site 998088008323 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 998088008324 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088008325 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088008326 Zn2+ binding site [ion binding]; other site 998088008327 Mg2+ binding site [ion binding]; other site 998088008328 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 998088008329 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088008330 Walker A motif; other site 998088008331 ATP binding site [chemical binding]; other site 998088008332 Walker B motif; other site 998088008333 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 998088008334 general secretion pathway protein C; Region: typeII_sec_gspC; TIGR01713 998088008335 general secretion pathway protein D; Region: type_II_gspD; TIGR02517 998088008336 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 998088008337 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 998088008338 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 998088008339 general secretory pathway protein E; Region: type_II_gspE; TIGR02533 998088008340 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 998088008341 Walker A motif; other site 998088008342 ATP binding site [chemical binding]; other site 998088008343 Walker B motif; other site 998088008344 general secretion pathway protein F; Region: GspF; TIGR02120 998088008345 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 998088008346 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 998088008347 Prokaryotic N-terminal methylation motif; Region: N_methyl; cl06830 998088008348 general secretion pathway protein G; Region: typeII_sec_gspG; TIGR01710 998088008349 Bacterial type II secretion system protein G; Region: GSPII_G; pfam08334 998088008350 general secretion pathway protein H; Region: typeII_sec_gspH; TIGR01708 998088008351 Type II transport protein GspH; Region: GspH; pfam12019 998088008352 Prokaryotic N-terminal methylation motif; Region: N_methyl; cl06830 998088008353 general secretion pathway protein I; Region: gspI; TIGR01707 998088008354 Bacterial type II secretion system protein I/J; Region: GSPII_IJ; pfam02501 998088008355 Prokaryotic N-terminal methylation motif; Region: N_methyl; cl06830 998088008356 general secretion pathway protein J; Region: gspJ; TIGR01711 998088008357 Pseudopilin GspJ; Region: GspJ; pfam11612 998088008358 General secretion pathway protein K; Region: GspK; pfam03934 998088008359 general secretion pathway protein L; Region: typeII_sec_gspL; TIGR01709 998088008360 GspL cytoplasmic actin-ATPase-like region; Region: GspL; pfam05134 998088008361 GspL periplasmic domain; Region: GspL_C; cl14909 998088008362 General secretion pathway, M protein; Region: GspM; cl01222 998088008363 Bacterial type II secretion system protein N; Region: GSPII_N; pfam01203 998088008364 PTS_IIB_chitobiose_lichenan: subunit IIB of enzyme II (EII) of the N,N-diacetylchitobiose-specific and lichenan-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In these systems, EII is either a lichenan- or an N,N-...; Region: PTS_IIB_chitobiose_lichenan; cd05564 998088008365 active site 998088008366 P-loop; other site 998088008367 phosphorylation site [posttranslational modification] 998088008368 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 998088008369 Glycosyl hydrolase family 1; Region: Glyco_hydro_1; pfam00232 998088008370 Beta-glucosidase/6-phospho-beta-glucosidase/beta- galactosidase [Carbohydrate transport and metabolism]; Region: BglB; cl01046 998088008371 PTS_IIA, PTS system, lactose/cellobiose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_lac; cd00215 998088008372 methionine cluster; other site 998088008373 active site 998088008374 phosphorylation site [posttranslational modification] 998088008375 metal binding site [ion binding]; metal-binding site 998088008376 DNA-binding transcriptional regulator ChbR; Provisional; Region: PRK10296 998088008377 Cupin domain; Region: Cupin_2; cl09118 998088008378 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088008379 Alpha-galactosidases/6-phospho-beta-glucosidases, family 4 of glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: CelF; COG1486 998088008380 Glycoside Hydrolases Family 4; Phospho-beta-glucosidase; Region: GH4_P_beta_glucosidase; cd05296 998088008381 NAD binding site [chemical binding]; other site 998088008382 sugar binding site [chemical binding]; other site 998088008383 divalent metal binding site [ion binding]; other site 998088008384 tetramer (dimer of dimers) interface [polypeptide binding]; other site 998088008385 dimer interface [polypeptide binding]; other site 998088008386 YdjC-like protein; Region: YdjC; cl01344 998088008387 YccA-like proteins; Region: YccA_like; cd10433 998088008388 hypothetical membrane protein, TIGR01666; Region: YCCS 998088008389 FUSC-like inner membrane protein yccS; Region: FUSC-like; pfam12805 998088008390 DsrC like protein; Region: DsrC; cl01101 998088008391 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 998088008392 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088008393 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088008394 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088008395 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 998088008396 substrate binding pocket [chemical binding]; other site 998088008397 dimerization interface [polypeptide binding]; other site 998088008398 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 998088008399 classical (c) SDRs; Region: SDR_c; cd05233 998088008400 NAD(P) binding site [chemical binding]; other site 998088008401 active site 998088008402 DinB superfamily; Region: DinB_2; cl00986 998088008403 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088008404 ligand binding site [chemical binding]; other site 998088008405 Histidine phosphatase superfamily (branch 2); Region: His_Phos_2; pfam00328 998088008406 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cl11399 998088008407 Fic/DOC family; Region: Fic; cl00960 998088008408 hypothetical protein; Provisional; Region: PRK01254 998088008409 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster...; Region: Radical_SAM; cl15259 998088008410 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 998088008411 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 998088008412 Protein export membrane protein; Region: SecD_SecF; cl14618 998088008413 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 998088008414 Cache domain; Region: Cache_1; pfam02743 998088008415 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088008416 metal binding site [ion binding]; metal-binding site 998088008417 active site 998088008418 I-site; other site 998088008419 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 998088008420 nucleophile elbow; other site 998088008421 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 998088008422 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 998088008423 non-specific DNA binding site [nucleotide binding]; other site 998088008424 salt bridge; other site 998088008425 sequence-specific DNA binding site [nucleotide binding]; other site 998088008426 Surface antigen; Region: Surface_Ag_2; cl01155 998088008427 outer membrane protein A; Reviewed; Region: PRK10808 998088008428 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088008429 ligand binding site [chemical binding]; other site 998088008430 outer membrane protein A; Reviewed; Region: PRK10808 998088008431 Surface antigen; Region: Surface_Ag_2; cl01155 998088008432 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088008433 ligand binding site [chemical binding]; other site 998088008434 outer membrane protein A; Reviewed; Region: PRK10808 998088008435 Surface antigen; Region: Surface_Ag_2; cl01155 998088008436 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088008437 ligand binding site [chemical binding]; other site 998088008438 malate dehydrogenase; Provisional; Region: PRK13529 998088008439 Malic enzyme, N-terminal domain; Region: malic; pfam00390 998088008440 NAD(P) binding domain of malic enzyme (ME), subgroup 1; Region: NAD_bind_1_malic_enz; cd05312 998088008441 NAD(P) binding site [chemical binding]; other site 998088008442 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 998088008443 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088008444 MatE; Region: MatE; cl10513 998088008445 MatE; Region: MatE; cl10513 998088008446 Protein of unknown function (DUF2498); Region: DUF2498; cl11671 998088008447 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088008448 metal binding site [ion binding]; metal-binding site 998088008449 active site 998088008450 I-site; other site 998088008451 Permease family; Region: Xan_ur_permease; pfam00860 998088008452 Sulfate transporter family; Region: Sulfate_transp; cl00967 998088008453 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 998088008454 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088008455 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 998088008456 Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and...; Region: Restriction_endonuclease_like; cl00277 998088008457 putative active site [active] 998088008458 Protein of unknown function (DUF3320); Region: DUF3320; pfam11784 998088008459 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 998088008460 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 998088008461 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase; Region: PLPDE_III_ODC; cd00622 998088008462 dimer interface [polypeptide binding]; other site 998088008463 active site 998088008464 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 998088008465 catalytic residues [active] 998088008466 substrate binding site [chemical binding]; other site 998088008467 putative calcium/sodium:proton antiporter; Provisional; Region: PRK10734 998088008468 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 998088008469 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 998088008470 Peroxiredoxin (PRX) family, PRX5-like subfamily; members are similar to the human protein, PRX5, a homodimeric TRX peroxidase, widely expressed in tissues and found cellularly in mitochondria, peroxisomes and the cytosol. The cellular location of PRX5...; Region: PRX5_like; cd03013 998088008471 catalytic triad [active] 998088008472 dimer interface [polypeptide binding]; other site 998088008473 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 998088008474 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or...; Region: Nudix_Hydrolase; cl00447 998088008475 nudix motif; other site 998088008476 Protein of unknown function (DUF1107); Region: DUF1107; pfam06526 998088008477 Protein of unknown function (DUF2845); Region: DUF2845; pfam11006 998088008478 peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK11570 998088008479 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 998088008480 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 998088008481 CutC family; Region: CutC; cl01218 998088008482 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 998088008483 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088008484 Coenzyme A binding pocket [chemical binding]; other site 998088008485 Peptidase family M48; Region: Peptidase_M48; cl12018 998088008486 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088008487 phosphate regulon sensor protein; Provisional; Region: phoR; PRK11006 998088008488 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 998088008489 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 998088008490 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 998088008491 dimer interface [polypeptide binding]; other site 998088008492 phosphorylation site [posttranslational modification] 998088008493 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088008494 ATP binding site [chemical binding]; other site 998088008495 Mg2+ binding site [ion binding]; other site 998088008496 G-X-G motif; other site 998088008497 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 998088008498 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088008499 active site 998088008500 phosphorylation site [posttranslational modification] 998088008501 intermolecular recognition site; other site 998088008502 dimerization interface [polypeptide binding]; other site 998088008503 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 998088008504 DNA binding site [nucleotide binding] 998088008505 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_16; cd07263 998088008506 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 998088008507 GAF domain; Region: GAF; cl00853 998088008508 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088008509 Walker A motif; other site 998088008510 ATP binding site [chemical binding]; other site 998088008511 Walker B motif; other site 998088008512 arginine finger; other site 998088008513 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 998088008514 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 998088008515 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 998088008516 NAD(P) binding site [chemical binding]; other site 998088008517 catalytic residues [active] 998088008518 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 998088008519 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 998088008520 EamA-like transporter family; Region: EamA; cl01037 998088008521 Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]; Region: CitB; COG4565 998088008522 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088008523 active site 998088008524 phosphorylation site [posttranslational modification] 998088008525 intermolecular recognition site; other site 998088008526 dimerization interface [polypeptide binding]; other site 998088008527 Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]; Region: CitA; COG3290 998088008528 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 998088008529 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 998088008530 malate dehydrogenase; Provisional; Region: PRK13529 998088008531 Malic enzyme, N-terminal domain; Region: malic; pfam00390 998088008532 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088008533 NAD(P) binding pocket [chemical binding]; other site 998088008534 2-hydroxycarboxylate transporter family; Region: 2HCT; cl01386 998088008535 transcriptional regulator SlyA; Provisional; Region: PRK03573 998088008536 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088008537 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 998088008538 Protein of unknown function (DUF2955); Region: DUF2955; pfam11168 998088008539 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088008540 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088008541 substrate binding pocket [chemical binding]; other site 998088008542 membrane-bound complex binding site; other site 998088008543 hinge residues; other site 998088008544 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; cl01604 998088008545 Gram-negative bacterial tonB protein; Region: TonB; cl10048 998088008546 Proteolipid membrane potential modulator; Region: Pmp3; cl00431 998088008547 anaerobic ribonucleoside-triphosphate reductase activating protein; Region: NrdG; TIGR02491 998088008548 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster...; Region: Radical_SAM; cd01335 998088008549 FeS/SAM binding site; other site 998088008550 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK09263 998088008551 ATP cone domain; Region: ATP-cone; pfam03477 998088008552 Class III ribonucleotide reductase; Region: RNR_III; cd01675 998088008553 effector binding site; other site 998088008554 active site 998088008555 Zn binding site [ion binding]; other site 998088008556 glycine loop; other site 998088008557 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG2984 998088008558 NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]; Region: Lig; COG0272 998088008559 NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction...; Region: LIGANc; cd00114 998088008560 nucleotide binding pocket [chemical binding]; other site 998088008561 K-X-D-G motif; other site 998088008562 catalytic site [active] 998088008563 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 998088008564 Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/...; Region: BRCT; cd00027 998088008565 Dimer interface [polypeptide binding]; other site 998088008566 BRCT sequence motif; other site 998088008567 cell division protein ZipA; Provisional; Region: PRK03427 998088008568 ZipA C-terminal domain. ZipA, a membrane-anchored protein, is one of at least nine essential gene products necessary for assembly of the septal ring which mediates cell division in E.coli. ZipA and FtsA directly bind FtsZ, a homolog of eukaryotic...; Region: ZipA; cl12038 998088008569 FtsZ protein binding site [polypeptide binding]; other site 998088008570 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 998088008571 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (...; Region: ABC_SMC_barmotin; cd03278 998088008572 Walker A/P-loop; other site 998088008573 ATP binding site [chemical binding]; other site 998088008574 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (...; Region: ABC_SMC_barmotin; cd03278 998088008575 ABC transporter signature motif; other site 998088008576 Walker B; other site 998088008577 D-loop; other site 998088008578 H-loop/switch region; other site 998088008579 Etoposide-induced protein 2.4 (EI24); Region: EI24; cl01126 998088008580 Predicted membrane protein [Function unknown]; Region: COG2860 998088008581 UPF0126 domain; Region: UPF0126; pfam03458 998088008582 UPF0126 domain; Region: UPF0126; pfam03458 998088008583 Peptidase M15; Region: Peptidase_M15_3; cl01194 998088008584 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 998088008585 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 998088008586 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 998088008587 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088008588 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088008589 substrate binding pocket [chemical binding]; other site 998088008590 membrane-bound complex binding site; other site 998088008591 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 998088008592 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 998088008593 Ligand binding site [chemical binding]; other site 998088008594 Putative Catalytic site [active] 998088008595 DXD motif; other site 998088008596 GtrA-like protein; Region: GtrA; cl00971 998088008597 alpha-amylase; Reviewed; Region: malS; PRK09505 998088008598 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 998088008599 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 998088008600 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 998088008601 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 998088008602 putative N-terminal domain interface [polypeptide binding]; other site 998088008603 putative dimer interface [polypeptide binding]; other site 998088008604 putative substrate binding pocket (H-site) [chemical binding]; other site 998088008605 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 998088008606 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088008607 active site 998088008608 phosphorylation site [posttranslational modification] 998088008609 intermolecular recognition site; other site 998088008610 dimerization interface [polypeptide binding]; other site 998088008611 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors...; Region: LuxR_C_like; cd06170 998088008612 DNA binding residues [nucleotide binding] 998088008613 dimerization interface [polypeptide binding]; other site 998088008614 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 998088008615 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088008616 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 998088008617 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 998088008618 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 998088008619 nucleophile elbow; other site 998088008620 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 998088008621 putative cation:proton antiport protein; Provisional; Region: PRK10669 998088008622 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 998088008623 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088008624 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088008625 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088008626 metal binding site [ion binding]; metal-binding site 998088008627 active site 998088008628 I-site; other site 998088008629 tRNA(Ile)-lysidine synthetase; Provisional; Region: tilS; PRK10660 998088008630 N-terminal domain of predicted ATPase of the PP-loop faimly implicated in cell cycle control [Cell division and chromosome partitioning]. This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases...; Region: PP-ATPase; cd01992 998088008631 Ligand Binding Site [chemical binding]; other site 998088008632 TilS substrate binding domain; Region: TilS; pfam09179 998088008633 B3/4 domain; Region: B3_4; cl11458 998088008634 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 998088008635 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 998088008636 active site 998088008637 Zn binding site [ion binding]; other site 998088008638 Periplasmic lysozyme inhibitor, I-type (PliI) and similar proteins; Region: PliI_like; cd09632 998088008639 dimer interface [polypeptide binding]; other site 998088008640 putative inhibitory loop; other site 998088008641 Pyridoxal kinase plays a key role in the synthesis of the active coenzyme pyridoxal-5'-phosphate (PLP), by catalyzing the phosphorylation of the precursor vitamin B6 in the presence of Zn2+ and ATP. Mammals are unable to synthesize PLP de novo and...; Region: pyridoxal_pyridoxamine_kinase; cd01173 998088008642 dimer interface [polypeptide binding]; other site 998088008643 pyridoxal binding site [chemical binding]; other site 998088008644 ATP binding site [chemical binding]; other site 998088008645 lysine decarboxylase CadA; Provisional; Region: PRK15400 998088008646 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cl09944 998088008647 Ornithine decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to ornithine decarboxylase (ODC), arginine decarboxylase (ADC) and...; Region: Orn_deC_like; cd00615 998088008648 homodimer interface [polypeptide binding]; other site 998088008649 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088008650 catalytic residue [active] 998088008651 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 998088008652 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 998088008653 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 998088008654 DNA-binding transcriptional activator CadC; Provisional; Region: PRK10153 998088008655 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 998088008656 DNA binding site [nucleotide binding] 998088008657 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 998088008658 LysR family transcriptional regulator; Provisional; Region: PRK14997 998088008659 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088008660 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 998088008661 putative effector binding pocket; other site 998088008662 dimerization interface [polypeptide binding]; other site 998088008663 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 998088008664 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088008665 membrane-bound complex binding site; other site 998088008666 hinge residues; other site 998088008667 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 998088008668 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 998088008669 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088008670 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088008671 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088008672 dimerization interface [polypeptide binding]; other site 998088008673 multidrug efflux pump VmrA; Reviewed; Region: vmrA; PRK09575 998088008674 MatE; Region: MatE; cl10513 998088008675 MatE; Region: MatE; cl10513 998088008676 acetolactate synthase; Reviewed; Region: PRK08617 998088008677 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 998088008678 PYR/PP interface [polypeptide binding]; other site 998088008679 dimer interface [polypeptide binding]; other site 998088008680 TPP binding site [chemical binding]; other site 998088008681 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 998088008682 Thiamine pyrophosphate (TPP) family, Acetolactate synthase (ALS) subfamily, TPP-binding module; composed of proteins similar to Klebsiella pneumoniae ALS, a catabolic enzyme required for butanediol fermentation. ALS catalyzes the conversion of 2...; Region: TPP_ALS; cd02010 998088008683 TPP-binding site [chemical binding]; other site 998088008684 dimer interface [polypeptide binding]; other site 998088008685 Alpha-acetolactate decarboxylase; Region: AAL_decarboxy; cl01408 998088008686 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 998088008687 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088008688 The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold; Region: PBP2_BudR; cd08451 998088008689 putative dimerization interface [polypeptide binding]; other site 998088008690 putative substrate binding pocket [chemical binding]; other site 998088008691 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 998088008692 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 998088008693 active site 998088008694 HIGH motif; other site 998088008695 dimer interface [polypeptide binding]; other site 998088008696 KMSKS motif; other site 998088008697 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 998088008698 putative peptidase; Provisional; Region: PRK11649 998088008699 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 998088008700 Peptidase family M23; Region: Peptidase_M23; pfam01551 998088008701 Uncharacterised protein family (UPF0075); Region: UPF0075; cl04217 998088008702 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 998088008703 homotrimer interaction site [polypeptide binding]; other site 998088008704 putative active site [active] 998088008705 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 998088008706 homotrimer interaction site [polypeptide binding]; other site 998088008707 putative active site [active] 998088008708 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 998088008709 homotrimer interaction site [polypeptide binding]; other site 998088008710 putative active site [active] 998088008711 transketolase; Reviewed; Region: PRK12753 998088008712 Thiamine pyrophosphate (TPP) family, Transketolase (TK) subfamily, TPP-binding module; TK catalyzes the transfer of a two-carbon unit from ketose phosphates to aldose phosphates. In heterotrophic organisms, TK provides a link between glycolysis and the...; Region: TPP_TK; cd02012 998088008713 TPP-binding site [chemical binding]; other site 998088008714 dimer interface [polypeptide binding]; other site 998088008715 Pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and related proteins; Region: TPP_PYR_DXS_TK_like; cd07033 998088008716 PYR/PP interface [polypeptide binding]; other site 998088008717 dimer interface [polypeptide binding]; other site 998088008718 TPP binding site [chemical binding]; other site 998088008719 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 998088008720 S-adenosylmethionine synthetase; Validated; Region: PRK05250 998088008721 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 998088008722 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 998088008723 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 998088008724 SprT homologues; Region: SprT; cl01182 998088008725 SprT-like family; Region: SprT-like; pfam10263 998088008726 Endonuclease I; Region: Endonuclease_1; cl01003 998088008727 RNA methyltransferase; Region: Methyltrans_RNA; cl00611 998088008728 glutathione synthetase; Provisional; Region: PRK05246 998088008729 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 998088008730 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 998088008731 Uncharacterized ACR, COG1678; Region: DUF179; cl00731 998088008732 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cl00243 998088008733 dipeptide/tripeptide permease B; Provisional; Region: PRK10207 998088008734 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cl11420 998088008735 DNA-binding transcriptional regulator YidZ; Provisional; Region: PRK10216 998088008736 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088008737 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 998088008738 substrate binding pocket [chemical binding]; other site 998088008739 dimerization interface [polypeptide binding]; other site 998088008740 multidrug efflux system protein MdtL; Provisional; Region: PRK10473 998088008741 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088008742 putative substrate translocation pore; other site 998088008743 MoxR-like ATPases [General function prediction only]; Region: COG0714 998088008744 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088008745 Walker A motif; other site 998088008746 ATP binding site [chemical binding]; other site 998088008747 Walker B motif; other site 998088008748 arginine finger; other site 998088008749 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 998088008750 Protein of unknown function DUF58; Region: DUF58; pfam01882 998088008751 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 998088008752 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 998088008753 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 998088008754 transaldolase-like protein; Provisional; Region: PTZ00411 998088008755 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 998088008756 active site 998088008757 dimer interface [polypeptide binding]; other site 998088008758 catalytic residue [active] 998088008759 Protein of unknown function (DUF3545); Region: DUF3545; pfam12065 998088008760 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 998088008761 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 998088008762 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 998088008763 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 998088008764 DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli...; Region: DnaE_OBF; cd04485 998088008765 generic binding surface II; other site 998088008766 generic binding surface I; other site 998088008767 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 998088008768 RNA/DNA hybrid binding site [nucleotide binding]; other site 998088008769 active site 998088008770 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 998088008771 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 998088008772 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 998088008773 UDP-N-acetylglucosamine O-acyltransferase (UDP-GlcNAc acyltransferase): Proteins in this family catalyze the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-GlcNAc. It is the first enzyme in the lipid A...; Region: LbH_UDP-GlcNAc_AT; cd03351 998088008774 active site 998088008775 FabZ is a 17kD beta-hydroxyacyl-acyl carrier protein (ACP) dehydratase that primarily catalyzes the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, the third step in the elongation phase of the bacterial/ plastid, type II, fatty-acid...; Region: FabZ; cd01288 998088008776 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 998088008777 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 998088008778 UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD): The enzyme catalyzes the transfer of 3-hydroxymyristic acid or 3-hydroxy-arachidic acid, depending on the organism, from the acyl carrier protein (ACP) to UDP-3-O-acyl-glucosamine to produce UDP-2,3-...; Region: LbH_LpxD; cd03352 998088008779 trimer interface [polypeptide binding]; other site 998088008780 active site 998088008781 UDP-GlcNAc binding site [chemical binding]; other site 998088008782 lipid binding site [chemical binding]; lipid-binding site 998088008783 periplasmic chaperone; Provisional; Region: PRK10780 998088008784 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 998088008785 outer membrane protein assembly factor YaeT; Provisional; Region: PRK11067 998088008786 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 998088008787 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 998088008788 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 998088008789 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 998088008790 Surface antigen; Region: Bac_surface_Ag; cl03097 998088008791 zinc metallopeptidase RseP; Provisional; Region: PRK10779 998088008792 RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. In Escherichia coli, the S2P homolog...; Region: S2P-M50_PDZ_RseP-like; cd06163 998088008793 active site 998088008794 PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most...; Region: PDZ_metalloprotease; cd00989 998088008795 protein binding site [polypeptide binding]; other site 998088008796 PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most...; Region: PDZ_metalloprotease; cd00989 998088008797 RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. In Escherichia coli, the S2P homolog...; Region: S2P-M50_PDZ_RseP-like; cd06163 998088008798 putative substrate binding region [chemical binding]; other site 998088008799 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 998088008800 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 998088008801 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 998088008802 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 998088008803 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 998088008804 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cd00475 998088008805 catalytic residue [active] 998088008806 putative FPP diphosphate binding site; other site 998088008807 putative FPP binding hydrophobic cleft; other site 998088008808 dimer interface [polypeptide binding]; other site 998088008809 putative IPP diphosphate binding site; other site 998088008810 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are 'recycled' and ready for another round of...; Region: RRF; cd00520 998088008811 hinge region; other site 998088008812 UMP kinase (UMPK)-Ec, the microbial/chloroplast uridine monophosphate kinase (uridylate kinase) enzyme that catalyzes UMP phosphorylation and plays a key role in pyrimidine nucleotide biosynthesis; regulation of this process is via feed-back control...; Region: AAK_UMPK-PyrH-Ec; cd04254 998088008813 putative nucleotide binding site [chemical binding]; other site 998088008814 uridine monophosphate binding site [chemical binding]; other site 998088008815 homohexameric interface [polypeptide binding]; other site 998088008816 elongation factor Ts; Provisional; Region: tsf; PRK09377 998088008817 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 998088008818 Elongation factor TS; Region: EF_TS; pfam00889 998088008819 Elongation factor TS; Region: EF_TS; pfam00889 998088008820 Ribosomal protein S2 (RPS2), involved in formation of the translation initiation complex, where it might contact the messenger RNA and several components of the ribosome. It has been shown that in Escherichia coli RPS2 is essential for the binding of...; Region: RPS2; cd01425 998088008821 rRNA interaction site [nucleotide binding]; other site 998088008822 S8 interaction site; other site 998088008823 putative laminin-1 binding site; other site 998088008824 methionine aminopeptidase; Reviewed; Region: PRK07281 998088008825 Methionine Aminopeptidase 1. E.C. 3.4.11.18. Also known as methionyl aminopeptidase and Peptidase M. Catalyzes release of N-terminal amino acids, preferentially methionine, from peptides and arylamides; Region: MetAP1; cd01086 998088008826 active site 998088008827 PII uridylyl-transferase; Provisional; Region: PRK05007 998088008828 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 998088008829 metal binding triad; other site 998088008830 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 998088008831 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 998088008832 ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains; Region: ACT_UUR-like_1; cd04900 998088008833 C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains; Region: ACT_ACR-UUR-like_2; cd04899 998088008834 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 998088008835 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (also called THP succinyltransferase): THDP N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA...; Region: LbH_THP_succinylT; cd03350 998088008836 trimer interface [polypeptide binding]; other site 998088008837 active site 998088008838 substrate binding site [chemical binding]; other site 998088008839 CoA binding site [chemical binding]; other site 998088008840 Protein of unknown function (DUF3461); Region: DUF3461; cl10125 998088008841 PTS system glucose-specific transporter subunits IIBC; Provisional; Region: PRK11089 998088008842 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 998088008843 PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIB_glc; cd00212 998088008844 active site turn [active] 998088008845 phosphorylation site [posttranslational modification] 998088008846 Maltose operon periplasmic protein precursor (MalM); Region: MalM; cl11647 998088008847 The Maltoporin-like channels (LamB porin) form a trimeric structure which facilitate the diffusion of maltodextrins and other sugars across the outer membrane of Gram-negative bacteria. The membrane channel is formed by an 18-strand antiparallel beta-...; Region: Maltoporin-like; cd01346 998088008848 trimer interface; other site 998088008849 sugar binding site [chemical binding]; other site 998088008850 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 998088008851 tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not...; Region: PseudoU_synth_TruC; cd02563 998088008852 probable active site [active] 998088008853 Domain of unknown function, DUF446; Region: DUF446; cl01187 998088008854 Protein of unknown function (DUF3549); Region: DUF3549; pfam12069 998088008855 Protein of unknown function (DUF3301); Region: DUF3301; pfam11743 998088008856 Protein of unknown function (DUF2789); Region: DUF2789; pfam10982 998088008857 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); Region: DUF2310; cl02380 998088008858 Syd protein; Region: Syd; cl06405 998088008859 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 998088008860 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 998088008861 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 998088008862 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088008863 metal binding site [ion binding]; metal-binding site 998088008864 active site 998088008865 I-site; other site 998088008866 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 998088008867 Domain of unknown function (DUF3412); Region: DUF3412; pfam11892 998088008868 flap endonuclease-like protein; Provisional; Region: PRK09482 998088008869 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 998088008870 active site 998088008871 metal binding site 1 [ion binding]; metal-binding site 998088008872 putative 5' ssDNA interaction site; other site 998088008873 metal binding site 3; metal-binding site 998088008874 metal binding site 2 [ion binding]; metal-binding site 998088008875 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 998088008876 putative DNA binding site [nucleotide binding]; other site 998088008877 putative metal binding site [ion binding]; other site 998088008878 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 998088008879 isocitrate dehydrogenase; Validated; Region: PRK06451 998088008880 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional; Region: PRK11760 998088008881 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 998088008882 Protein of unknown function (DUF423); Region: DUF423; cl01008 998088008883 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG3571 998088008884 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 998088008885 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088008886 HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 998088008887 dimerization interface [polypeptide binding]; other site 998088008888 substrate binding pocket [chemical binding]; other site 998088008889 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 998088008890 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cd06225 998088008891 dimerization interface [polypeptide binding]; other site 998088008892 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088008893 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088008894 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 998088008895 active site 998088008896 DNA polymerase IV; Validated; Region: PRK02406 998088008897 DNA binding site [nucleotide binding] 998088008898 Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1; Region: GATase1_DJ-1; cd03135 998088008899 conserved cys residue [active] 998088008900 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088008901 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 998088008902 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 998088008903 Protein of unknown function (DUF520); Region: DUF520; cl00723 998088008904 Nucleoside-specific channel-forming protein, Tsx; Region: Channel_Tsx; cl04114 998088008905 muropeptide transporter; Reviewed; Region: ampG; PRK11902 998088008906 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cl11420 998088008907 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cl00197 998088008908 active site 998088008909 Uncharacterized lipoprotein; Region: Lipoprotein_16; pfam03923 998088008910 SAM-dependent 23S ribosomal RNA mG1835 methyltransferase; Provisional; Region: PRK15001 998088008911 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cd02440 998088008912 S-adenosylmethionine binding site [chemical binding]; other site 998088008913 BolA-like protein; Region: BolA; cl00386 998088008914 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 998088008915 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 998088008916 RnfE family; Region: NQR2_RnfD_RnfE; cl00779 998088008917 Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrC [Energy production and conversion]; Region: NqrC; COG2869 998088008918 FMN-binding domain; Region: FMN_bind; cl01081 998088008919 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 998088008920 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 998088008921 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 998088008922 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 998088008923 catalytic loop [active] 998088008924 iron binding site [ion binding]; other site 998088008925 Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) FAD/NADH binding domain. (Na+-NQR) provides a means of storing redox reaction energy via the transmembrane translocation of Na2+ ions. The C-terminal domain resembles ferredoxin:NADP+...; Region: NADH_quinone_reductase; cd06188 998088008926 FAD binding pocket [chemical binding]; other site 998088008927 FAD binding motif [chemical binding]; other site 998088008928 phosphate binding motif [ion binding]; other site 998088008929 beta-alpha-beta structure motif; other site 998088008930 NAD binding pocket [chemical binding]; other site 998088008931 ApbE family; Region: ApbE; cl00643 998088008932 Protein of unknown function (DUF539); Region: DUF539; cl01129 998088008933 Protein of unknown function (DUF3833); Region: DUF3833; pfam12915 998088008934 Tryptophan-rich protein (DUF2389); Region: DUF2389; cl09726 998088008935 Protein of unknown function (DUF2878); Region: DUF2878; pfam11086 998088008936 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 998088008937 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cd02440 998088008938 S-adenosylmethionine binding site [chemical binding]; other site 998088008939 Protein of unknown function (DUF1365); Region: DUF1365; cl01388 998088008940 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 998088008941 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088008942 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088008943 NAD(P) binding site [chemical binding]; other site 998088008944 active site 998088008945 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 998088008946 deoxyribodipyrimidine photolyase; Provisional; Region: PRK10674 998088008947 DNA photolyase; Region: DNA_photolyase; pfam00875 998088008948 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 998088008949 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 998088008950 DNA binding residues [nucleotide binding] 998088008951 Protein of unknown function (DUF523); Region: DUF523; cl00733 998088008952 Protein of unknown function (DUF1722); Region: DUF1722; cl01284 998088008953 Protein of unknown function (DUF3157); Region: DUF3157; pfam11355 998088008954 ATP-utilizing enzymes of the PP-loop superfamily [General function prediction only]; Region: COG1606 998088008955 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 998088008956 Ligand Binding Site [chemical binding]; other site 998088008957 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 998088008958 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cd01427 998088008959 motif II; other site 998088008960 bifunctional chorismate mutase/prephenate dehydratase; Provisional; Region: pheA; PRK10622 998088008961 Chorismate mutase type II; Region: CM_2; cl00693 998088008962 Prephenate dehydratase; Region: PDT; pfam00800 998088008963 C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme; Region: ACT_CM-PDT; cd04905 998088008964 putative L-Phe binding site [chemical binding]; other site 998088008965 Protein of unknown function, DUF400; Region: DUF400; cl01141 998088008966 Curli production assembly/transport component CsgG; Region: CsgG; cl00639 998088008967 Domain of unknown function (DUF932); Region: DUF932; cl12129 998088008968 Phage-related protein, predicted endonuclease [DNA replication, recombination, and repair]; Region: COG5377 998088008969 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 998088008970 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 998088008971 non-specific DNA binding site [nucleotide binding]; other site 998088008972 salt bridge; other site 998088008973 sequence-specific DNA binding site [nucleotide binding]; other site 998088008974 Protein of unknown function (DUF2787); Region: DUF2787; pfam10980 998088008975 Mpr1p, Pad1p N-terminal (MPN) domains; Region: MPN; cl13996 998088008976 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 998088008977 Queuine tRNA-ribosyltransferase; Region: TGT; cl00409 998088008978 DGQHR domain; Region: DGQHR; cl14002 998088008979 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088008980 Lhr-like helicases [General function prediction only]; Region: Lhr; COG1201 998088008981 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088008982 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 998088008983 ATP-binding site [chemical binding]; other site 998088008984 DEAD-like helicases superfamily; Region: DEXDc; smart00487 998088008985 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 998088008986 ATP binding site [chemical binding]; other site 998088008987 putative Mg++ binding site [ion binding]; other site 998088008988 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 998088008989 nucleotide binding region [chemical binding]; other site 998088008990 ATP-binding site [chemical binding]; other site 998088008991 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 998088008992 ATP binding site [chemical binding]; other site 998088008993 putative Mg++ binding site [ion binding]; other site 998088008994 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 998088008995 nucleotide binding region [chemical binding]; other site 998088008996 ATP-binding site [chemical binding]; other site 998088008997 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (...; Region: S24_LexA-like; cd06529 998088008998 Catalytic site [active] 998088008999 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 998088009000 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 998088009001 active site 998088009002 DNA binding site [nucleotide binding] 998088009003 Fic family protein [Function unknown]; Region: COG3177 998088009004 Fic/DOC family; Region: Fic; cl00960 998088009005 Protein of unknown function (DUF3296); Region: DUF3296; pfam11726 998088009006 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 998088009007 integrase; Provisional; Region: PRK09692 998088009008 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 998088009009 active site 998088009010 Int/Topo IB signature motif; other site 998088009011 cell division protein MukB; Provisional; Region: mukB; PRK04863 998088009012 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088009013 outer membrane porin, OprD family; Region: OprD; pfam03573 998088009014 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 998088009015 short chain dehydrogenase; Provisional; Region: PRK05693 998088009016 NADP binding site [chemical binding]; other site 998088009017 active site 998088009018 steroid binding site; other site 998088009019 Domain of unknown function (DUF1904); Region: DUF1904; pfam08921 998088009020 TraB family; Region: TraB; cl12050 998088009021 Protein of unknown function (DUF3149); Region: DUF3149; pfam11346 998088009022 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 998088009023 Smr domain; Region: Smr; cl02619 998088009024 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 998088009025 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 998088009026 active site 998088009027 Zn binding site [ion binding]; other site 998088009028 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 998088009029 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 998088009030 Tfp pilus assembly protein PilV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilV; COG4967 998088009031 Prepilin peptidase dependent protein C; Region: DUF3728; cl08108 998088009032 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 998088009033 Type II transport protein GspH; Region: GspH; pfam12019 998088009034 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 998088009035 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 998088009036 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 998088009037 AlkA N-terminal domain; Region: AlkA_N; cl05528 998088009038 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]; Region: AlkA; COG0122 998088009039 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 998088009040 minor groove reading motif; other site 998088009041 helix-hairpin-helix signature motif; other site 998088009042 substrate binding pocket [chemical binding]; other site 998088009043 active site 998088009044 methylated-DNA--protein-cysteine methyltransferase; Provisional; Region: PRK00901 998088009045 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 998088009046 The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases...; Region: ATase; cd06445 998088009047 DNA binding site [nucleotide binding] 998088009048 active site 998088009049 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 998088009050 Peptidase family U32; Region: Peptidase_U32; cl03113 998088009051 Collagenase; Region: DUF3656; pfam12392 998088009052 LysE type translocator; Region: LysE; cl00565 998088009053 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088009054 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088009055 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 998088009056 substrate binding pocket [chemical binding]; other site 998088009057 dimerization interface [polypeptide binding]; other site 998088009058 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK12879 998088009059 Ketoacyl-acyl carrier protein synthase III (KASIII) initiates the elongation in type II fatty acid synthase systems. It is found in bacteria and plants. Elongation of fatty acids in the type II systems occurs by Claisen condensation of malonyl-acyl...; Region: KAS_III; cd00830 998088009060 dimer interface [polypeptide binding]; other site 998088009061 active site 998088009062 CoA binding pocket [chemical binding]; other site 998088009063 Response regulator receiver domain; Region: Response_reg; pfam00072 998088009064 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088009065 active site 998088009066 phosphorylation site [posttranslational modification] 998088009067 intermolecular recognition site; other site 998088009068 dimerization interface [polypeptide binding]; other site 998088009069 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 998088009070 anti sigma factor interaction site; other site 998088009071 regulatory phosphorylation site [posttranslational modification]; other site 998088009072 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 998088009073 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 998088009074 putative binding surface; other site 998088009075 active site 998088009076 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 998088009077 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088009078 ATP binding site [chemical binding]; other site 998088009079 Mg2+ binding site [ion binding]; other site 998088009080 G-X-G motif; other site 998088009081 CheA regulatory domain; CheA is a histidine protein kinase present in bacteria and archea. Activated by the chemotaxis receptor a histidine phosphoryl group from CheA is passed directly to an aspartate in the response regulator CheY. This signalling...; Region: CheA_reg; cd00731 998088009082 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 998088009083 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 998088009084 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088009085 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088009086 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088009087 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 998088009088 putative CheA interaction surface; other site 998088009089 methyl-accepting chemotaxis protein I; Provisional; Region: PRK15041 998088009090 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088009091 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 998088009092 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 998088009093 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 998088009094 CheD chemotactic sensory transduction; Region: CheD; cl00810 998088009095 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 998088009096 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088009097 active site 998088009098 phosphorylation site [posttranslational modification] 998088009099 intermolecular recognition site; other site 998088009100 dimerization interface [polypeptide binding]; other site 998088009101 CheB methylesterase; Region: CheB_methylest; pfam01339 998088009102 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 998088009103 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 998088009104 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 998088009105 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 998088009106 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 998088009107 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 998088009108 Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to...; Region: PNPase_KH; cd02393 998088009109 putative nucleic acid binding region [nucleotide binding]; other site 998088009110 G-X-X-G motif; other site 998088009111 S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA...; Region: S1_PNPase; cd04472 998088009112 RNA binding site [nucleotide binding]; other site 998088009113 domain interface; other site 998088009114 Ribosomal protein S15 (prokaryotic)_S13 (eukaryotic) binds the central domain of 16S rRNA and is required for assembly of the small ribosomal subunit and for intersubunit association, thus representing a key element in the assembly of the whole...; Region: Ribosomal_S15p_S13e; cd00353 998088009115 16S/18S rRNA binding site [nucleotide binding]; other site 998088009116 S13e-L30e interaction site [polypeptide binding]; other site 998088009117 25S rRNA binding site [nucleotide binding]; other site 998088009118 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 998088009119 PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of...; Region: PseudoU_synth_EcTruB; cd02573 998088009120 RNA binding site [nucleotide binding]; other site 998088009121 active site 998088009122 Pseudouridine synthase II TruB, C-terminal; Region: TruB-C_2; pfam09157 998088009123 Ribosome-binding factor A; Region: RBFA; cl00542 998088009124 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 998088009125 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 998088009126 translation initiation factor IF-2; Region: IF-2; TIGR00487 998088009127 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 998088009128 IF2/eIF5B (initiation factors 2/ eukaryotic initiation factor 5B) subfamily. IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits. As seen in other GTPases...; Region: IF2_eIF5B; cd01887 998088009129 G1 box; other site 998088009130 putative GEF interaction site [polypeptide binding]; other site 998088009131 GTP/Mg2+ binding site [chemical binding]; other site 998088009132 Switch I region; other site 998088009133 G2 box; other site 998088009134 G3 box; other site 998088009135 Switch II region; other site 998088009136 G4 box; other site 998088009137 G5 box; other site 998088009138 This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the...; Region: IF2_mtIF2_II; cd03702 998088009139 Translation-initiation factor 2; Region: IF-2; pfam11987 998088009140 mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation...; Region: mtIF2_IVc; cd03692 998088009141 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 998088009142 NusA N-terminal domain; Region: NusA_N; pfam08529 998088009143 S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and...; Region: S1_NusA; cd04455 998088009144 RNA binding site [nucleotide binding]; other site 998088009145 homodimer interface [polypeptide binding]; other site 998088009146 NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of...; Region: NusA_KH; cd02134 998088009147 G-X-X-G motif; other site 998088009148 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 998088009149 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 998088009150 ribosome maturation protein RimP; Reviewed; Region: PRK00092 998088009151 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members...; Region: Sm_like; cl00259 998088009152 YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix...; Region: YlxS_C; cd01734 998088009153 Sm1 motif; other site 998088009154 predicted subunit interaction site [polypeptide binding]; other site 998088009155 RNA binding pocket [nucleotide binding]; other site 998088009156 Sm2 motif; other site 998088009157 Preprotein translocase SecG subunit; Region: SecG; cl09123 998088009158 Triosephosphate isomerase (TIM) is a glycolytic enzyme that catalyzes the interconversion of dihydroxyacetone phosphate and D-glyceraldehyde-3-phosphate. The reaction is very efficient and requires neither cofactors nor metal ions. TIM, usually...; Region: TIM; cd00311 998088009159 substrate binding site [chemical binding]; other site 998088009160 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 998088009161 GlmM is a bacterial phosphoglucosamine mutase (PNGM) that belongs to the alpha-D-phosphohexomutase superfamily. It is required for the interconversion of glucosamine-6-phosphate and glucosamine-1-phosphate in the biosynthetic pathway of UDP-N-...; Region: GlmM; cd05802 998088009162 active site 998088009163 substrate binding site [chemical binding]; other site 998088009164 metal binding site [ion binding]; metal-binding site 998088009165 DHPS subgroup of Pterin binding enzymes. DHPS (dihydropteroate synthase), a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and...; Region: DHPS; cd00739 998088009166 dihydropteroate synthase; Region: DHPS; TIGR01496 998088009167 substrate binding pocket [chemical binding]; other site 998088009168 dimer interface [polypeptide binding]; other site 998088009169 inhibitor binding site; inhibition site 998088009170 ATP-dependent metalloprotease; Reviewed; Region: hflB; PRK10733 998088009171 FtsH Extracellular; Region: FtsH_ext; pfam06480 998088009172 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088009173 Walker A motif; other site 998088009174 ATP binding site [chemical binding]; other site 998088009175 Walker B motif; other site 998088009176 arginine finger; other site 998088009177 Peptidase family M41; Region: Peptidase_M41; pfam01434 998088009178 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cd02440 998088009179 S-adenosylmethionine binding site [chemical binding]; other site 998088009180 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; cl00663 998088009181 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 998088009182 domain; Region: GreA_GreB_N; pfam03449 998088009183 C-term; Region: GreA_GreB; pfam01272 998088009184 flagellar motor protein MotB; Reviewed; Region: motB; PRK08944 998088009185 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088009186 ligand binding site [chemical binding]; other site 998088009187 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 998088009188 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 998088009189 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 998088009190 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 998088009191 substrate binding pocket [chemical binding]; other site 998088009192 chain length determination region; other site 998088009193 substrate-Mg2+ binding site; other site 998088009194 catalytic residues [active] 998088009195 aspartate-rich region 1; other site 998088009196 active site lid residues [active] 998088009197 aspartate-rich region 2; other site 998088009198 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 998088009199 TPP-binding module; 1-Deoxy-D-xylulose-5-phosphate synthase (DXS) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. Terpeniods are plant natural products with important pharmaceutical activity. DXS...; Region: TPP_DXS; cd02007 998088009200 TPP-binding site; other site 998088009201 Pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and related proteins; Region: TPP_PYR_DXS_TK_like; cd07033 998088009202 PYR/PP interface [polypeptide binding]; other site 998088009203 dimer interface [polypeptide binding]; other site 998088009204 TPP binding site [chemical binding]; other site 998088009205 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 998088009206 bifunctional UDP-sugar hydrolase/5'-nucleotidase periplasmic precursor; Reviewed; Region: ushA; PRK09558 998088009207 Escherichia coli UshA and related proteins, N-terminal metallophosphatase domain; Region: MPP_UshA_N; cd07405 998088009208 active site 998088009209 metal binding site [ion binding]; metal-binding site 998088009210 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 998088009211 Protein of unknown function (DUF2956); Region: DUF2956; pfam11169 998088009212 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 998088009213 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088009214 active site 998088009215 phosphorylation site [posttranslational modification] 998088009216 intermolecular recognition site; other site 998088009217 dimerization interface [polypeptide binding]; other site 998088009218 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088009219 Walker A motif; other site 998088009220 ATP binding site [chemical binding]; other site 998088009221 Walker B motif; other site 998088009222 arginine finger; other site 998088009223 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 998088009224 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 998088009225 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 998088009226 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 998088009227 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues...; Region: WD40; cl02567 998088009228 structural tetrad; other site 998088009229 SlyX; Region: SlyX; cl01090 998088009230 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 998088009231 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088009232 dimer interface [polypeptide binding]; other site 998088009233 conserved gate region; other site 998088009234 putative PBP binding loops; other site 998088009235 ABC-ATPase subunit interface; other site 998088009236 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 998088009237 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088009238 dimer interface [polypeptide binding]; other site 998088009239 conserved gate region; other site 998088009240 putative PBP binding loops; other site 998088009241 ABC-ATPase subunit interface; other site 998088009242 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 998088009243 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_2; cd08498 998088009244 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 998088009245 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 998088009246 Walker A/P-loop; other site 998088009247 ATP binding site [chemical binding]; other site 998088009248 Q-loop/lid; other site 998088009249 ABC transporter signature motif; other site 998088009250 Walker B; other site 998088009251 D-loop; other site 998088009252 H-loop/switch region; other site 998088009253 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 998088009254 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 998088009255 Walker A/P-loop; other site 998088009256 ATP binding site [chemical binding]; other site 998088009257 Q-loop/lid; other site 998088009258 ABC transporter signature motif; other site 998088009259 Walker B; other site 998088009260 D-loop; other site 998088009261 H-loop/switch region; other site 998088009262 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 998088009263 tetramer interfaces [polypeptide binding]; other site 998088009264 binuclear metal-binding site [ion binding]; other site 998088009265 thiamine monophosphate kinase; Provisional; Region: PRK05731 998088009266 ThiL (Thiamine-monophosphate kinase) plays a dual role in de novo biosynthesis and in salvage of exogenous thiamine. Thiamine salvage occurs in two steps, with thiamine kinase catalyzing the formation of thiamine phosphate, and ThiL catalyzing the...; Region: ThiL; cd02194 998088009267 ATP binding site [chemical binding]; other site 998088009268 dimerization interface [polypeptide binding]; other site 998088009269 Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus...; Region: Terminator_NusB; cd00619 998088009270 putative RNA binding site [nucleotide binding]; other site 998088009271 lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2); type-I; Region: Lumazine_synthase-I; cd09209 998088009272 homopentamer interface [polypeptide binding]; other site 998088009273 active site 998088009274 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 998088009275 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 998088009276 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cl00522 998088009277 dimerization interface [polypeptide binding]; other site 998088009278 active site 998088009279 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 998088009280 Lumazine binding domain; Region: Lum_binding; pfam00677 998088009281 Lumazine binding domain; Region: Lum_binding; pfam00677 998088009282 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 998088009283 Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the...; Region: Riboflavin_deaminase-reductase; cd01284 998088009284 catalytic motif [active] 998088009285 Zn binding site [ion binding]; other site 998088009286 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5,10-...; Region: DHFR; cl00161 998088009287 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 998088009288 ATP cone domain; Region: ATP-cone; pfam03477 998088009289 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 998088009290 Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of...; Region: SHMT; cd00378 998088009291 dimer interface [polypeptide binding]; other site 998088009292 glycine-pyridoxal phosphate binding site [chemical binding]; other site 998088009293 active site 998088009294 folate binding site [chemical binding]; other site 998088009295 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 998088009296 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088009297 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 998088009298 dimer interface [polypeptide binding]; other site 998088009299 phosphorylation site [posttranslational modification] 998088009300 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088009301 ATP binding site [chemical binding]; other site 998088009302 Mg2+ binding site [ion binding]; other site 998088009303 G-X-G motif; other site 998088009304 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088009305 active site 998088009306 phosphorylation site [posttranslational modification] 998088009307 intermolecular recognition site; other site 998088009308 dimerization interface [polypeptide binding]; other site 998088009309 TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria; Region: PBP1_TorT-like; cd06306 998088009310 putative ligand binding site [chemical binding]; other site 998088009311 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 998088009312 DNA-binding transcriptional regulator TorR; Provisional; Region: PRK10766 998088009313 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088009314 active site 998088009315 phosphorylation site [posttranslational modification] 998088009316 intermolecular recognition site; other site 998088009317 dimerization interface [polypeptide binding]; other site 998088009318 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 998088009319 DNA binding site [nucleotide binding] 998088009320 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl09485 998088009321 trimethylamine N-oxide reductase cytochrome c-type subunit; Provisional; Region: PRK15032 998088009322 trimethylamine N-oxide reductase I catalytic subunit; Provisional; Region: PRK15102 998088009323 The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_DMSOR-BSOR-TMAOR; cd02769 998088009324 molybdopterin cofactor binding site [chemical binding]; other site 998088009325 substrate binding site [chemical binding]; other site 998088009326 The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_CT_DMSOR-BSOR-TMAOR; cd02793 998088009327 molybdopterin cofactor binding site; other site 998088009328 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 998088009329 PAS fold; Region: PAS_4; pfam08448 998088009330 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 998088009331 PAS domain S-box; Region: sensory_box; TIGR00229 998088009332 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 998088009333 putative active site [active] 998088009334 heme pocket [chemical binding]; other site 998088009335 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088009336 metal binding site [ion binding]; metal-binding site 998088009337 active site 998088009338 I-site; other site 998088009339 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 998088009340 acetyl-CoA synthetase; Provisional; Region: PRK00174 998088009341 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 998088009342 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 998088009343 Dehydroquinase (DHQase), type II. Dehydroquinase (or 3-dehydroquinate dehydratase) catalyzes the reversible dehydration of 3-dehydroquinate to form 3-dehydroshikimate. This reaction is part of two metabolic pathways: the biosynthetic shikimate pathway...; Region: DHQase_II; cd00466 998088009344 active site 998088009345 trimer interface [polypeptide binding]; other site 998088009346 dimer interface [polypeptide binding]; other site 998088009347 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 998088009348 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase...; Region: biotinyl_domain; cd06850 998088009349 carboxyltransferase (CT) interaction site; other site 998088009350 biotinylation site [posttranslational modification]; other site 998088009351 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 998088009352 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 998088009353 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 998088009354 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 998088009355 Protein of unknown function (DUF997); Region: DUF997; cl01614 998088009356 Sodium:solute symporter family; Region: SSF; cl00456 998088009357 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 998088009358 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 998088009359 PTS system, N-acetylglucosamine-specific IIBC component; Region: PTS-II-BC-nag; TIGR01998 998088009360 PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIB_glc; cl00164 998088009361 active site turn [active] 998088009362 phosphorylation site [posttranslational modification] 998088009363 LysR family transcriptional regulator; Provisional; Region: PRK14997 998088009364 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088009365 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 998088009366 putative effector binding pocket; other site 998088009367 dimerization interface [polypeptide binding]; other site 998088009368 Arginate lyase and other MDR family members; Region: AL_MDR; cd08252 998088009369 zinc-binding alcohol dehydrogenase family protein; Region: adh_fam_1; TIGR02817 998088009370 putative NAD(P) binding site [chemical binding]; other site 998088009371 dimer interface [polypeptide binding]; other site 998088009372 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 998088009373 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 998088009374 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 998088009375 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088009376 maltose O-acetyltransferase; Provisional; Region: PRK10092 998088009377 Maltose O-acetyltransferase (MAT) and Galactoside O-acetyltransferase (GAT): MAT and GAT catalyze the CoA-dependent acetylation of the 6-hydroxyl group of their respective sugar substrates. MAT acetylates maltose and glucose exclusively at the C6...; Region: LbH_MAT_GAT; cd03357 998088009378 active site 998088009379 substrate binding site [chemical binding]; other site 998088009380 trimer interface [polypeptide binding]; other site 998088009381 CoA binding site [chemical binding]; other site 998088009382 Nitroreductase-like family which includes NADH oxidase and arsenite oxidiase. NADH oxidase catalyses the oxidation of NAD(P)H and accepts a wide broad range of compounds as electron acceptors, such as nitrocompound. Arsenite oxidase in a beta-...; Region: Arsenite_oxidase; cd02135 998088009383 putative FMN binding site [chemical binding]; other site 998088009384 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 998088009385 2,4-dienoyl-CoA reductase (DCR) FMN-binding domain. DCR in E. coli is an iron-sulfur flavoenzyme which contains FMN, FAD, and a 4Fe-4S cluster. It is also a monomer, unlike that of its eukaryotic counterparts which form homotetramers and lack the...; Region: DCR_FMN; cd02930 998088009386 active site 998088009387 FMN binding site [chemical binding]; other site 998088009388 2,4-decadienoyl-CoA binding site; other site 998088009389 catalytic residue [active] 998088009390 4Fe-4S cluster binding site [ion binding]; other site 998088009391 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 998088009392 protease 4; Provisional; Region: PRK10949 998088009393 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 998088009394 tandem repeat interface [polypeptide binding]; other site 998088009395 oligomer interface [polypeptide binding]; other site 998088009396 active site residues [active] 998088009397 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 998088009398 tandem repeat interface [polypeptide binding]; other site 998088009399 oligomer interface [polypeptide binding]; other site 998088009400 active site residues [active] 998088009401 L,D-transpeptidase; Provisional; Region: PRK10190 998088009402 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 998088009403 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 998088009404 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 998088009405 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi...; Region: TPR; cd00189 998088009406 binding surface 998088009407 TPR motif; other site 998088009408 Gram-negative bacterial tonB protein; Region: TonB; cl10048 998088009409 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 998088009410 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 998088009411 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 998088009412 Protein of unknown function (DUF3450); Region: DUF3450; pfam11932 998088009413 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 998088009414 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 998088009415 N-terminal plug; other site 998088009416 ligand-binding site [chemical binding]; other site 998088009417 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 998088009418 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088009419 dimer interface [polypeptide binding]; other site 998088009420 conserved gate region; other site 998088009421 putative PBP binding loops; other site 998088009422 ABC-ATPase subunit interface; other site 998088009423 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 998088009424 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088009425 dimer interface [polypeptide binding]; other site 998088009426 conserved gate region; other site 998088009427 putative PBP binding loops; other site 998088009428 ABC-ATPase subunit interface; other site 998088009429 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_14; cd08497 998088009430 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 998088009431 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 998088009432 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 998088009433 Walker A/P-loop; other site 998088009434 ATP binding site [chemical binding]; other site 998088009435 Q-loop/lid; other site 998088009436 ABC transporter signature motif; other site 998088009437 Walker B; other site 998088009438 D-loop; other site 998088009439 H-loop/switch region; other site 998088009440 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 998088009441 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 998088009442 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 998088009443 Walker A/P-loop; other site 998088009444 ATP binding site [chemical binding]; other site 998088009445 Q-loop/lid; other site 998088009446 ABC transporter signature motif; other site 998088009447 Walker B; other site 998088009448 D-loop; other site 998088009449 H-loop/switch region; other site 998088009450 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 998088009451 Uncharacterized conserved protein [Function unknown]; Region: COG1284 998088009452 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 998088009453 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088009454 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 998088009455 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088009456 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 998088009457 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 998088009458 putative NAD(P) binding site [chemical binding]; other site 998088009459 active site 998088009460 putative substrate binding site [chemical binding]; other site 998088009461 Uncharacterized protein conserved in bacteria (DUF2076); Region: DUF2076; cl01353 998088009462 Uncharacterized protein conserved in bacteria (DUF2076); Region: DUF2076; cl01353 998088009463 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 998088009464 N-acetyl-D-glucosamine binding site [chemical binding]; other site 998088009465 catalytic residue [active] 998088009466 Bacterial inner membrane protein; Region: Imp-YgjV; pfam10688 998088009467 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 998088009468 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 998088009469 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 998088009470 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088009471 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 998088009472 ABC transporter; Region: ABC_tran_2; pfam12848 998088009473 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 998088009474 Sulfate transporter family; Region: Sulfate_transp; cl00967 998088009475 Permease family; Region: Xan_ur_permease; pfam00860 998088009476 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 998088009477 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 998088009478 HIGH motif; other site 998088009479 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 998088009480 active site 998088009481 KMSKS motif; other site 998088009482 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cd06225 998088009483 dimerization interface [polypeptide binding]; other site 998088009484 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088009485 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088009486 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 998088009487 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein...; Region: CSP_CDS; cd04458 998088009488 DNA-binding site [nucleotide binding]; DNA binding site 998088009489 RNA-binding motif; other site 998088009490 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 998088009491 putative active site [active] 998088009492 putative substrate binding site [chemical binding]; other site 998088009493 catalytic site [active] 998088009494 dimer interface [polypeptide binding]; other site 998088009495 GTPase RsgA; Reviewed; Region: PRK12288 998088009496 YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence...; Region: YjeQ_engC; cd01854 998088009497 GTPase/OB domain interface [polypeptide binding]; other site 998088009498 GTPase/Zn-binding domain interface [polypeptide binding]; other site 998088009499 GTP/Mg2+ binding site [chemical binding]; other site 998088009500 G4 box; other site 998088009501 G5 box; other site 998088009502 G1 box; other site 998088009503 Switch I region; other site 998088009504 G2 box; other site 998088009505 G3 box; other site 998088009506 Switch II region; other site 998088009507 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 998088009508 Uncharacterized conserved protein (DUF2132); Region: DUF2132; cl01894 998088009509 Protein of unknown function (DUF2960); Region: DUF2960; pfam11173 998088009510 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 998088009511 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 998088009512 putative catalytic cysteine [active] 998088009513 gamma-glutamyl kinase; Provisional; Region: PRK05429 998088009514 AAK_G5K_ProB: Glutamate-5-kinase (G5K) catalyzes glutamate-dependent ATP cleavage; G5K transfers the terminal phosphoryl group of ATP to the gamma-carboxyl group of glutamate, in the first and controlling step of proline (and, in mammals, ornithine)...; Region: AAK_G5K_ProB; cd04242 998088009515 homotetrameric interface [polypeptide binding]; other site 998088009516 putative phosphate binding site [ion binding]; other site 998088009517 putative allosteric binding site; other site 998088009518 nucleotide binding site [chemical binding]; other site 998088009519 PUA domain; Region: PUA; cl00607 998088009520 Transcriptional regulator Crl; Region: Crl; cl11653 998088009521 fermentation/respiration switch protein; Reviewed; Region: frsA; PRK05077 998088009522 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 998088009523 aminoacyl-histidine dipeptidase; Region: aa-his-dipept; TIGR01893 998088009524 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 998088009525 metal binding site [ion binding]; metal-binding site 998088009526 dimer interface [polypeptide binding]; other site 998088009527 Dna-J like membrane chaperone protein; Provisional; Region: djlA; PRK09430 998088009528 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 998088009529 putative metal binding site [ion binding]; other site 998088009530 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of...; Region: DnaJ; cd06257 998088009531 HSP70 interaction site [polypeptide binding]; other site 998088009532 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 998088009533 Substrate binding site [chemical binding]; other site 998088009534 metal binding site [ion binding]; metal-binding site 998088009535 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 998088009536 Phosphotransferase enzyme family; Region: APH; pfam01636 998088009537 LPS assembly outer membrane complex protein LptD; Provisional; Region: PRK03761 998088009538 OstA-like protein; Region: OstA; cl00844 998088009539 Organic solvent tolerance protein; Region: OstA_C; pfam04453 998088009540 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 998088009541 SurA N-terminal domain; Region: SurA_N; pfam09312 998088009542 PPIC-type PPIASE domain; Region: Rotamase; cl08278 998088009543 PPIC-type PPIASE domain; Region: Rotamase; cl08278 998088009544 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 998088009545 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 998088009546 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 998088009547 Protein of unknown function (DUF525); Region: DUF525; cl01119 998088009548 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 998088009549 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 998088009550 active site 998088009551 metal binding site [ion binding]; metal-binding site 998088009552 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 998088009553 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 998088009554 non-specific DNA binding site [nucleotide binding]; other site 998088009555 salt bridge; other site 998088009556 sequence-specific DNA binding site [nucleotide binding]; other site 998088009557 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 998088009558 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 998088009559 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cd00347 998088009560 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3314 998088009561 Nucleoside recognition; Region: Gate; cl00486 998088009562 GTPase CgtA; Reviewed; Region: obgE; PRK12298 998088009563 GTP1/OBG; Region: GTP1_OBG; pfam01018 998088009564 Obg subfamily. The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins...; Region: Obg; cd01898 998088009565 G1 box; other site 998088009566 GTP/Mg2+ binding site [chemical binding]; other site 998088009567 Switch I region; other site 998088009568 G2 box; other site 998088009569 G3 box; other site 998088009570 Switch II region; other site 998088009571 G4 box; other site 998088009572 G5 box; other site 998088009573 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 998088009574 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 998088009575 octaprenyl diphosphate synthase; Provisional; Region: PRK10888 998088009576 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 998088009577 substrate binding pocket [chemical binding]; other site 998088009578 chain length determination region; other site 998088009579 substrate-Mg2+ binding site; other site 998088009580 catalytic residues [active] 998088009581 aspartate-rich region 1; other site 998088009582 active site lid residues [active] 998088009583 aspartate-rich region 2; other site 998088009584 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; cl01275 998088009585 FtsH protease regulator HflC; Provisional; Region: PRK11029 998088009586 Band_7_HflC: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfC (High frequency of lysogenization C). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflC; cd03405 998088009587 FtsH protease regulator HflK; Provisional; Region: PRK10930 998088009588 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 998088009589 Band_7_HflK: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfK (High frequency of lysogenization K). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflK; cd03404 998088009590 GTPase HflX; Provisional; Region: PRK11058 998088009591 HflX subfamily. A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual...; Region: HflX; cd01878 998088009592 G1 box; other site 998088009593 GTP/Mg2+ binding site [chemical binding]; other site 998088009594 Switch I region; other site 998088009595 G2 box; other site 998088009596 G3 box; other site 998088009597 Switch II region; other site 998088009598 G4 box; other site 998088009599 G5 box; other site 998088009600 Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that...; Region: Hfq; cd01716 998088009601 Sm1 motif; other site 998088009602 intra - hexamer interaction site; other site 998088009603 inter - hexamer interaction site [polypeptide binding]; other site 998088009604 nucleotide binding pocket [chemical binding]; other site 998088009605 Sm2 motif; other site 998088009606 IPP transferase; Region: IPPT; cl00403 998088009607 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 998088009608 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088009609 ATP binding site [chemical binding]; other site 998088009610 Mg2+ binding site [ion binding]; other site 998088009611 G-X-G motif; other site 998088009612 MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL. EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second...; Region: MutL_Trans_MutL; cd03482 998088009613 ATP binding site [chemical binding]; other site 998088009614 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 998088009615 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 998088009616 Localisation of periplasmic protein complexes; Region: AMIN; pfam11741 998088009617 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 998088009618 N-acetylmuramoyl-L-alanine amidase or MurNAc-LAA (also known as peptidoglycan aminohydrolase, NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan amidase; EC 3.5.1.28) is an autolysin that hydrolyzes the amide bond between N-acetylmuramoyl and L-amino...; Region: MurNAc-LAA; cd02696 998088009619 active site 998088009620 metal binding site [ion binding]; metal-binding site 998088009621 invasion associated secreted endopeptidase; Provisional; Region: PRK13914 998088009622 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 998088009623 putative peptidoglycan binding site; other site 998088009624 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 998088009625 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 998088009626 putative peptidoglycan binding site; other site 998088009627 Uncharacterised P-loop hydrolase UPF0079; Region: UPF0079; cl00520 998088009628 putative carbohydrate kinase; Provisional; Region: PRK10565 998088009629 YjeF-related protein N-terminus; Region: YjeF_N; cl00318 998088009630 B.subtilis YXKO protein of unknown function and related proteins. Based on the conservation of the ATP binding site, the substrate binding site and the Mg2+binding site and structural homology this group is a member of the ribokinase-like superfamily; Region: YXKO-related; cd01171 998088009631 putative substrate binding site [chemical binding]; other site 998088009632 putative ATP binding site [chemical binding]; other site 998088009633 Uncharacterized Fe-S protein [Energy production and conversion]; Region: COG1600 998088009634 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 998088009635 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 998088009636 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 998088009637 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 998088009638 MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport. Other members of this system include the MetP permease and the MetQ substrate binding protein; Region: ABC_MetN_methionine_transporter; cd03258 998088009639 Walker A/P-loop; other site 998088009640 ATP binding site [chemical binding]; other site 998088009641 Q-loop/lid; other site 998088009642 ABC transporter signature motif; other site 998088009643 Walker B; other site 998088009644 D-loop; other site 998088009645 H-loop/switch region; other site 998088009646 NIL domain; Region: NIL; cl09633 998088009647 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088009648 dimer interface [polypeptide binding]; other site 998088009649 conserved gate region; other site 998088009650 ABC-ATPase subunit interface; other site 998088009651 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 998088009652 transcriptional activator RfaH; Provisional; Region: rfaH; PRK09014 998088009653 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; Region: NGN_SP_RfaH; cd09892 998088009654 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 998088009655 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088009656 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088009657 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088009658 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088009659 Response regulator receiver domain; Region: Response_reg; pfam00072 998088009660 active site 998088009661 phosphorylation site [posttranslational modification] 998088009662 intermolecular recognition site; other site 998088009663 dimerization interface [polypeptide binding]; other site 998088009664 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 998088009665 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cl15306 998088009666 substrate binding pocket [chemical binding]; other site 998088009667 membrane-bound complex binding site; other site 998088009668 hinge residues; other site 998088009669 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 998088009670 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088009671 substrate binding pocket [chemical binding]; other site 998088009672 membrane-bound complex binding site; other site 998088009673 hinge residues; other site 998088009674 PAS fold; Region: PAS_4; pfam08448 998088009675 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: VicK; COG5002 998088009676 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 998088009677 dimer interface [polypeptide binding]; other site 998088009678 phosphorylation site [posttranslational modification] 998088009679 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088009680 ATP binding site [chemical binding]; other site 998088009681 Mg2+ binding site [ion binding]; other site 998088009682 G-X-G motif; other site 998088009683 Response regulator receiver domain; Region: Response_reg; pfam00072 998088009684 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088009685 active site 998088009686 phosphorylation site [posttranslational modification] 998088009687 intermolecular recognition site; other site 998088009688 dimerization interface [polypeptide binding]; other site 998088009689 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 998088009690 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 998088009691 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01096 998088009692 aerobic respiration control sensor protein ArcB; Provisional; Region: PRK11091 998088009693 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 998088009694 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 998088009695 dimer interface [polypeptide binding]; other site 998088009696 phosphorylation site [posttranslational modification] 998088009697 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088009698 ATP binding site [chemical binding]; other site 998088009699 Mg2+ binding site [ion binding]; other site 998088009700 G-X-G motif; other site 998088009701 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088009702 active site 998088009703 phosphorylation site [posttranslational modification] 998088009704 intermolecular recognition site; other site 998088009705 dimerization interface [polypeptide binding]; other site 998088009706 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 998088009707 Protein of unknown function (DUF2860); Region: DUF2860; pfam11059 998088009708 Protein of unknown function (DUF3334); Region: DUF3334; pfam11813 998088009709 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the...; Region: HIT_like; cl00228 998088009710 Uncharacterized protein conserved in bacteria (DUF2057); Region: DUF2057; cl11437 998088009711 LysR family transcriptional regulator; Provisional; Region: PRK14997 998088009712 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088009713 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 998088009714 putative effector binding pocket; other site 998088009715 dimerization interface [polypeptide binding]; other site 998088009716 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088009717 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 998088009718 NAD(P) binding site [chemical binding]; other site 998088009719 active site 998088009720 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 998088009721 ATP binding site [chemical binding]; other site 998088009722 active site 998088009723 substrate binding site [chemical binding]; other site 998088009724 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]; Region: NlpB; COG3317 998088009725 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 998088009726 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 998088009727 dihydrodipicolinate synthase; Region: dapA; TIGR00674 998088009728 dimer interface [polypeptide binding]; other site 998088009729 active site 998088009730 catalytic residue [active] 998088009731 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 998088009732 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains; Region: ACT_GcvR_1; cd04893 998088009733 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-...; Region: CBS_pair; cl09141 998088009734 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by...; Region: PRX_BCP; cd03017 998088009735 catalytic triad [active] 998088009736 YfbU domain; Region: YfbU; cl01137 998088009737 Protein of unknown function, DUF412; Region: DUF412; cl01183 998088009738 Acetokinase family; Region: Acetate_kinase; cl01029 998088009739 phosphate acetyltransferase; Reviewed; Region: PRK05632 998088009740 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 998088009741 DRTGG domain; Region: DRTGG; cl12147 998088009742 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 998088009743 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 998088009744 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 998088009745 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 998088009746 active site 998088009747 tetramer interface [polypeptide binding]; other site 998088009748 amino acid/peptide transporter (Peptide:H+ symporter), bacterial; Region: yjdL_sub1_fam; TIGR00924 998088009749 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088009750 putative substrate translocation pore; other site 998088009751 response regulator of RpoS; Provisional; Region: PRK10693 998088009752 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088009753 active site 998088009754 phosphorylation site [posttranslational modification] 998088009755 intermolecular recognition site; other site 998088009756 dimerization interface [polypeptide binding]; other site 998088009757 Phd_YefM; Region: PhdYeFM; cl09153 998088009758 hypothetical protein; Validated; Region: PRK08116 998088009759 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088009760 Walker A motif; other site 998088009761 ATP binding site [chemical binding]; other site 998088009762 Walker B motif; other site 998088009763 atypical (a) SDRs, subgroup 5; Region: SDR_a5; cd05243 998088009764 NAD(P) binding site [chemical binding]; other site 998088009765 putative active site [active] 998088009766 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 998088009767 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 998088009768 ABC-2 type transporter; Region: ABC2_membrane; cl11417 998088009769 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 998088009770 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 998088009771 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 998088009772 Outer membrane efflux protein; Region: OEP; pfam02321 998088009773 Outer membrane efflux protein; Region: OEP; pfam02321 998088009774 tRNA-dihydrouridine synthase B; Provisional; Region: PRK10415 998088009775 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and...; Region: DUS_like_FMN; cd02801 998088009776 FMN binding site [chemical binding]; other site 998088009777 active site 998088009778 catalytic residues [active] 998088009779 substrate binding site [chemical binding]; other site 998088009780 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 998088009781 EamA-like transporter family; Region: EamA; cl01037 998088009782 Protein of unknown function (DUF3100); Region: DUF3100; pfam11299 998088009783 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 998088009784 M20 Peptidase Aminoacylase 1 family; Region: M20_Acy1; cd03886 998088009785 metal binding site [ion binding]; metal-binding site 998088009786 dimer interface [polypeptide binding]; other site 998088009787 transcriptional regulator CysB; Reviewed; Region: cysB; PRK12681 998088009788 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088009789 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 998088009790 substrate binding site [chemical binding]; other site 998088009791 dimerization interface [polypeptide binding]; other site 998088009792 LysE type translocator; Region: LysE; cl00565 998088009793 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 998088009794 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 998088009795 putative valine binding site [chemical binding]; other site 998088009796 dimer interface [polypeptide binding]; other site 998088009797 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 998088009798 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06466 998088009799 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 998088009800 PYR/PP interface [polypeptide binding]; other site 998088009801 dimer interface [polypeptide binding]; other site 998088009802 TPP binding site [chemical binding]; other site 998088009803 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 998088009804 Thiamine pyrophosphate (TPP) family, Acetohydroxyacid synthase (AHAS) subfamily, TPP-binding module; composed of proteins similar to the large catalytic subunit of AHAS. AHAS catalyzes the condensation of two molecules of pyruvate to give the...; Region: TPP_AHAS; cd02015 998088009805 TPP-binding site [chemical binding]; other site 998088009806 dimer interface [polypeptide binding]; other site 998088009807 conserved hypothetical protein; Region: MJ1255; TIGR00661 998088009808 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cl00474 998088009809 active site 998088009810 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 998088009811 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088009812 2-isopropylmalate synthase; Validated; Region: PRK00915 998088009813 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 998088009814 active site 998088009815 catalytic residues [active] 998088009816 metal binding site [ion binding]; metal-binding site 998088009817 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 998088009818 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 998088009819 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 998088009820 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 998088009821 substrate binding site [chemical binding]; other site 998088009822 ligand binding site [chemical binding]; other site 998088009823 Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate 3-...; Region: IPMI_Swivel; cd01577 998088009824 substrate binding site [chemical binding]; other site 998088009825 PilZ domain; Region: PilZ; cl01260 998088009826 ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]; Region: TbpA; COG4143 998088009827 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088009828 thiamine transporter membrane protein; Reviewed; Region: thiP; PRK09433 998088009829 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088009830 dimer interface [polypeptide binding]; other site 998088009831 conserved gate region; other site 998088009832 putative PBP binding loops; other site 998088009833 ABC-ATPase subunit interface; other site 998088009834 thiamine transporter ATP-binding subunit; Provisional; Region: thiQ; PRK10771 998088009835 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088009836 Walker A/P-loop; other site 998088009837 ATP binding site [chemical binding]; other site 998088009838 Q-loop/lid; other site 998088009839 ABC transporter signature motif; other site 998088009840 Walker B; other site 998088009841 D-loop; other site 998088009842 H-loop/switch region; other site 998088009843 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 998088009844 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 998088009845 putative active site [active] 998088009846 PhoH-like protein; Region: PhoH; cl12134 998088009847 TSCPD domain; Region: TSCPD; cl14834 998088009848 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 998088009849 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; Region: NrdJ_Z; TIGR02504 998088009850 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 998088009851 active site 998088009852 dimer interface [polypeptide binding]; other site 998088009853 effector binding site; other site 998088009854 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 998088009855 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088009856 metal binding site [ion binding]; metal-binding site 998088009857 active site 998088009858 I-site; other site 998088009859 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 998088009860 Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the...; Region: SO_family_Moco; cl00199 998088009861 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 998088009862 GroEL_like type I chaperonin. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. The symmetry of type I is seven-fold and they are found...; Region: GroEL; cd03344 998088009863 ring oligomerisation interface [polypeptide binding]; other site 998088009864 ATP/Mg binding site [chemical binding]; other site 998088009865 stacking interactions; other site 998088009866 hinge regions; other site 998088009867 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts...; Region: cpn10; cd00320 998088009868 oligomerisation interface [polypeptide binding]; other site 998088009869 mobile loop; other site 998088009870 roof hairpin; other site 998088009871 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 998088009872 MatE; Region: MatE; cl10513 998088009873 MatE; Region: MatE; cl10513 998088009874 FxsA cytoplasmic membrane protein; Region: FxsA; cl01148 998088009875 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 998088009876 Aspartase; Region: Aspartase; cd01357 998088009877 active sites [active] 998088009878 tetramer interface [polypeptide binding]; other site 998088009879 Anaerobic c4-dicarboxylate membrane transporter; Region: DcuA_DcuB; cl01040 998088009880 UGMP family protein; Validated; Region: PRK09604 998088009881 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 998088009882 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 998088009883 GatB domain; Region: GatB_Yqey; cl11497 998088009884 DNA primase; Validated; Region: dnaG; PRK05667 998088009885 CHC2 zinc finger; Region: zf-CHC2; cl02597 998088009886 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 998088009887 TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_DnaG_primases; cd03364 998088009888 active site 998088009889 metal binding site [ion binding]; metal-binding site 998088009890 interdomain interaction site; other site 998088009891 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 998088009892 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; cl07879 998088009893 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 998088009894 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 998088009895 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 998088009896 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 998088009897 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 998088009898 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 998088009899 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial...; Region: Sigma70_r4; cd06171 998088009900 DNA binding residues [nucleotide binding] 998088009901 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria...; Region: Cytochrome_b_N; cl00859 998088009902 Cytochrome b562; Region: Cytochrom_B562; cl01546 998088009903 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 998088009904 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 998088009905 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 998088009906 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 998088009907 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 998088009908 Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates 5-aminoimidazole-4-carboxamide-; Region: IMPCH; cd01421 998088009909 purine monophosphate binding site [chemical binding]; other site 998088009910 dimer interface [polypeptide binding]; other site 998088009911 putative catalytic residues [active] 998088009912 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 998088009913 zinc-responsive transcriptional regulator; Provisional; Region: zntR; PRK09514 998088009914 Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; Region: HTH_HMRTR; cd04770 998088009915 DNA binding residues [nucleotide binding] 998088009916 dimer interface [polypeptide binding]; other site 998088009917 metal binding site [ion binding]; metal-binding site 998088009918 Domain of unknown function; Region: DUF331; cl01149 998088009919 HemN family oxidoreductase; Provisional; Region: PRK05660 998088009920 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster...; Region: Radical_SAM; cd01335 998088009921 FeS/SAM binding site; other site 998088009922 HemN C-terminal region; Region: HemN_C; pfam06969 998088009923 NTPase/HAM1. This family consists of the HAM1 protein and pyrophosphate-releasing xanthosine/ inosine triphosphatase. HAM1 protects the cell against mutagenesis by the base analog 6-N-hydroxylaminopurine (HAP) in E. Coli and S. cerevisiae. A Ham1-...; Region: HAM1; cd00515 998088009924 active site 998088009925 dimerization interface [polypeptide binding]; other site 998088009926 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088009927 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 998088009928 putative substrate translocation pore; other site 998088009929 putative oxidoreductase; Provisional; Region: PRK11579 998088009930 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088009931 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 998088009932 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 998088009933 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088009934 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 998088009935 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088009936 Fungalysin/Thermolysin Propeptide Motif; Region: FTP; pfam07504 998088009937 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 998088009938 Peptidase M4 family includes thermolysin, protealysin, aureolysin and neutral protease; Region: M4_neutral_protease; cd09597 998088009939 active site 998088009940 Zn binding site [ion binding]; other site 998088009941 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 998088009942 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088009943 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088009944 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 998088009945 dimerization interface [polypeptide binding]; other site 998088009946 multidrug resistance protein MdtH; Provisional; Region: PRK11646 998088009947 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088009948 putative substrate translocation pore; other site 998088009949 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088009950 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088009951 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 998088009952 RF3 subfamily. Peptide chain release factor 3 (RF3) is a protein involved in the termination step of translation in bacteria. Termination occurs when class I release factors (RF1 or RF2) recognize the stop codon at the A-site of the ribosome and...; Region: RF3; cd04169 998088009953 G1 box; other site 998088009954 putative GEF interaction site [polypeptide binding]; other site 998088009955 GTP/Mg2+ binding site [chemical binding]; other site 998088009956 Switch I region; other site 998088009957 G2 box; other site 998088009958 G3 box; other site 998088009959 Switch II region; other site 998088009960 G4 box; other site 998088009961 G5 box; other site 998088009962 RF3_II: this subfamily represents the domain II of bacterial Release Factor 3 (RF3). Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the...; Region: RF3_II; cd03689 998088009963 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 998088009964 classical (c) SDRs; Region: SDR_c; cd05233 998088009965 NAD(P) binding site [chemical binding]; other site 998088009966 active site 998088009967 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088009968 metal binding site [ion binding]; metal-binding site 998088009969 active site 998088009970 I-site; other site 998088009971 hypothetical protein; Provisional; Region: yieM; PRK10997 998088009972 VWA YIEM type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-...; Region: VWA_YIEM_type; cd01462 998088009973 metal ion-dependent adhesion site (MIDAS); other site 998088009974 regulatory ATPase RavA; Provisional; Region: PRK13531 998088009975 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088009976 Walker A motif; other site 998088009977 ATP binding site [chemical binding]; other site 998088009978 Walker B motif; other site 998088009979 arginine finger; other site 998088009980 Protein of unknown function (DUF3763); Region: DUF3763; pfam12592 998088009981 ribosomal-protein-alanine N-acetyltransferase; Provisional; Region: rimI; PRK09491 998088009982 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088009983 Coenzyme A binding pocket [chemical binding]; other site 998088009984 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 998088009985 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 998088009986 Glutamate-cysteine ligase; Region: Glu_cys_ligase; cl01099 998088009987 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 998088009988 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 998088009989 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 998088009990 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 998088009991 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 998088009992 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 998088009993 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 998088009994 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 998088009995 alcohol dehydrogenase and quinone reductase-like medium chain degydrogenases/reductases; Region: MDR_like_2; cd05289 998088009996 putative NAD(P) binding site [chemical binding]; other site 998088009997 ferredoxin-NADP reductase; Provisional; Region: PRK10926 998088009998 Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently...; Region: FNR1; cd06195 998088009999 FAD binding pocket [chemical binding]; other site 998088010000 FAD binding motif [chemical binding]; other site 998088010001 phosphate binding motif [ion binding]; other site 998088010002 beta-alpha-beta structure motif; other site 998088010003 NAD binding pocket [chemical binding]; other site 998088010004 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 998088010005 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 998088010006 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 998088010007 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 998088010008 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 998088010009 Natural resistance-associated macrophage protein; Region: Nramp; cl00836 998088010010 Predicted metal-dependent hydrolases related to alanyl-tRNA synthetase HxxxH domain [General function prediction only]; Region: COG2872 998088010011 Predicted membrane protein [Function unknown]; Region: COG4125 998088010012 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 998088010013 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 998088010014 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-...; Region: HU_IHF; cd00591 998088010015 IHF dimer interface [polypeptide binding]; other site 998088010016 IHF - DNA interface [nucleotide binding]; other site 998088010017 Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ; Region: Rsd_AlgQ; cl11478 998088010018 PilZ domain; Region: PilZ; cl01260 998088010019 DNA repair protein RadA; Provisional; Region: PRK11823 998088010020 Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of...; Region: Sms; cd01121 998088010021 Walker A motif/ATP binding site; other site 998088010022 ATP binding site [chemical binding]; other site 998088010023 Walker B motif; other site 998088010024 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 998088010025 PilZ domain; Region: PilZ; cl01260 998088010026 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 998088010027 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 998088010028 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 998088010029 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cd01427 998088010030 motif II; other site 998088010031 Bacterial virulence factor haemolysin; Region: SMP_2; cl11479 998088010032 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 998088010033 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 998088010034 Sulfatase; Region: Sulfatase; cl10460 998088010035 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 998088010036 thymidine phosphorylase; Reviewed; Region: deoA; PRK05820 998088010037 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 998088010038 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 998088010039 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; cl06734 998088010040 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 998088010041 intersubunit interface [polypeptide binding]; other site 998088010042 active site 998088010043 catalytic residue [active] 998088010044 Protein of unknown function (DUF1427); Region: DUF1427; cl01771 998088010045 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 998088010046 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 998088010047 Nucleoside recognition; Region: Gate; cl00486 998088010048 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 998088010049 putative deoxyribonuclease YjjV; Provisional; Region: PRK11449 998088010050 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 998088010051 active site 998088010052 S-Ribosylhomocysteinase (LuxS); Region: LuxS; cl00802 998088010053 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 998088010054 N-acetyl-D-glucosamine binding site [chemical binding]; other site 998088010055 catalytic residue [active] 998088010056 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl00412 998088010057 NAD synthetase; Provisional; Region: PRK13981 998088010058 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 998088010059 multimer interface [polypeptide binding]; other site 998088010060 active site 998088010061 catalytic triad [active] 998088010062 protein interface 1 [polypeptide binding]; other site 998088010063 NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to...; Region: NAD_synthase; cd00553 998088010064 homodimer interface [polypeptide binding]; other site 998088010065 NAD binding pocket [chemical binding]; other site 998088010066 ATP binding pocket [chemical binding]; other site 998088010067 Mg binding site [ion binding]; other site 998088010068 active-site loop [active] 998088010069 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 998088010070 Type II transport protein GspH; Region: GspH; pfam12019 998088010071 Type II transport protein GspH; Region: GspH; pfam12019 998088010072 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 998088010073 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 998088010074 type IV pilus modification protein PilV; Region: type_IV_pilV; TIGR02523 998088010075 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 998088010076 Prokaryotic N-terminal methylation motif; Region: N_methyl; cl06830 998088010077 LytB protein; Region: LYTB; cl00507 998088010078 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 998088010079 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 998088010080 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 998088010081 lipoprotein signal peptidase; Provisional; Region: PRK14787 998088010082 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 998088010083 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 998088010084 active site 998088010085 HIGH motif; other site 998088010086 nucleotide binding site [chemical binding]; other site 998088010087 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 998088010088 active site 998088010089 KMSKS motif; other site 998088010090 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 998088010091 tRNA binding surface [nucleotide binding]; other site 998088010092 anticodon binding site; other site 998088010093 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 998088010094 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 998088010095 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 998088010096 active site 998088010097 Riboflavin kinase; Region: Flavokinase; cl03312 998088010098 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 998088010099 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 998088010100 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088010101 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 998088010102 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088010103 The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA gene, encoding Na+/H+ antiporter, contains the type 2 periplasmic binding fold; Region: PBP2_NhaR; cd08429 998088010104 putative dimerization interface [polypeptide binding]; other site 998088010105 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088010106 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 998088010107 Thymidylate synthase and pyrimidine hydroxymethylase: Thymidylate synthase (TS) and deoxycytidylate hydroxymethylase (dCMP-HMase) are homologs that catalyze analogous alkylation of C5 of pyrimidine nucleotides. Both enzymes are involved in the...; Region: TS_Pyrimidine_HMase; cd00351 998088010108 dimerization interface [polypeptide binding]; other site 998088010109 active site 998088010110 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 998088010111 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional; Region: PRK11061 998088010112 GAF domain; Region: GAF; cl00853 998088010113 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 998088010114 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 998088010115 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 998088010116 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where...; Region: Ap4A_hydrolase_plant_like; cd03671 998088010117 putative active site [active] 998088010118 Ap4A binding site [chemical binding]; other site 998088010119 nudix motif; other site 998088010120 putative metal binding site [ion binding]; other site 998088010121 MutH is a 28kD endonuclease involved in methyl-directed DNA mismatch repair in gram negative bacteria. MutH is both sequence-specific and methylation-specific, introducing a nick in the unmethylated strand of a hemi-methylated d(GATC) DNA duplex; Region: MutH_Sau3AI; cd00583 998088010122 putative DNA-binding cleft [nucleotide binding]; other site 998088010123 putative DNA clevage site; other site 998088010124 molecular lever; other site 998088010125 E or 'early' set of sugar utilizing enzymes which may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end; Region: E_set; cl09101 998088010126 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 998088010127 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 998088010128 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 998088010129 RimM N-terminal domain; Region: RimM; pfam01782 998088010130 Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to...; Region: PRCH; cl09959 998088010131 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 998088010132 signal recognition particle protein; Provisional; Region: PRK10867 998088010133 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 998088010134 The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The...; Region: SRP; cd03115 998088010135 P loop; other site 998088010136 GTP binding site [chemical binding]; other site 998088010137 Signal peptide binding domain; Region: SRP_SPB; pfam02978 998088010138 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 998088010139 hypothetical protein; Provisional; Region: PRK11573 998088010140 Domain of unknown function DUF21; Region: DUF21; pfam01595 998088010141 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in...; Region: CBS_pair_CorC_HlyC_assoc; cd04590 998088010142 Transporter associated domain; Region: CorC_HlyC; cl08393 998088010143 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088010144 Rrf2 family protein; Region: rrf2_super; TIGR00738 998088010145 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional; Region: PRK13289 998088010146 Globins are heme proteins, which bind and transport oxygen. This family summarizes a diverse set of homologous protein domains, including: (1) tetrameric vertebrate hemoglobins, which are the major protein component of erythrocytes and transport oxygen...; Region: globin; cd01040 998088010147 heme-binding site [chemical binding]; other site 998088010148 FAD_NAD(P)H binding domain of flavohemoglobin. Flavohemoglobins have a globin domain containing a B-type heme fused with a ferredoxin reductase-like FAD/NAD-binding domain. Flavohemoglobins detoxify nitric oxide (NO) via an NO dioxygenase reaction. The...; Region: flavohem_like_fad_nad_binding; cd06184 998088010149 FAD binding pocket [chemical binding]; other site 998088010150 FAD binding motif [chemical binding]; other site 998088010151 phosphate binding motif [ion binding]; other site 998088010152 beta-alpha-beta structure motif; other site 998088010153 NAD binding pocket [chemical binding]; other site 998088010154 Heme binding pocket [chemical binding]; other site 998088010155 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 998088010156 malate dehydrogenase; Provisional; Region: PRK05086 998088010157 Glyoxysomal and mitochondrial malate dehydrogenases; Region: MDH_glyoxysomal_mitochondrial; cd01337 998088010158 NAD binding site [chemical binding]; other site 998088010159 dimerization interface [polypeptide binding]; other site 998088010160 Substrate binding site [chemical binding]; other site 998088010161 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088010162 dimer interface [polypeptide binding]; other site 998088010163 conserved gate region; other site 998088010164 putative PBP binding loops; other site 998088010165 ABC-ATPase subunit interface; other site 998088010166 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 998088010167 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088010168 dimer interface [polypeptide binding]; other site 998088010169 conserved gate region; other site 998088010170 putative PBP binding loops; other site 998088010171 ABC-ATPase subunit interface; other site 998088010172 putative ABC transporter arginine-biding protein; Provisional; Region: PRK15007 998088010173 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088010174 substrate binding pocket [chemical binding]; other site 998088010175 membrane-bound complex binding site; other site 998088010176 hinge residues; other site 998088010177 arginine transporter ATP-binding subunit; Provisional; Region: artP; PRK11124 998088010178 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP; Region: ABC_HisP_GlnQ_permeases; cd03262 998088010179 Walker A/P-loop; other site 998088010180 ATP binding site [chemical binding]; other site 998088010181 Q-loop/lid; other site 998088010182 ABC transporter signature motif; other site 998088010183 Walker B; other site 998088010184 D-loop; other site 998088010185 H-loop/switch region; other site 998088010186 Arginine repressor, DNA binding domain; Region: Arg_repressor; pfam01316 998088010187 Arginine repressor, C-terminal domain; Region: Arg_repressor_C; pfam02863 998088010188 Dyp-type peroxidase family; Region: Dyp_perox; cl01067 998088010189 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 998088010190 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088010191 Walker A/P-loop; other site 998088010192 ATP binding site [chemical binding]; other site 998088010193 Q-loop/lid; other site 998088010194 ABC transporter signature motif; other site 998088010195 Walker B; other site 998088010196 D-loop; other site 998088010197 H-loop/switch region; other site 998088010198 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088010199 dimer interface [polypeptide binding]; other site 998088010200 conserved gate region; other site 998088010201 putative PBP binding loops; other site 998088010202 ABC-ATPase subunit interface; other site 998088010203 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cl00427 998088010204 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088010205 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl00412 998088010206 RF-1 domain; Region: RF-1; cl02875 998088010207 methylated-DNA--protein-cysteine methyltransferase; Provisional; Region: PRK00901 998088010208 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 998088010209 The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases...; Region: ATase; cd06445 998088010210 DNA binding site [nucleotide binding] 998088010211 active site 998088010212 Protein of unknown function (DUF328); Region: DUF328; cl01143 998088010213 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 998088010214 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088010215 Walker A motif; other site 998088010216 ATP binding site [chemical binding]; other site 998088010217 Walker B motif; other site 998088010218 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 998088010219 Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism...; Region: PilT; cd01131 998088010220 Walker A motif; other site 998088010221 ATP binding site [chemical binding]; other site 998088010222 Walker B motif; other site 998088010223 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 998088010224 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 998088010225 catalytic residue [active] 998088010226 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 998088010227 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088010228 YGGT family; Region: YGGT; cl00508 998088010229 YGGT family; Region: YGGT; cl00508 998088010230 Uncharacterised ACR, YggU family COG1872; Region: DUF167; cl00811 998088010231 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 998088010232 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 998088010233 Nucleoside recognition; Region: Gate; cl00486 998088010234 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 998088010235 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088010236 LysR family transcriptional regulator; Provisional; Region: PRK14997 998088010237 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 998088010238 putative effector binding pocket; other site 998088010239 dimerization interface [polypeptide binding]; other site 998088010240 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue...; Region: GSH_Peroxidase; cd00340 998088010241 catalytic residues [active] 998088010242 dimer interface [polypeptide binding]; other site 998088010243 NnrU protein; Region: NnrU; cl01697 998088010244 Glycerate kinase family; Region: Gly_kinase; cl00841 998088010245 H+/gluconate symporter and related permeases [Carbohydrate transport and metabolism / Amino acid transport and metabolism]; Region: GntT; COG2610 998088010246 GntP family permease; Region: GntP_permease; cl15264 998088010247 Sugar diacid utilization regulator [Transcription / Signal transduction mechanisms]; Region: CdaR; COG3835 998088010248 Putative sugar diacid recognition; Region: Diacid_rec; pfam05651 998088010249 Uncharacterised protein family (UPF0231); Region: UPF0231; cl11474 998088010250 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088010251 substrate binding pocket [chemical binding]; other site 998088010252 membrane-bound complex binding site; other site 998088010253 hinge residues; other site 998088010254 CAAX amino terminal protease self- immunity; Region: Abi; cl00558 998088010255 Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine; Region: nSMase; cd09078 998088010256 putative catalytic site [active] 998088010257 metal binding site A [ion binding]; metal-binding site 998088010258 phosphate binding site [ion binding]; other site 998088010259 metal binding site C [ion binding]; metal-binding site 998088010260 metal binding site B [ion binding]; metal-binding site 998088010261 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 998088010262 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 998088010263 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088010264 ATP binding site [chemical binding]; other site 998088010265 putative Mg++ binding site [ion binding]; other site 998088010266 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 998088010267 nucleotide binding region [chemical binding]; other site 998088010268 ATP-binding site [chemical binding]; other site 998088010269 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cl15306 998088010270 substrate binding pocket [chemical binding]; other site 998088010271 membrane-bound complex binding site; other site 998088010272 hinge residues; other site 998088010273 Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a...; Region: PRX_Atyp2cys; cd03014 998088010274 dimer interface [polypeptide binding]; other site 998088010275 catalytic triad [active] 998088010276 peroxidatic and resolving cysteines [active] 998088010277 zinc/cadmium/mercury/lead-transporting ATPase; Provisional; Region: zntA; PRK11033 998088010278 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 998088010279 metal-binding site [ion binding] 998088010280 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 998088010281 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 998088010282 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 998088010283 Bacterial pullanase-associated domain; Region: PUD; pfam03714 998088010284 alpha-1,6-glucosidases, pullulanase-type; Region: pullul_strch; TIGR02103 998088010285 Pullulanase domain N-terminus. Pullulanase (AKA dextrinase; alpha-dextrin endo-1,6-alpha glucosidase) is an enzyme with action similar to that of isoamylase; it cleaves 1,6-alpha-glucosidic linkages in pullulan, amylopectin, and glycogen, and in alpha-...; Region: Pullulanase_N_term; cd02860 998088010286 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 998088010287 Domain of unknown function (DUF3372); Region: DUF3372; pfam11852 998088010288 Cation efflux family; Region: Cation_efflux; cl00316 998088010289 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 998088010290 Transcriptional regulators RcnR and FrmR, and related domains; this domain family was previously known as part of DUF156; Region: RcnR-FrmR-like_DUF156; cd10153 998088010291 putative metal binding site [ion binding]; other site 998088010292 putative homotetramer interface [polypeptide binding]; other site 998088010293 putative homodimer interface [polypeptide binding]; other site 998088010294 putative homodimer-homodimer interface [polypeptide binding]; other site 998088010295 putative allosteric switch controlling residues; other site 998088010296 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 998088010297 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088010298 homodimer interface [polypeptide binding]; other site 998088010299 catalytic residue [active] 998088010300 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088010301 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088010302 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 998088010303 substrate binding pocket [chemical binding]; other site 998088010304 dimerization interface [polypeptide binding]; other site 998088010305 Domain of unknown function (DUF1820); Region: DUF1820; cl11545 998088010306 glycine radical enzyme activase, YjjW family; Region: activase_YjjW; TIGR04041 998088010307 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster...; Region: Radical_SAM; cl15259 998088010308 hypothetical protein; Provisional; Region: PRK10977 998088010309 Glycine radical; Region: Gly_radical; cl12026 998088010310 Branched-chain amino acid transport protein (AzlD); Region: AzlD; cl00735 998088010311 AzlC protein; Region: AzlC; cl00570 998088010312 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 998088010313 Uncharacterized protein related to the periplasmic component of the Tol biopolymer transport system [Function unknown]; Region: COG4946 998088010314 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 998088010315 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 998088010316 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-...; Region: PDZ_serine_protease; cd00987 998088010317 protein binding site [polypeptide binding]; other site 998088010318 Tricorn protease; serine protease family S41; Region: Peptidase_S41_TRI; cd07562 998088010319 Domain interface; other site 998088010320 Peptide binding site; other site 998088010321 Active site tetrad [active] 998088010322 Predicted ferric reductase [Inorganic ion transport and metabolism]; Region: COG4097 998088010323 Ferric reductase like transmembrane component; Region: Ferric_reduct; cl01043 998088010324 NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) domain, which varies in orientation with respect to the NAD(P)...; Region: FNR_like_3; cd06198 998088010325 FAD binding pocket [chemical binding]; other site 998088010326 FAD binding motif [chemical binding]; other site 998088010327 phosphate binding motif [ion binding]; other site 998088010328 beta-alpha-beta structure motif; other site 998088010329 NAD binding pocket [chemical binding]; other site 998088010330 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 998088010331 PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_glc; cl00162 998088010332 CESA_like is the cellulose synthase superfamily; Region: CESA_like; cd06423 998088010333 DXD motif; other site 998088010334 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 998088010335 Peptidase M3-like family, a zincin metallopeptidase, includes M3 and M32 families; Region: M3_like; cd06258 998088010336 active site 998088010337 Zn binding site [ion binding]; other site 998088010338 Cache domain; Region: Cache_2; cl07034 998088010339 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 998088010340 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088010341 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088010342 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088010343 N-acetylglucosamine-binding protein A; Reviewed; Region: PRK13211 998088010344 Chitin binding domain; Region: Chitin_bind_3; cl03871 998088010345 Predicted membrane protein [Function unknown]; Region: COG3174 998088010346 maltose O-acetyltransferase; Provisional; Region: PRK10092 998088010347 Maltose O-acetyltransferase (MAT) and Galactoside O-acetyltransferase (GAT): MAT and GAT catalyze the CoA-dependent acetylation of the 6-hydroxyl group of their respective sugar substrates. MAT acetylates maltose and glucose exclusively at the C6...; Region: LbH_MAT_GAT; cd03357 998088010348 active site 998088010349 substrate binding site [chemical binding]; other site 998088010350 trimer interface [polypeptide binding]; other site 998088010351 CoA binding site [chemical binding]; other site 998088010352 Protein of unknown function (DUF1294); Region: DUF1294; cl01311 998088010353 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 998088010354 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cd01427 998088010355 motif II; other site 998088010356 adenosine nucleotide hydrolase NudE; Provisional; Region: nudE; PRK11762 998088010357 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as...; Region: ADPRase_NUDT5; cd03424 998088010358 dimer interface [polypeptide binding]; other site 998088010359 ADP-ribose binding site [chemical binding]; other site 998088010360 active site 998088010361 nudix motif; other site 998088010362 metal binding site [ion binding]; metal-binding site 998088010363 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in cysteine...; Region: CysQ; cd01638 998088010364 active site 998088010365 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 998088010366 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 998088010367 tRNA-binding-domain-containing CsaA-like proteins. CsaA is a molecular chaperone with export related activities. CsaA has a putative tRNA binding activity. The functional unit of CsaA is a homodimer and this domain acts as a dimerization domain; Region: tRNA_bind_CsaA; cd02798 998088010368 dimer interface [polypeptide binding]; other site 998088010369 putative tRNA-binding site [nucleotide binding]; other site 998088010370 Cupin domain; Region: Cupin_2; cl09118 998088010371 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 998088010372 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088010373 Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence; Region: Met_repressor_MetJ; cd00490 998088010374 dimerization interface [polypeptide binding]; other site 998088010375 DNA binding site [nucleotide binding] 998088010376 corepressor binding sites; other site 998088010377 O-succinylhomoserine (thiol)-lyase; Region: O_succ_thio_ly; TIGR02080 998088010378 CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of...; Region: CGS_like; cd00614 998088010379 homodimer interface [polypeptide binding]; other site 998088010380 substrate-cofactor binding pocket; other site 998088010381 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088010382 catalytic residue [active] 998088010383 bifunctional aspartate kinase II/homoserine dehydrogenase II; Provisional; Region: metL; PRK09466 998088010384 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 998088010385 nucleotide binding site [chemical binding]; other site 998088010386 substrate binding site [chemical binding]; other site 998088010387 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088010388 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 998088010389 Phosphate transporter family; Region: PHO4; cl00396 998088010390 Phosphate transporter family; Region: PHO4; cl00396 998088010391 Protein of unknown function DUF47; Region: PhoU_div; pfam01865 998088010392 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 998088010393 putative active site [active] 998088010394 putative metal binding residues [ion binding]; other site 998088010395 signature motif; other site 998088010396 putative triphosphate binding site [ion binding]; other site 998088010397 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 998088010398 dihydrodipicolinate synthase; Region: dapA; TIGR00674 998088010399 dimer interface [polypeptide binding]; other site 998088010400 active site 998088010401 catalytic residue [active] 998088010402 16S ribosomal RNA m2G1207 methyltransferase; Provisional; Region: rsmC; PRK09489 998088010403 Methyltransferase small domain N-terminal; Region: MTS_N; pfam08468 998088010404 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cd02440 998088010405 S-adenosylmethionine binding site [chemical binding]; other site 998088010406 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00844 998088010407 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 998088010408 ligand binding site [chemical binding]; other site 998088010409 oligomer interface [polypeptide binding]; other site 998088010410 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and rate-...; Region: LbH_G1P_AT_C; cd04651 998088010411 dimer interface [polypeptide binding]; other site 998088010412 N-terminal domain interface [polypeptide binding]; other site 998088010413 sulfate 1 binding site; other site 998088010414 glycogen synthase; Provisional; Region: glgA; PRK00654 998088010415 This family is most closely related to the GT1 family of glycosyltransferases. Glycogen synthase catalyzes the formation and elongation of the alpha-1,4-glucose backbone using ADP-glucose, the second and key step of glycogen biosynthesis. This family...; Region: GT1_Glycogen_synthase_DULL1_like; cd03791 998088010416 ADP-binding pocket [chemical binding]; other site 998088010417 homodimer interface [polypeptide binding]; other site 998088010418 Late competence development protein ComFB; Region: ComFB; pfam10719 998088010419 Na+/H+ antiporter NhaC; Region: antiport_nhaC; TIGR00931 998088010420 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088010421 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 998088010422 ClC chloride channel EriC. This domain is found in the EriC chloride transporters that mediate the extreme acid resistance response in eubacteria and archaea. This response allows bacteria to survive in the acidic environments by decarboxylation-...; Region: EriC; cd01031 998088010423 Voltage gated chloride channel; Region: Voltage_CLC; pfam00654 998088010424 Cl- selectivity filter; other site 998088010425 Cl- binding residues [ion binding]; other site 998088010426 pore gating glutamate residue; other site 998088010427 dimer interface [polypeptide binding]; other site 998088010428 H+/Cl- coupling transport residue; other site 998088010429 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 998088010430 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase...; Region: OAT_like; cd00610 998088010431 inhibitor-cofactor binding pocket; inhibition site 998088010432 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088010433 catalytic residue [active] 998088010434 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 998088010435 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 998088010436 DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a...; Region: DsbA_Com1_like; cd03023 998088010437 catalytic residues [active] 998088010438 ATP-dependent helicase HepA; Validated; Region: PRK04914 998088010439 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 998088010440 ATP binding site [chemical binding]; other site 998088010441 putative Mg++ binding site [ion binding]; other site 998088010442 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 998088010443 nucleotide binding region [chemical binding]; other site 998088010444 ATP-binding site [chemical binding]; other site 998088010445 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF...; Region: PseudoU_synth_RluCD_like; cd02869 998088010446 active site 998088010447 maltose O-acetyltransferase; Provisional; Region: PRK10092 998088010448 Maltose O-acetyltransferase (MAT) and Galactoside O-acetyltransferase (GAT): MAT and GAT catalyze the CoA-dependent acetylation of the 6-hydroxyl group of their respective sugar substrates. MAT acetylates maltose and glucose exclusively at the C6...; Region: LbH_MAT_GAT; cd03357 998088010449 active site 998088010450 substrate binding site [chemical binding]; other site 998088010451 trimer interface [polypeptide binding]; other site 998088010452 CoA binding site [chemical binding]; other site 998088010453 trehalose-6-phosphate hydrolase; Provisional; Region: PRK10933 998088010454 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 998088010455 PTS system trehalose(maltose)-specific transporter subunits IIBC; Provisional; Region: PRK11007 998088010456 PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIB_glc; cd00212 998088010457 active site turn [active] 998088010458 phosphorylation site [posttranslational modification] 998088010459 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 998088010460 trehalose repressor; Provisional; Region: treR; PRK09492 998088010461 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 998088010462 DNA binding site [nucleotide binding] 998088010463 domain linker motif; other site 998088010464 Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_TreR_like; cd01542 998088010465 dimerization interface [polypeptide binding]; other site 998088010466 ligand binding site [chemical binding]; other site 998088010467 Membrane transport protein; Region: Mem_trans; cl09117 998088010468 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 998088010469 metal-binding site [ion binding] 998088010470 Asparaginase (amidohydrolase): Asparaginases are tetrameric enzymes that catalyze the hydrolysis of asparagine to aspartic acid and ammonia. In bacteria, there are two classes of amidohydrolases, one highly specific for asparagine and localised to the...; Region: Asparaginase; cd00411 998088010471 active site/substrate binding site [active] 998088010472 tetramer interface [polypeptide binding]; other site 998088010473 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 998088010474 Domain of unknown function DUF21; Region: DUF21; pfam01595 998088010475 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in...; Region: CBS_pair_CorC_HlyC_assoc; cd04590 998088010476 Transporter associated domain; Region: CorC_HlyC; cl08393 998088010477 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 998088010478 Beta-lactamase; Region: Beta-lactamase; cl01009 998088010479 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 998088010480 Global regulator protein family; Region: CsrA; cl00670 998088010481 aspartate kinase; Reviewed; Region: PRK06635 998088010482 AAK_AKii-LysC-BS: Amino Acid Kinase Superfamily (AAK), AKii; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, and the lysine plus threonine-sensitive...; Region: AAK_AKii-LysC-BS; cd04261 998088010483 putative nucleotide binding site [chemical binding]; other site 998088010484 putative catalytic residues [active] 998088010485 putative Mg ion binding site [ion binding]; other site 998088010486 putative aspartate binding site [chemical binding]; other site 998088010487 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins; Region: ACT_AKii-LysC-BS-like_1; cd04913 998088010488 putative allosteric regulatory site; other site 998088010489 ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains; Region: ACT_AKii-LysC-BS-like_2; cd04936 998088010490 putative allosteric regulatory residue; other site 998088010491 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 998088010492 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation...; Region: AlaRS_core; cd00673 998088010493 motif 1; other site 998088010494 active site 998088010495 motif 2; other site 998088010496 motif 3; other site 998088010497 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 998088010498 DHHA1 domain; Region: DHHA1; pfam02272 998088010499 RecX family; Region: RecX; cl00936 998088010500 recombinase A; Provisional; Region: recA; PRK09354 998088010501 RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange; Region: recA; cd00983 998088010502 hexamer interface [polypeptide binding]; other site 998088010503 Walker A motif; other site 998088010504 ATP binding site [chemical binding]; other site 998088010505 Walker B motif; other site 998088010506 Competence-damaged protein; Region: CinA; cl00666 998088010507 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 998088010508 MutS domain I; Region: MutS_I; pfam01624 998088010509 MutS domain II; Region: MutS_II; pfam05188 998088010510 MutS family domain IV; Region: MutS_IV; pfam05190 998088010511 MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal...; Region: ABC_MutS1; cd03284 998088010512 Walker A/P-loop; other site 998088010513 ATP binding site [chemical binding]; other site 998088010514 Q-loop/lid; other site 998088010515 ABC transporter signature motif; other site 998088010516 Walker B; other site 998088010517 D-loop; other site 998088010518 H-loop/switch region; other site 998088010519 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: COG4667 998088010520 Hypothetical patatin similar to yjju protein of Escherichia coli; Region: Pat_hypo_Ecoli_yjju_like; cd07208 998088010521 active site 998088010522 nucleophile elbow; other site 998088010523 LrgB-like family; Region: LrgB; cl00596 998088010524 LrgA family; Region: LrgA; cl00608 998088010525 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088010526 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088010527 The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; Region: PBP2_CidR; cd08438 998088010528 putative dimerization interface [polypeptide binding]; other site 998088010529 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]; Region: HisJ; COG0834 998088010530 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cl01709 998088010531 This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia coli and other related bacterial proteins. These trans-acting, single-domain proteins are homologs of ProX and also the cis-acting prolyl-tRNA synthetase (ProRS); Region: YbaK_deacylase; cd00002 998088010532 putative deacylase active site [active] 998088010533 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088010534 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 998088010535 non-specific DNA binding site [nucleotide binding]; other site 998088010536 salt bridge; other site 998088010537 sequence-specific DNA binding site [nucleotide binding]; other site 998088010538 Domain of unknown function (DUF955); Region: DUF955; cl01076 998088010539 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09240 998088010540 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster...; Region: Radical_SAM; cd01335 998088010541 FeS/SAM binding site; other site 998088010542 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 998088010543 Thiazole synthase (ThiG) is the tetrameric enzyme that is involved in the formation of the thiazole moiety of thiamin pyrophosphate, an essential ubiquitous cofactor that plays an important role in carbohydrate and amino acid metabolism. ThiG catalyzes...; Region: ThiG; cd04728 998088010544 ThiS interaction site; other site 998088010545 putative active site [active] 998088010546 tetramer interface [polypeptide binding]; other site 998088010547 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 998088010548 thiS-thiF/thiG interaction site; other site 998088010549 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 998088010550 ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of...; Region: ThiF_MoeB_HesA_family; cd00757 998088010551 ATP binding site [chemical binding]; other site 998088010552 substrate interface [chemical binding]; other site 998088010553 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of...; Region: HMPP_kinase; cd01169 998088010554 dimer interface [polypeptide binding]; other site 998088010555 HMP-P kinase/thiamin-monophosphate pyrophosphorylase; Region: PLN02898 998088010556 substrate binding site [chemical binding]; other site 998088010557 ATP binding site [chemical binding]; other site 998088010558 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-...; Region: TMP_TenI; cd00564 998088010559 thiamine phosphate binding site [chemical binding]; other site 998088010560 active site 998088010561 pyrophosphate binding site [ion binding]; other site 998088010562 ThiC family; Region: ThiC; cl08031 998088010563 Aerolysin/Pertussis toxin (APT) domain; Region: APT; pfam03440 998088010564 Aerolysin toxin; Region: Aerolysin; cl03107 998088010565 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 998088010566 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088010567 active site 998088010568 phosphorylation site [posttranslational modification] 998088010569 intermolecular recognition site; other site 998088010570 dimerization interface [polypeptide binding]; other site 998088010571 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 998088010572 DNA binding site [nucleotide binding] 998088010573 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 998088010574 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cl00080 998088010575 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 998088010576 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 998088010577 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 998088010578 Homocysteine/selenocysteine methylase (S-methylmethionine-dependent) [Amino acid transport and metabolism]; Region: MHT1; cl14105 998088010579 MeTr subgroup of pterin binding enzymes. This family includes cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). Cobalamin-dependent...; Region: MeTr; cd00740 998088010580 substrate binding pocket [chemical binding]; other site 998088010581 B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy); Region: methionine_synthase_B12_BD; cd02069 998088010582 B12 binding site [chemical binding]; other site 998088010583 cobalt ligand [ion binding]; other site 998088010584 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 998088010585 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 998088010586 Transcriptional regulators [Transcription]; Region: PurR; COG1609 998088010587 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 998088010588 DNA binding site [nucleotide binding] 998088010589 domain linker motif; other site 998088010590 Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism; Region: PBP1_GalS_like; cd06270 998088010591 dimerization interface (closed form) [polypeptide binding]; other site 998088010592 ligand binding site [chemical binding]; other site 998088010593 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088010594 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088010595 aspartate aminotransferase; Provisional; Region: PRK08361 998088010596 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 998088010597 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088010598 homodimer interface [polypeptide binding]; other site 998088010599 catalytic residue [active] 998088010600 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 998088010601 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088010602 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 998088010603 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 998088010604 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This...; Region: Alpha_ANH_like_IV; cd01994 998088010605 Ligand Binding Site [chemical binding]; other site 998088010606 metabolite-proton symporter; Region: 2A0106; TIGR00883 998088010607 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088010608 putative substrate translocation pore; other site 998088010609 MarC family integral membrane protein; Region: MarC; cl00919 998088010610 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 998088010611 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 998088010612 Predicted amidohydrolase [General function prediction only]; Region: COG0388 998088010613 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 998088010614 putative active site [active] 998088010615 catalytic triad [active] 998088010616 dimer interface [polypeptide binding]; other site 998088010617 TIGR02099 family protein; Region: TIGR02099 998088010618 ribonuclease G; Provisional; Region: PRK11712 998088010619 S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and...; Region: S1_RNase_E; cd04453 998088010620 homodimer interface [polypeptide binding]; other site 998088010621 oligonucleotide binding site [chemical binding]; other site 998088010622 Maf-like protein; Region: Maf; pfam02545 998088010623 Nucleotide binding protein Maf. Maf has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea, but homologs in B.subtilis and S.cerevisiae are nonessential for cell division. Maf has been predicted to be a nucleotide- or...; Region: Maf; cd00555 998088010624 active site 998088010625 dimer interface [polypeptide binding]; other site 998088010626 rod shape-determining protein MreD; Region: MreD; cl01087 998088010627 rod shape-determining protein MreC; Region: mreC; TIGR00219 998088010628 rod shape-determining protein MreC; Region: MreC; pfam04085 998088010629 rod shape-determining protein MreB; Provisional; Region: PRK13927 998088010630 hypothetical protein; Provisional; Region: PRK10039 998088010631 Cell division protein FtsA; Region: FtsA; cl11496 998088010632 legume lectins; Region: lectin_L-type; cl14058 998088010633 homotetramer interaction site [polypeptide binding]; other site 998088010634 homodimer interaction site [polypeptide binding]; other site 998088010635 carbohydrate binding site [chemical binding]; other site 998088010636 metal binding site [ion binding]; metal-binding site 998088010637 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 998088010638 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 998088010639 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 998088010640 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 998088010641 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 998088010642 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 998088010643 Walker A motif; other site 998088010644 ATP binding site [chemical binding]; other site 998088010645 Walker B motif; other site 998088010646 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi...; Region: TPR; cd00189 998088010647 binding surface 998088010648 TPR motif; other site 998088010649 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088010650 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 998088010651 outer membrane porin HofQ; Provisional; Region: hofQ; PRK10560 998088010652 Secretin N-terminal domain; Region: Secretin_N_2; pfam07655 998088010653 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 998088010654 type III secretion apparatus protein, YscD/HrpQ family; Region: type_III_yscD; TIGR02500 998088010655 Tfp pilus assembly protein, ATPase PilM [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilM; COG4972 998088010656 1-aminocyclopropane-1-carboxylate deaminase [Amino acid transport and metabolism]; Region: Acd; COG2515 998088010657 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD)...; Region: Trp-synth-beta_II; cl00342 998088010658 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 998088010659 catalytic residue [active] 998088010660 regulatory protein CsrD; Provisional; Region: PRK11059 998088010661 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088010662 metal binding site [ion binding]; metal-binding site 998088010663 active site 998088010664 I-site; other site 998088010665 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 998088010666 Predicted signal transduction protein containing sensor and EAL domains [Signal transduction mechanisms]; Region: COG4943 998088010667 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 998088010668 calcium/sodium:proton antiporter; Provisional; Region: PRK10599 998088010669 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 998088010670 tyrosine 2,3-aminomutase; Region: Tyr_2_3_mutase; TIGR03832 998088010671 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 998088010672 active sites [active] 998088010673 tetramer interface [polypeptide binding]; other site 998088010674 urocanate hydratase; Provisional; Region: PRK05414 998088010675 urocanate hydratase; Region: hutU; TIGR01228 998088010676 Arginase family; Region: Arginase; cl00306 998088010677 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 998088010678 Imidazolonepropionase/imidazolone-5-propionate hydrolase (Imidazolone-5PH) catalyzes the third step in the histidine degradation pathway, the hydrolysis of (S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate to N-formimidoyl-L-glutamate. In bacteria...; Region: Imidazolone-5PH; cd01296 998088010679 active site 998088010680 histidine utilization repressor, proteobacterial; Region: his_ut_repres; TIGR02018 998088010681 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 998088010682 DNA-binding site [nucleotide binding]; DNA binding site 998088010683 UTRA domain; Region: UTRA; cl01230 998088010684 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeA; cd00883 998088010685 active site clefts [active] 998088010686 zinc binding site [ion binding]; other site 998088010687 dimer interface [polypeptide binding]; other site 998088010688 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 998088010689 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 998088010690 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial...; Region: Sigma70_r4; cd06171 998088010691 DNA binding residues [nucleotide binding] 998088010692 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 998088010693 FtsX-like permease family; Region: FtsX; pfam02687 998088010694 cell division protein FtsE; Provisional; Region: PRK10908 998088010695 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088010696 Walker A/P-loop; other site 998088010697 ATP binding site [chemical binding]; other site 998088010698 Q-loop/lid; other site 998088010699 ABC transporter signature motif; other site 998088010700 Walker B; other site 998088010701 D-loop; other site 998088010702 H-loop/switch region; other site 998088010703 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 998088010704 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 998088010705 The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The...; Region: SRP; cd03115 998088010706 P loop; other site 998088010707 GTP binding site [chemical binding]; other site 998088010708 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cd02440 998088010709 S-adenosylmethionine binding site [chemical binding]; other site 998088010710 Protein of unknown function (DUF1145); Region: DUF1145; cl11481 998088010711 Predicted transcriptional regulator [Transcription]; Region: COG2378 998088010712 Invasion gene expression up-regulator, SirB; Region: SirB; cl01184 998088010713 glutathione-regulated potassium-efflux system protein KefC; Provisional; Region: PRK03562 998088010714 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 998088010715 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088010716 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 998088010717 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088010718 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088010719 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 998088010720 dimerization interface [polypeptide binding]; other site 998088010721 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088010722 NAD(P) binding site [chemical binding]; other site 998088010723 active site 998088010724 Protein of unknown function, DUF; Region: DUF411; cl01142 998088010725 protease 2; Provisional; Region: PRK10115 998088010726 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 998088010727 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 998088010728 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 998088010729 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088010730 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088010731 Domain of unknown function (DUF3394); Region: DUF3394; pfam11874 998088010732 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 998088010733 putative active site [active] 998088010734 catalytic site [active] 998088010735 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 998088010736 putative active site [active] 998088010737 catalytic site [active] 998088010738 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088010739 substrate binding pocket [chemical binding]; other site 998088010740 membrane-bound complex binding site; other site 998088010741 hinge residues; other site 998088010742 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 998088010743 N-acetyl-D-glucosamine binding site [chemical binding]; other site 998088010744 catalytic residue [active] 998088010745 Protein of unknown function (DUF406); Region: DUF406; cl11449 998088010746 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 998088010747 DNA-binding transcriptional regulator YidZ; Provisional; Region: PRK10216 998088010748 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088010749 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 998088010750 substrate binding pocket [chemical binding]; other site 998088010751 dimerization interface [polypeptide binding]; other site 998088010752 MarC family integral membrane protein; Region: MarC; cl00919 998088010753 Protein of unknown function (DUF2492); Region: DUF2492; cl11278 998088010754 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 998088010755 LysR family transcriptional regulator; Provisional; Region: PRK14997 998088010756 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088010757 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 998088010758 putative effector binding pocket; other site 998088010759 dimerization interface [polypeptide binding]; other site 998088010760 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 998088010761 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 998088010762 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 998088010763 putative substrate translocation pore; other site 998088010764 YhhN-like protein; Region: YhhN; cl01505 998088010765 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 998088010766 Di-iron ligands [ion binding]; other site 998088010767 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 998088010768 DNA-binding transcriptional repressor FabR; Provisional; Region: PRK11202 998088010769 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088010770 Protein of unknown function (DUF1422); Region: DUF1422; cl11649 998088010771 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cd01427 998088010772 active site 998088010773 motif I; other site 998088010774 motif II; other site 998088010775 elongation factor Tu; Reviewed; Region: PRK00049 998088010776 EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors; Region: EF_Tu; cd01884 998088010777 G1 box; other site 998088010778 GEF interaction site [polypeptide binding]; other site 998088010779 GTP/Mg2+ binding site [chemical binding]; other site 998088010780 Switch I region; other site 998088010781 G2 box; other site 998088010782 G3 box; other site 998088010783 Switch II region; other site 998088010784 G4 box; other site 998088010785 G5 box; other site 998088010786 EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the...; Region: EFTU_II; cd03697 998088010787 Domain III of elongation factor (EF) Tu. Ef-Tu consists of three structural domains, designated I, II and III. Domain III adopts a beta barrel structure. Domain III is involved in binding to both charged tRNA and binding to elongation factor Ts (EF-Ts)...; Region: EFTU_III; cd03707 998088010788 Antibiotic Binding Site [chemical binding]; other site 998088010789 elongation factor G; Reviewed; Region: PRK00007 998088010790 Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved...; Region: EF-G; cd01886 998088010791 G1 box; other site 998088010792 putative GEF interaction site [polypeptide binding]; other site 998088010793 GTP/Mg2+ binding site [chemical binding]; other site 998088010794 Switch I region; other site 998088010795 G2 box; other site 998088010796 G3 box; other site 998088010797 Switch II region; other site 998088010798 G4 box; other site 998088010799 G5 box; other site 998088010800 EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide...; Region: EFG_mtEFG_II; cd04088 998088010801 EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor...; Region: EFG_mtEFG1_IV; cd01434 998088010802 EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor...; Region: EFG_mtEFG_C; cd03713 998088010803 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 998088010804 S12-like family, 30S ribosomal protein S12 subfamily; S12 is located at the interface of the large and small ribosomal subunits of prokaryotes, chloroplasts and mitochondria, where it plays an important role in both tRNA and ribosomal subunit...; Region: Ribosomal_S12; cd03368 998088010805 S17 interaction site [polypeptide binding]; other site 998088010806 S8 interaction site; other site 998088010807 16S rRNA interaction site [nucleotide binding]; other site 998088010808 streptomycin interaction site [chemical binding]; other site 998088010809 23S rRNA interaction site [nucleotide binding]; other site 998088010810 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 998088010811 DsrE/DsrF-like family; Region: DrsE; cl00672 998088010812 DsrE/DsrF-like family; Region: DrsE; cl00672 998088010813 DsrE/DsrF-like family; Region: DrsE; cl00672 998088010814 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 998088010815 homotrimer interaction site [polypeptide binding]; other site 998088010816 putative active site [active] 998088010817 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2964 998088010818 YheO-like PAS domain; Region: PAS_6; pfam08348 998088010819 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 998088010820 DNA-directed RNA polymerase, beta' subunit, predominant form; Region: rpoC_TIGR; TIGR02386 998088010821 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 998088010822 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 998088010823 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 998088010824 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 998088010825 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 998088010826 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 998088010827 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 998088010828 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 998088010829 DNA binding site [nucleotide binding] 998088010830 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 998088010831 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl04593 998088010832 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 998088010833 RNA polymerase beta subunit; Region: RNA_pol_Rpb2_1; cl04591 998088010834 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cd00653 998088010835 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl04593 998088010836 RPB11 interaction site [polypeptide binding]; other site 998088010837 RPB12 interaction site [polypeptide binding]; other site 998088010838 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cd00653 998088010839 RPB3 interaction site [polypeptide binding]; other site 998088010840 RPB1 interaction site [polypeptide binding]; other site 998088010841 RPB11 interaction site [polypeptide binding]; other site 998088010842 RPB10 interaction site [polypeptide binding]; other site 998088010843 Ribosomal protein L7/L12. Ribosomal protein L7/L12 refers to the large ribosomal subunit proteins L7 and L12, which are identical except that L7 is acetylated at the N terminus. It is a component of the L7/L12 stalk, which is located at the surface of...; Region: Ribosomal_L7_L12; cd00387 998088010844 core dimer interface [polypeptide binding]; other site 998088010845 peripheral dimer interface [polypeptide binding]; other site 998088010846 L10 interface [polypeptide binding]; other site 998088010847 L11 interface [polypeptide binding]; other site 998088010848 putative EF-Tu interaction site [polypeptide binding]; other site 998088010849 putative EF-G interaction site [polypeptide binding]; other site 998088010850 Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11...; Region: Ribosomal_L10; cd05797 998088010851 23S rRNA interface [nucleotide binding]; other site 998088010852 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 998088010853 Ribosomal protein L1. The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA. In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that...; Region: Ribosomal_L1; cd00403 998088010854 mRNA/rRNA interface [nucleotide binding]; other site 998088010855 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 998088010856 Ribosomal protein L11. Ribosomal protein L11, together with proteins L10 and L7/L12, and 23S rRNA, form the L7/L12 stalk on the surface of the large subunit of the ribosome. The homologous eukaryotic cytoplasmic protein is also called 60S ribosomal...; Region: Ribosomal_L11; cd00349 998088010857 23S rRNA interface [nucleotide binding]; other site 998088010858 L7/L12 interface [polypeptide binding]; other site 998088010859 putative thiostrepton binding site; other site 998088010860 L25 interface [polypeptide binding]; other site 998088010861 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 998088010862 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 998088010863 putative homodimer interface [polypeptide binding]; other site 998088010864 KOW motif; Region: KOW; cl00354 998088010865 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 998088010866 elongation factor Tu; Reviewed; Region: PRK00049 998088010867 EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors; Region: EF_Tu; cd01884 998088010868 G1 box; other site 998088010869 GEF interaction site [polypeptide binding]; other site 998088010870 GTP/Mg2+ binding site [chemical binding]; other site 998088010871 Switch I region; other site 998088010872 G2 box; other site 998088010873 G3 box; other site 998088010874 Switch II region; other site 998088010875 G4 box; other site 998088010876 G5 box; other site 998088010877 EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the...; Region: EFTU_II; cd03697 998088010878 Domain III of elongation factor (EF) Tu. Ef-Tu consists of three structural domains, designated I, II and III. Domain III adopts a beta barrel structure. Domain III is involved in binding to both charged tRNA and binding to elongation factor Ts (EF-Ts)...; Region: EFTU_III; cd03707 998088010879 Antibiotic Binding Site [chemical binding]; other site 998088010880 pantothenate kinase; Provisional; Region: PRK05439 998088010881 Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway. The reaction carried out by this enzyme is a key regulatory point in...; Region: PanK; cd02025 998088010882 ATP-binding site [chemical binding]; other site 998088010883 CoA-binding site [chemical binding]; other site 998088010884 Mg2+-binding site [ion binding]; other site 998088010885 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088010886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 998088010887 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 998088010888 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 998088010889 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 998088010890 FAD binding domain; Region: FAD_binding_4; pfam01565 998088010891 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 998088010892 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 998088010893 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088010894 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088010895 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 998088010896 Cation transport protein; Region: TrkH; cl10514 998088010897 Cation transport protein; Region: TrkH; cl10514 998088010898 Cupin domain; Region: Cupin_2; cl09118 998088010899 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 998088010900 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 998088010901 Protein of unknown function, DUF417; Region: DUF417; cl01162 998088010902 DNA topoisomerase III; Provisional; Region: PRK07726 998088010903 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by:...; Region: TOPRIM_TopoIA_TopoIII; cd03362 998088010904 active site 998088010905 putative interdomain interaction site [polypeptide binding]; other site 998088010906 putative metal-binding site [ion binding]; other site 998088010907 putative nucleotide binding site [chemical binding]; other site 998088010908 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded...; Region: TOP1Ac; cd00186 998088010909 domain I; other site 998088010910 DNA binding groove [nucleotide binding] 998088010911 phosphate binding site [ion binding]; other site 998088010912 domain II; other site 998088010913 domain III; other site 998088010914 nucleotide binding site [chemical binding]; other site 998088010915 catalytic site [active] 998088010916 domain IV; other site 998088010917 Response regulator receiver domain; Region: Response_reg; pfam00072 998088010918 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088010919 active site 998088010920 phosphorylation site [posttranslational modification] 998088010921 intermolecular recognition site; other site 998088010922 dimerization interface [polypeptide binding]; other site 998088010923 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cl09944 998088010924 active site 998088010925 phosphorylation site [posttranslational modification] 998088010926 intermolecular recognition site; other site 998088010927 dimerization interface [polypeptide binding]; other site 998088010928 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 998088010929 ligand binding site [chemical binding]; other site 998088010930 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 998088010931 flexible hinge region; other site 998088010932 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cl00080 998088010933 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 998088010934 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088010935 ATP binding site [chemical binding]; other site 998088010936 Mg2+ binding site [ion binding]; other site 998088010937 G-X-G motif; other site 998088010938 trimethylamine-N-oxide reductase c-type cytochrome TorC; Region: torC; TIGR02162 998088010939 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl09485 998088010940 The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_DMSOR-BSOR-TMAOR; cd02769 998088010941 molybdopterin guanine dinucleotide-containing S/N-oxide reductases; Region: bisC_fam; TIGR00509 998088010942 molybdopterin cofactor binding site [chemical binding]; other site 998088010943 substrate binding site [chemical binding]; other site 998088010944 The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_CT_DMSOR-BSOR-TMAOR; cd02793 998088010945 molybdopterin cofactor binding site; other site 998088010946 sensor protein PhoQ; Provisional; Region: PRK10815 998088010947 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088010948 ATP binding site [chemical binding]; other site 998088010949 Mg2+ binding site [ion binding]; other site 998088010950 G-X-G motif; other site 998088010951 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 998088010952 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088010953 active site 998088010954 phosphorylation site [posttranslational modification] 998088010955 intermolecular recognition site; other site 998088010956 dimerization interface [polypeptide binding]; other site 998088010957 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 998088010958 DNA binding site [nucleotide binding] 998088010959 Ferric reductase like transmembrane component; Region: Ferric_reduct; cl01043 998088010960 Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the...; Region: SO_family_Moco; cl00199 998088010961 Moco binding site; other site 998088010962 metal coordination site [ion binding]; other site 998088010963 Protein of unknown function (DUF1097); Region: DUF1097; pfam06496 998088010964 response regulator GlrR; Provisional; Region: PRK15115 998088010965 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088010966 active site 998088010967 phosphorylation site [posttranslational modification] 998088010968 intermolecular recognition site; other site 998088010969 dimerization interface [polypeptide binding]; other site 998088010970 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088010971 Walker A motif; other site 998088010972 ATP binding site [chemical binding]; other site 998088010973 Walker B motif; other site 998088010974 arginine finger; other site 998088010975 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 998088010976 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088010977 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 998088010978 dimer interface [polypeptide binding]; other site 998088010979 phosphorylation site [posttranslational modification] 998088010980 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088010981 ATP binding site [chemical binding]; other site 998088010982 Mg2+ binding site [ion binding]; other site 998088010983 G-X-G motif; other site 998088010984 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088010985 dihydromonapterin reductase; Provisional; Region: PRK06483 998088010986 NAD(P) binding site [chemical binding]; other site 998088010987 active site 998088010988 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-...; Region: CBS_pair_16; cd04629 998088010989 Uncharacterized integral membrane protein (DUF2301); Region: DUF2301; cl02241 998088010990 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088010991 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088010992 substrate binding pocket [chemical binding]; other site 998088010993 membrane-bound complex binding site; other site 998088010994 hinge residues; other site 998088010995 DNA-binding transcriptional regulator AsnC; Provisional; Region: PRK11179 998088010996 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088010997 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 998088010998 motif 1; other site 998088010999 dimer interface [polypeptide binding]; other site 998088011000 active site 998088011001 motif 2; other site 998088011002 motif 3; other site 998088011003 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 998088011004 Clp amino terminal domain; Region: Clp_N; pfam02861 998088011005 Clp amino terminal domain; Region: Clp_N; pfam02861 998088011006 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088011007 Walker A motif; other site 998088011008 ATP binding site [chemical binding]; other site 998088011009 Walker B motif; other site 998088011010 arginine finger; other site 998088011011 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088011012 Walker A motif; other site 998088011013 ATP binding site [chemical binding]; other site 998088011014 Walker B motif; other site 998088011015 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 998088011016 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 998088011017 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 998088011018 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 998088011019 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 998088011020 RNA binding surface [nucleotide binding]; other site 998088011021 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF...; Region: PseudoU_synth_RluCD_like; cd02869 998088011022 active site 998088011023 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 998088011024 coenzyme A disulfide reductase; Reviewed; Region: PRK09564 998088011025 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088011026 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 998088011027 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 998088011028 L-cysteine desulfidase [Amino acid transport and metabolism]; Region: COG3681 998088011029 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 998088011030 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 998088011031 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2964 998088011032 YheO-like PAS domain; Region: PAS_6; pfam08348 998088011033 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088011034 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088011035 substrate binding pocket [chemical binding]; other site 998088011036 membrane-bound complex binding site; other site 998088011037 hinge residues; other site 998088011038 NAD(P) transhydrogenase beta subunit; Region: PNTB; cl00566 998088011039 NAD(P) transhydrogenase subunit alpha; Provisional; Region: pntA; PRK09424 998088011040 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; pfam05222 998088011041 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088011042 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 998088011043 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 998088011044 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 998088011045 dimer interface [polypeptide binding]; other site 998088011046 active site 998088011047 metal binding site [ion binding]; metal-binding site 998088011048 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 998088011049 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088011050 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 998088011051 Lipocalin / cytosolic fatty-acid binding protein family; Region: Lipocalin; cl01150 998088011052 Cache domain; Region: Cache_1; pfam02743 998088011053 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088011054 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088011055 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088011056 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 998088011057 active site 998088011058 metal binding site [ion binding]; metal-binding site 998088011059 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088011060 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088011061 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 998088011062 dimerization interface [polypeptide binding]; other site 998088011063 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 998088011064 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 998088011065 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088011066 aspartate carbamoyltransferase regulatory subunit; Reviewed; Region: PRK00893 998088011067 Aspartate carbamoyltransferase regulatory chain, allosteric domain; Region: PyrI; pfam01948 998088011068 Aspartate carbamoyltransferase regulatory chain, metal binding domain; Region: PyrI_C; pfam02748 998088011069 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 998088011070 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 998088011071 ornithine decarboxylase; Provisional; Region: PRK13578 998088011072 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cl09944 998088011073 Ornithine decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to ornithine decarboxylase (ODC), arginine decarboxylase (ADC) and...; Region: Orn_deC_like; cd00615 998088011074 homodimer interface [polypeptide binding]; other site 998088011075 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088011076 catalytic residue [active] 998088011077 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 998088011078 ornithine carbamoyltransferase; Validated; Region: PRK02102 998088011079 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 998088011080 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088011081 carbamate kinase; Reviewed; Region: PRK09411 998088011082 AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP. Both CK (this CD) and nonhomologous CP synthetase synthesize carbamoyl phosphate, an...; Region: AAK_CK; cd04235 998088011083 putative substrate binding site [chemical binding]; other site 998088011084 nucleotide binding site [chemical binding]; other site 998088011085 nucleotide binding site [chemical binding]; other site 998088011086 homodimer interface [polypeptide binding]; other site 998088011087 Amidinotransferase; Region: Amidinotransf; cl12043 998088011088 ParA-like protein; Provisional; Region: PHA02518 998088011089 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following...; Region: ParA; cd02042 998088011090 P-loop; other site 998088011091 Magnesium ion binding site [ion binding]; other site 998088011092 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 998088011093 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster...; Region: Radical_SAM; cd01335 998088011094 FeS/SAM binding site; other site 998088011095 HemN C-terminal region; Region: HemN_C; pfam06969 998088011096 Protein of unknown function (DUF2489); Region: DUF2489; pfam10675 998088011097 Protein of unknown function, DUF414; Region: DUF414; cl01172 998088011098 Cytochrome c; Region: Cytochrom_C; cl11414 998088011099 Cytochrome c; Region: Cytochrom_C; cl11414 998088011100 The YihA (EngB) subfamily. This subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and...; Region: YihA_EngB; cd01876 998088011101 G1 box; other site 998088011102 GTP/Mg2+ binding site [chemical binding]; other site 998088011103 Switch I region; other site 998088011104 G2 box; other site 998088011105 G3 box; other site 998088011106 Switch II region; other site 998088011107 G4 box; other site 998088011108 G5 box; other site 998088011109 Protein of unknown function (DUF1488); Region: DUF1488; pfam07369 998088011110 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 998088011111 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 998088011112 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 998088011113 shikimate binding site; other site 998088011114 NAD(P) binding site [chemical binding]; other site 998088011115 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl00433 998088011116 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 998088011117 AIR carboxylase; Region: AIRC; cl00310 998088011118 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 998088011119 Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]; Region: TopA; COG0551 998088011120 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 998088011121 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 998088011122 Protein of unknown function (DUF494); Region: DUF494; cl01103 998088011123 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 998088011124 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 998088011125 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 998088011126 Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(...; Region: Pep_deformylase; cd00487 998088011127 active site 998088011128 catalytic residues [active] 998088011129 metal binding site [ion binding]; metal-binding site 998088011130 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 998088011131 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 998088011132 putative active site [active] 998088011133 substrate binding site [chemical binding]; other site 998088011134 putative cosubstrate binding site; other site 998088011135 catalytic site [active] 998088011136 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 998088011137 substrate binding site [chemical binding]; other site 998088011138 16S rRNA methyltransferase B; Provisional; Region: PRK10901 998088011139 N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine transferase Sun, also known as RrmB or Fmu shares the RNA-binding non-catalytic domain with the transcription termination factor NusB. The precise biological...; Region: Methyltransferase_Sun; cd00620 998088011140 putative RNA binding site [nucleotide binding]; other site 998088011141 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cd02440 998088011142 S-adenosylmethionine binding site [chemical binding]; other site 998088011143 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 998088011144 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088011145 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088011146 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088011147 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 998088011148 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 998088011149 Cation transport protein; Region: TrkH; cl10514 998088011150 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 998088011151 TypA (tyrosine phosphorylated protein A)/BipA subfamily. BipA is a protein belonging to the ribosome-binding family of GTPases and is widely distributed in bacteria and plants. BipA was originally described as a protein that is induced in Salmonella...; Region: TypA_BipA; cd01891 998088011152 G1 box; other site 998088011153 putative GEF interaction site [polypeptide binding]; other site 998088011154 GTP/Mg2+ binding site [chemical binding]; other site 998088011155 Switch I region; other site 998088011156 G2 box; other site 998088011157 G3 box; other site 998088011158 Switch II region; other site 998088011159 G4 box; other site 998088011160 G5 box; other site 998088011161 BipA_TypA_II: domain II of BipA (also called TypA) having homology to domain II of the elongation factors (EFs) EF-G and EF-Tu. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a...; Region: BipA_TypA_II; cd03691 998088011162 BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants. BipA is a...; Region: BipA_TypA_C; cd03710 998088011163 glutamine synthetase; Provisional; Region: glnA; PRK09469 998088011164 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 998088011165 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 998088011166 nitrogen regulation protein NR(II); Provisional; Region: glnL; PRK11073 998088011167 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 998088011168 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088011169 ATP binding site [chemical binding]; other site 998088011170 Mg2+ binding site [ion binding]; other site 998088011171 G-X-G motif; other site 998088011172 nitrogen regulation protein NR(I); Provisional; Region: glnG; PRK10923 998088011173 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088011174 active site 998088011175 phosphorylation site [posttranslational modification] 998088011176 intermolecular recognition site; other site 998088011177 dimerization interface [polypeptide binding]; other site 998088011178 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 998088011179 Walker A motif; other site 998088011180 ATP binding site [chemical binding]; other site 998088011181 Walker B motif; other site 998088011182 arginine finger; other site 998088011183 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 998088011184 Adenosine deaminase (ADA) is a monomeric zinc dependent enzyme which catalyzes the irreversible hydrolytic deamination of both adenosine, as well as desoxyadenosine, to ammonia and inosine or desoxyinosine, respectively. ADA plays an important role in...; Region: ADA; cd01320 998088011185 active site 998088011186 purine riboside binding site [chemical binding]; other site 998088011187 RmuC family; Region: RmuC; pfam02646 998088011188 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved alpha-; Region: HCP_like; cl14655 998088011189 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 998088011190 Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Energy production and conversion]; Region: NuoI; COG1143 998088011191 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088011192 Rrf2 family protein; Region: rrf2_super; TIGR00738 998088011193 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, 2-...; Region: ribokinase_pfkB_like; cl00192 998088011194 substrate binding site [chemical binding]; other site 998088011195 ATP binding site [chemical binding]; other site 998088011196 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12682 998088011197 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088011198 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088011199 dimerization interface [polypeptide binding]; other site 998088011200 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 998088011201 catalytic triad [active] 998088011202 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 998088011203 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 998088011204 tetrameric interface [polypeptide binding]; other site 998088011205 NAD binding site [chemical binding]; other site 998088011206 catalytic residues [active] 998088011207 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 998088011208 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase...; Region: OAT_like; cd00610 998088011209 inhibitor-cofactor binding pocket; inhibition site 998088011210 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088011211 catalytic residue [active] 998088011212 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 998088011213 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 998088011214 non-specific DNA binding site [nucleotide binding]; other site 998088011215 salt bridge; other site 998088011216 sequence-specific DNA binding site [nucleotide binding]; other site 998088011217 Cupin domain; Region: Cupin_2; cl09118 998088011218 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase; Provisional; Region: PRK09847 998088011219 Escherichia coli NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC-like; Region: ALDH_GABALDH-PuuC; cd07112 998088011220 NAD(P) binding site [chemical binding]; other site 998088011221 catalytic residues [active] 998088011222 putative chloramphenical resistance permease RarD; Provisional; Region: PRK15430 998088011223 EamA-like transporter family; Region: EamA; cl01037 998088011224 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088011225 putative inner membrane protein; Provisional; Region: PRK11099 998088011226 putative inner membrane protein; Provisional; Region: PRK11099 998088011227 outer membrane protein A; Reviewed; Region: PRK10808 998088011228 Surface antigen; Region: Surface_Ag_2; cl01155 998088011229 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088011230 ligand binding site [chemical binding]; other site 998088011231 threonine dehydratase; Reviewed; Region: PRK09224 998088011232 Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly...; Region: Thr-dehyd; cd01562 998088011233 tetramer interface [polypeptide binding]; other site 998088011234 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088011235 catalytic residue [active] 998088011236 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 998088011237 putative Ile/Val binding site [chemical binding]; other site 998088011238 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 998088011239 putative Ile/Val binding site [chemical binding]; other site 998088011240 Dehydratase family; Region: ILVD_EDD; cl00340 998088011241 dihydroxy-acid dehydratase; Region: ilvD; TIGR00110 998088011242 branched-chain amino acid aminotransferase; Provisional; Region: PRK12479 998088011243 BCAT_beta_family: Branched-chain aminotransferase catalyses the transamination of the branched-chain amino acids leusine, isoleucine and valine to their respective alpha-keto acids, alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and alpha-...; Region: BCAT_beta_family; cd01557 998088011244 homodimer interface [polypeptide binding]; other site 998088011245 substrate-cofactor binding pocket; other site 998088011246 catalytic residue [active] 998088011247 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-...; Region: CBS_pair; cl09141 998088011248 acetolactate synthase 2 catalytic subunit; Reviewed; Region: PRK08978 998088011249 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 998088011250 PYR/PP interface [polypeptide binding]; other site 998088011251 dimer interface [polypeptide binding]; other site 998088011252 TPP binding site [chemical binding]; other site 998088011253 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 998088011254 Thiamine pyrophosphate (TPP) family, Acetohydroxyacid synthase (AHAS) subfamily, TPP-binding module; composed of proteins similar to the large catalytic subunit of AHAS. AHAS catalyzes the condensation of two molecules of pyruvate to give the...; Region: TPP_AHAS; cd02015 998088011255 TPP-binding site [chemical binding]; other site 998088011256 dimer interface [polypeptide binding]; other site 998088011257 Mg chelatase-related protein; Region: TIGR00368 998088011258 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 998088011259 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 998088011260 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 998088011261 putative acyl-acceptor binding pocket; other site 998088011262 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 998088011263 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 998088011264 putative acyl-acceptor binding pocket; other site 998088011265 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or...; Region: Nudix_Hydrolase; cl00447 998088011266 Nicotinamidase/pyrazinamidase (PZase). Nicotinamidase, a ubiquitous enzyme in prokaryotes, converts nicotinamide to nicotinic acid (niacin) and ammonia, which in turn can be recycled to make nicotinamide adenine dinucleotide (NAD). The same enzyme is...; Region: nicotinamidase; cd01011 998088011267 catalytic triad [active] 998088011268 metal binding site [ion binding]; metal-binding site 998088011269 conserved cis-peptide bond; other site 998088011270 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 998088011271 Nicotinate phosphoribosyltransferase (NAPRTase), related to PncB. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting...; Region: PncB_like; cd01401 998088011272 active site 998088011273 DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol...; Region: DsbA_DsbA; cd03019 998088011274 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 998088011275 catalytic residues [active] 998088011276 hinge region; other site 998088011277 alpha helical domain; other site 998088011278 Phosphotransferase enzyme family; Region: APH; pfam01636 998088011279 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 998088011280 active site 998088011281 ATP binding site [chemical binding]; other site 998088011282 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 998088011283 4Fe-4S binding domain; Region: Fer4_5; pfam12801 998088011284 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved alpha-; Region: HCP_like; cl14655 998088011285 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 998088011286 Protein of unknown function (DUF1040); Region: DUF1040; cl01176 998088011287 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088011288 metal binding site [ion binding]; metal-binding site 998088011289 active site 998088011290 I-site; other site 998088011291 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 998088011292 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 998088011293 DNA binding residues [nucleotide binding] 998088011294 dimer interface [polypeptide binding]; other site 998088011295 copper binding site [ion binding]; other site 998088011296 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 998088011297 metal-binding site [ion binding] 998088011298 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 998088011299 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 998088011300 metal-binding site [ion binding] 998088011301 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 998088011302 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cd01427 998088011303 motif II; other site 998088011304 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 998088011305 ribonuclease PH; Reviewed; Region: rph; PRK00173 998088011306 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 998088011307 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 998088011308 hypothetical protein; Provisional; Region: PRK11820 998088011309 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 998088011310 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 998088011311 LysR family transcriptional regulator; Provisional; Region: PRK14997 998088011312 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like_1; cd08470 998088011313 putative effector binding pocket; other site 998088011314 putative dimerization interface [polypeptide binding]; other site 998088011315 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 998088011316 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase; Region: adh_III_F_hyde; TIGR02818 998088011317 substrate binding site [chemical binding]; other site 998088011318 catalytic Zn binding site [ion binding]; other site 998088011319 NAD binding site [chemical binding]; other site 998088011320 structural Zn binding site [ion binding]; other site 998088011321 dimer interface [polypeptide binding]; other site 998088011322 Predicted esterase [General function prediction only]; Region: COG0627 998088011323 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 998088011324 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 998088011325 DinB superfamily; Region: DinB_2; cl00986 998088011326 TIGR03440 family protein; Region: unchr_TIGR03440 998088011327 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; cl00556 998088011328 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cd02440 998088011329 S-adenosylmethionine binding site [chemical binding]; other site 998088011330 Membrane transport protein; Region: Mem_trans; cl09117 998088011331 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 998088011332 The tRNA binding domain is also known as the Myf domain in literature. This domain is found in a diverse collection of tRNA binding proteins, including prokaryotic phenylalanyl tRNA synthetases (PheRS), methionyl-tRNA synthetases (MetRS), human tyrosyl-; Region: tRNA_bindingDomain; cl00320 998088011333 putative tRNA-binding site [nucleotide binding]; other site 998088011334 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 998088011335 Domain of unknown function (DUF386); Region: DUF386; cl01047 998088011336 cryptic beta-D-galactosidase subunit alpha; Reviewed; Region: ebgA; PRK10340 998088011337 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 998088011338 domain; Region: Glyco_hydro_2; pfam00703 998088011339 Beta galactosidase small chain; Region: Bgal_small_N; cl03787 998088011340 DNA-binding transcriptional repressor EbgR; Provisional; Region: PRK10339 998088011341 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 998088011342 DNA binding site [nucleotide binding] 998088011343 domain linker motif; other site 998088011344 Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism; Region: PBP1_GalR; cd01544 998088011345 putative dimerization interface [polypeptide binding]; other site 998088011346 putative ligand binding site [chemical binding]; other site 998088011347 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 998088011348 Gamma carbonic anhydrase-like: This family is composed of gamma carbonic anhydrase (CA), Ferripyochelin Binding Protein (FBP), E. coli paaY protein, and similar proteins. CAs are zinc-containing enzymes that catalyze the reversible hydration of carbon...; Region: LbH_gamma_CA_like; cd04645 998088011349 trimer interface [polypeptide binding]; other site 998088011350 putative metal binding site [ion binding]; other site 998088011351 DNA polymerase I; Provisional; Region: PRK05755 998088011352 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 998088011353 active site 998088011354 metal binding site 1 [ion binding]; metal-binding site 998088011355 putative 5' ssDNA interaction site; other site 998088011356 metal binding site 3; metal-binding site 998088011357 metal binding site 2 [ion binding]; metal-binding site 998088011358 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 998088011359 putative DNA binding site [nucleotide binding]; other site 998088011360 putative metal binding site [ion binding]; other site 998088011361 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases; Region: DNA_polA_I_Ecoli_like_exo; cd06139 998088011362 active site 998088011363 catalytic site [active] 998088011364 substrate binding site [chemical binding]; other site 998088011365 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 998088011366 active site 998088011367 DNA binding site [nucleotide binding] 998088011368 catalytic site [active] 998088011369 Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1; Region: GATase1_ES1; cd03133 998088011370 conserved cys residue [active] 998088011371 Protein of unknown function (DUF904); Region: DUF904; cl11531 998088011372 serine acetyltransferase; Provisional; Region: cysE; PRK11132 998088011373 Serine acetyltransferase, N-terminal; Region: SATase_N; cl05762 998088011374 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of L-...; Region: LbH_SAT; cd03354 998088011375 trimer interface [polypeptide binding]; other site 998088011376 active site 998088011377 substrate binding site [chemical binding]; other site 998088011378 CoA binding site [chemical binding]; other site 998088011379 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 998088011380 Cation efflux family; Region: Cation_efflux; cl00316 998088011381 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088011382 active site 998088011383 phosphorylation site [posttranslational modification] 998088011384 intermolecular recognition site; other site 998088011385 dimerization interface [polypeptide binding]; other site 998088011386 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 998088011387 DNA binding site [nucleotide binding] 998088011388 two-component sensor protein; Provisional; Region: cpxA; PRK09470 998088011389 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088011390 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 998088011391 dimer interface [polypeptide binding]; other site 998088011392 phosphorylation site [posttranslational modification] 998088011393 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088011394 ATP binding site [chemical binding]; other site 998088011395 Mg2+ binding site [ion binding]; other site 998088011396 G-X-G motif; other site 998088011397 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 998088011398 putative efflux protein, MATE family; Region: matE; TIGR00797 998088011399 MatE; Region: MatE; cl10513 998088011400 MatE; Region: MatE; cl10513 998088011401 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 998088011402 Cu(I) binding site [ion binding]; other site 998088011403 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088011404 LexA repressor; Validated; Region: PRK00215 998088011405 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (...; Region: S24_LexA-like; cd06529 998088011406 Catalytic site [active] 998088011407 Glycerol-3-phosphate O-acyltransferase [Lipid metabolism]; Region: PlsB; COG2937 998088011408 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT-like; Region: LPLAT_DHAPAT-like; cd07993 998088011409 putative acyl-acceptor binding pocket; other site 998088011410 UbiA prenyltransferase family; Region: UbiA; cl00337 998088011411 UTRA domain; Region: UTRA; cl01230 998088011412 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 998088011413 Protein of unknown function (DUF2799); Region: DUF2799; pfam10973 998088011414 Yhdh putative quinone oxidoreductases; Region: MDR_yhdh; cd08288 998088011415 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 998088011416 NADP binding site [chemical binding]; other site 998088011417 dimer interface [polypeptide binding]; other site 998088011418 Transcriptional regulators [Transcription]; Region: PurR; COG1609 998088011419 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 998088011420 DNA binding site [nucleotide binding] 998088011421 domain linker motif; other site 998088011422 Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_GntR; cd01575 998088011423 putative dimerization interface [polypeptide binding]; other site 998088011424 putative ligand binding site [chemical binding]; other site 998088011425 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 998088011426 active site 998088011427 phosphorylation site [posttranslational modification] 998088011428 PTS_IIB_ascorbate: subunit IIB of enzyme II (EII) of the L-ascorbate-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is an L-ascorbate-specific permease with two cytoplasmic subunits (IIA and IIB) and a...; Region: PTS_IIB_ascorbate; cd05563 998088011429 P-loop; other site 998088011430 active site 998088011431 phosphorylation site [posttranslational modification] 998088011432 PTS system sugar-specific permease component; Region: EIIC-GAT; cl04451 998088011433 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 998088011434 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 998088011435 Glycosyl transferases group 1; Region: Glycos_transf_1; cl12012 998088011436 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 998088011437 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 998088011438 putative active site [active] 998088011439 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 998088011440 putative metal binding site [ion binding]; other site 998088011441 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 998088011442 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 998088011443 putative active site [active] 998088011444 Nicotinic acid mononucleotide adenylyltransferase [Coenzyme metabolism]; Region: NadD; COG1057 998088011445 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 998088011446 active site 998088011447 (T/H)XGH motif; other site 998088011448 Protein of unknown function (DUF535); Region: DUF535; cl01128 998088011449 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 998088011450 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 998088011451 DNA binding site [nucleotide binding] 998088011452 catalytic residue [active] 998088011453 H2TH interface [polypeptide binding]; other site 998088011454 putative catalytic residues [active] 998088011455 turnover-facilitating residue; other site 998088011456 intercalation triad [nucleotide binding]; other site 998088011457 8OG recognition residue [nucleotide binding]; other site 998088011458 putative reading head residues; other site 998088011459 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 998088011460 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 998088011461 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 998088011462 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 998088011463 hypothetical protein; Reviewed; Region: PRK00024 998088011464 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 998088011465 MPN+ (JAMM) motif; other site 998088011466 Zinc-binding site [ion binding]; other site 998088011467 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 998088011468 Flavoprotein; Region: Flavoprotein; cl08021 998088011469 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 998088011470 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 998088011471 trimer interface [polypeptide binding]; other site 998088011472 active site 998088011473 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 998088011474 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 998088011475 DNA binding site [nucleotide binding] 998088011476 Int/Topo IB signature motif; other site 998088011477 active site 998088011478 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 998088011479 RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA...; Region: RT_Bac_retron_II; cd03487 998088011480 putative active site [active] 998088011481 putative NTP binding site [chemical binding]; other site 998088011482 putative nucleic acid binding site [nucleotide binding]; other site 998088011483 Domain in histone-like proteins of HNS family; Region: HNS; cl09251 998088011484 DNA binding protein, nucleoid-associated; Provisional; Region: PRK10328 998088011485 Fic family protein [Function unknown]; Region: COG3177 998088011486 Fic/DOC family; Region: Fic; cl00960 998088011487 Fic/DOC family; Region: Fic; cl00960 998088011488 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088011489 RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons...; Region: RT_like; cl02808 998088011490 active site 998088011491 NTP binding site [chemical binding]; other site 998088011492 nucleic acid binding site [nucleotide binding]; other site 998088011493 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cl00493 998088011494 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 998088011495 active site 998088011496 division inhibitor protein; Provisional; Region: slmA; PRK09480 998088011497 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088011498 mechanosensitive channel MscS; Provisional; Region: PRK10334 998088011499 Conserved TM helix; Region: TM_helix; pfam05552 998088011500 Mechanosensitive ion channel; Region: MS_channel; pfam00924 998088011501 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 998088011502 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the first SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of...; Region: SIS_PGI_1; cd05015 998088011503 active site 998088011504 dimer interface [polypeptide binding]; other site 998088011505 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the second SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of...; Region: SIS_PGI_2; cd05016 998088011506 dimer interface [polypeptide binding]; other site 998088011507 active site 998088011508 ketol-acid reductoisomerase; Validated; Region: PRK05225 998088011509 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088011510 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 998088011511 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 998088011512 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088011513 DNA-binding transcriptional regulator IlvY; Provisional; Region: PRK11716 998088011514 The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic bindin; Region: PBP2_IlvY; cd08430 998088011515 putative dimerization interface [polypeptide binding]; other site 998088011516 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088011517 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 998088011518 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088011519 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 998088011520 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 998088011521 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 998088011522 Cation transport protein; Region: TrkH; cl10514 998088011523 hypothetical protein; Provisional; Region: PRK11568 998088011524 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 998088011525 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 998088011526 proline dipeptidase; Provisional; Region: PRK13607 998088011527 Prolidase. E.C. 3.4.13.9. Also known as Xaa-Pro dipeptidase, X-Pro dipeptidase, proline dipeptidase., imidodipeptidase, peptidase D, gamma-peptidase. Catalyses hydrolysis of Xaa-Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action...; Region: Prolidase; cd01087 998088011528 active site 998088011529 acetoacetyl-CoA synthetase; Provisional; Region: PRK03584 998088011530 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 998088011531 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadB; PRK11730 998088011532 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase...; Region: crotonase-like; cd06558 998088011533 substrate binding site [chemical binding]; other site 998088011534 oxyanion hole (OAH) forming residues; other site 998088011535 trimer interface [polypeptide binding]; other site 998088011536 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 998088011537 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 998088011538 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 998088011539 3-ketoacyl-CoA thiolase; Reviewed; Region: fadA; PRK08947 998088011540 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 998088011541 dimer interface [polypeptide binding]; other site 998088011542 active site 998088011543 osmolarity response regulator; Provisional; Region: ompR; PRK09468 998088011544 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088011545 active site 998088011546 phosphorylation site [posttranslational modification] 998088011547 intermolecular recognition site; other site 998088011548 dimerization interface [polypeptide binding]; other site 998088011549 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 998088011550 DNA binding site [nucleotide binding] 998088011551 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088011552 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 998088011553 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088011554 ATP binding site [chemical binding]; other site 998088011555 Mg2+ binding site [ion binding]; other site 998088011556 G-X-G motif; other site 998088011557 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 998088011558 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 998088011559 SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A...; Region: SirA; cd03423 998088011560 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_2; cd06150 998088011561 homotrimer interaction site [polypeptide binding]; other site 998088011562 putative active site [active] 998088011563 putative outer membrane lipoprotein; Provisional; Region: PRK10510 998088011564 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088011565 ligand binding site [chemical binding]; other site 998088011566 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 998088011567 glycyl-tRNA synthetase, tetrameric type, alpha subunit; Region: glyQ; TIGR00388 998088011568 Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes and in arabidopsis. It is responsible for the...; Region: GlyRS_alpha_core; cd00733 998088011569 dimer interface [polypeptide binding]; other site 998088011570 motif 1; other site 998088011571 active site 998088011572 motif 2; other site 998088011573 motif 3; other site 998088011574 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 998088011575 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 998088011576 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 998088011577 Electron transfer DM13; Region: DM13; cl02735 998088011578 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 998088011579 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088011580 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 998088011581 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 998088011582 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 998088011583 DNA-binding site [nucleotide binding]; DNA binding site 998088011584 UTRA domain; Region: UTRA; cl01230 998088011585 PTS system, alpha-glucoside-specific IIBC component; Region: PTS-IIBC-alpha; TIGR02005 998088011586 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 998088011587 PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIB_glc; cd00212 998088011588 active site turn [active] 998088011589 phosphorylation site [posttranslational modification] 998088011590 Alpha-galactosidases/6-phospho-beta-glucosidases, family 4 of glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: CelF; COG1486 998088011591 Glycoside Hydrolases Family 4; GlvA- and pagL-like glycosidases; Region: GH4_GlvA_pagL_like; cd05298 998088011592 NAD binding site [chemical binding]; other site 998088011593 sugar binding site [chemical binding]; other site 998088011594 divalent metal binding site [ion binding]; other site 998088011595 putative tetramer (dimer of dimers) interface [polypeptide binding]; other site 998088011596 dimer interface [polypeptide binding]; other site 998088011597 DNA-binding transcriptional repressor PurR; Provisional; Region: PRK10703 998088011598 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 998088011599 DNA binding site [nucleotide binding] 998088011600 domain linker motif; other site 998088011601 Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli; Region: PBP1_PurR; cd06275 998088011602 dimerization interface [polypeptide binding]; other site 998088011603 ligand binding site [chemical binding]; other site 998088011604 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 998088011605 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 998088011606 dimerization interface [polypeptide binding]; other site 998088011607 ligand binding site [chemical binding]; other site 998088011608 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 998088011609 TM-ABC transporter signature motif; other site 998088011610 leucine/isoleucine/valine transporter permease subunit; Provisional; Region: livM; PRK11301 998088011611 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 998088011612 TM-ABC transporter signature motif; other site 998088011613 leucine/isoleucine/valine transporter ATP-binding subunit; Provisional; Region: livG; PRK11300 998088011614 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 998088011615 Walker A/P-loop; other site 998088011616 ATP binding site [chemical binding]; other site 998088011617 Q-loop/lid; other site 998088011618 ABC transporter signature motif; other site 998088011619 Walker B; other site 998088011620 D-loop; other site 998088011621 H-loop/switch region; other site 998088011622 leucine/isoleucine/valine transporter ATP-binding subunit; Provisional; Region: livF; PRK11614 998088011623 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 998088011624 Walker A/P-loop; other site 998088011625 ATP binding site [chemical binding]; other site 998088011626 Q-loop/lid; other site 998088011627 ABC transporter signature motif; other site 998088011628 Walker B; other site 998088011629 D-loop; other site 998088011630 H-loop/switch region; other site 998088011631 GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily. Unlike other rhodanese sulfurtransferases, GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a...; Region: GlpE_ST; cd01444 998088011632 active site residue [active] 998088011633 intramembrane serine protease GlpG; Provisional; Region: PRK10907 998088011634 Protein of unknown function (DUF3582); Region: DUF3582; pfam12122 998088011635 Rhomboid family; Region: Rhomboid; cl11446 998088011636 extracellular lipase, Pla-1/cef family; Region: lipase_Pla1_cef; TIGR03502 998088011637 Bacterial virulence factor lipase N-terminal; Region: Lipase_bact_N; pfam12262 998088011638 Membrane fusogenic activity; Region: BMFP; cl01115 998088011639 putative diguanylate cyclase; Provisional; Region: PRK09776 998088011640 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088011641 metal binding site [ion binding]; metal-binding site 998088011642 active site 998088011643 I-site; other site 998088011644 FMN reductase; Validated; Region: fre; PRK08051 998088011645 NAD(P)H dependent flavin oxidoreductases use flavin as a substrate in mediating electron transfer from iron complexes or iron proteins. Structurally similar to ferredoxin reductases, but with only 15% sequence identity, flavin reductases reduce FAD...; Region: flavin_oxioreductase; cd06189 998088011646 FAD binding pocket [chemical binding]; other site 998088011647 FAD binding motif [chemical binding]; other site 998088011648 phosphate binding motif [ion binding]; other site 998088011649 beta-alpha-beta structure motif; other site 998088011650 NAD binding pocket [chemical binding]; other site 998088011651 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 998088011652 transcription termination factor Rho; Provisional; Region: rho; PRK09376 998088011653 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 998088011654 Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent...; Region: Rho_CSD; cd04459 998088011655 RNA binding site [nucleotide binding]; other site 998088011656 Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of...; Region: rho_factor; cd01128 998088011657 multimer interface [polypeptide binding]; other site 998088011658 Walker A motif; other site 998088011659 ATP binding site [chemical binding]; other site 998088011660 Walker B motif; other site 998088011661 TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947 998088011662 catalytic residues [active] 998088011663 ATP-dependent RNA helicase RhlB; Provisional; Region: PRK04837 998088011664 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (...; Region: DEADc; cd00268 998088011665 ATP binding site [chemical binding]; other site 998088011666 Mg++ binding site [ion binding]; other site 998088011667 motif III; other site 998088011668 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 998088011669 nucleotide binding region [chemical binding]; other site 998088011670 ATP-binding site [chemical binding]; other site 998088011671 guanosine pentaphosphate phosphohydrolase; Provisional; Region: PRK11031 998088011672 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 998088011673 Modulator of Rho-dependent transcription termination (ROF); Region: ROF; cl09210 998088011674 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cd02440 998088011675 S-adenosylmethionine binding site [chemical binding]; other site 998088011676 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088011677 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088011678 substrate binding pocket [chemical binding]; other site 998088011679 membrane-bound complex binding site; other site 998088011680 hinge residues; other site 998088011681 PAS domain S-box; Region: sensory_box; TIGR00229 998088011682 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 998088011683 putative active site [active] 998088011684 heme pocket [chemical binding]; other site 998088011685 PAS domain S-box; Region: sensory_box; TIGR00229 998088011686 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 998088011687 putative active site [active] 998088011688 heme pocket [chemical binding]; other site 998088011689 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088011690 metal binding site [ion binding]; metal-binding site 998088011691 active site 998088011692 I-site; other site 998088011693 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 998088011694 oligopeptidase A; Provisional; Region: PRK10911 998088011695 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 998088011696 active site 998088011697 Zn binding site [ion binding]; other site 998088011698 Glycosyl hydrolases family 18; Region: Glyco_hydro_18; pfam00704 998088011699 GH18 domain of Chitinase D (ChiD). ChiD, a chitinase found in Bacillus circulans, hydrolyzes the 1,4-beta-linkages of N-acetylglucosamine in chitin and chitodextrins. The domain architecture of ChiD includes a catalytic glycosyl hydrolase family 18 (...; Region: GH18_chitinase_D-like; cd02871 998088011700 putative active site [active] 998088011701 Bacterial Ig-like domain (group 3); Region: Big_3; pfam07523 998088011702 Chitin/cellulose binding domain. Putative carbohydrate binding domain found in many different glycosyl hydrolase enzymes. May occur in tandem arrangements; Region: ChtBD3; cd00036 998088011703 chitin/cellulose binding site [chemical binding]; other site 998088011704 N-acetylglucosamine-binding protein A; Reviewed; Region: PRK13211 998088011705 Chitin/cellulose binding domain. Putative carbohydrate binding domain found in many different glycosyl hydrolase enzymes. May occur in tandem arrangements; Region: ChtBD3; cl00046 998088011706 ToxR activated gene A lipoprotein; Region: TagA; pfam12561 998088011707 N-acetylglucosamine-binding protein A; Reviewed; Region: PRK13211 998088011708 Chitin/cellulose binding domain. Putative carbohydrate binding domain found in many different glycosyl hydrolase enzymes. May occur in tandem arrangements; Region: ChtBD3; cl00046 998088011709 Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the...; Region: ALAD_PBGS_aspartate_rich; cd04823 998088011710 dimer interface [polypeptide binding]; other site 998088011711 allosteric magnesium binding site [ion binding]; other site 998088011712 active site 998088011713 aspartate-rich active site metal binding site; other site 998088011714 Schiff base residues; other site 998088011715 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 998088011716 putative deoxyribonuclease YjjV; Provisional; Region: PRK11449 998088011717 active site 998088011718 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 998088011719 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 998088011720 sec-independent translocase; Provisional; Region: tatB; PRK00404 998088011721 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 998088011722 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 998088011723 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 998088011724 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 998088011725 ubiE/COQ5 methyltransferase family; Region: Ubie_methyltran; pfam01209 998088011726 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cd02440 998088011727 S-adenosylmethionine binding site [chemical binding]; other site 998088011728 CrcB-like protein; Region: CRCB; cl09114 998088011729 Cytosine deaminase and related metal-dependent hydrolases [Nucleotide transport and metabolism / General function prediction only]; Region: SsnA; COG0402 998088011730 Bacterial cytosine deaminase and related metal-dependent hydrolases. Cytosine deaminases (CDs) catalyze the deamination of cytosine, producing uracil and ammonia. They play an important role in pyrimidine salvage. CDs are present in prokaryotes and...; Region: Bact_CD; cd01293 998088011731 active site 998088011732 Purine-cytosine permease and related proteins [Nucleotide transport and metabolism]; Region: CodB; COG1457 998088011733 Sodium:solute symporter family; Region: SSF; cl00456 998088011734 Gram-negative bacterial tonB protein; Region: TonB; cl10048 998088011735 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 998088011736 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 998088011737 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 998088011738 Protein of unknown function (DUF3450); Region: DUF3450; pfam11932 998088011739 DNA-binding transcriptional activator SdiA; Provisional; Region: PRK10188 998088011740 Autoinducer binding domain; Region: Autoind_bind; pfam03472 998088011741 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors...; Region: LuxR_C_like; cd06170 998088011742 DNA binding residues [nucleotide binding] 998088011743 dimerization interface [polypeptide binding]; other site 998088011744 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 998088011745 Glutamine amidotransferases class-II (Gn-AT)_GFAT-type. This domain is found at the N-terminus of glucosamine-6P synthase (GlmS, or GFAT in humans). The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate...; Region: GFAT; cd00714 998088011746 glutaminase active site [active] 998088011747 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_1; cd05008 998088011748 dimer interface [polypeptide binding]; other site 998088011749 active site 998088011750 SIS (Sugar ISomerase) domain repeat 2 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_2; cd05009 998088011751 dimer interface [polypeptide binding]; other site 998088011752 active site 998088011753 DNA-bindng transcriptional repressor SrlR; Provisional; Region: srlR; PRK10434 998088011754 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 998088011755 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 998088011756 DNA-binding response regulator CreB; Provisional; Region: PRK11083 998088011757 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 998088011758 active site 998088011759 phosphorylation site [posttranslational modification] 998088011760 intermolecular recognition site; other site 998088011761 dimerization interface [polypeptide binding]; other site 998088011762 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 998088011763 DNA binding site [nucleotide binding] 998088011764 sensory histidine kinase CreC; Provisional; Region: PRK11100 998088011765 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 998088011766 dimer interface [polypeptide binding]; other site 998088011767 phosphorylation site [posttranslational modification] 998088011768 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 998088011769 ATP binding site [chemical binding]; other site 998088011770 Mg2+ binding site [ion binding]; other site 998088011771 G-X-G motif; other site 998088011772 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 998088011773 Protein of unknown function (DUF1566); Region: DUF1566; pfam07603 998088011774 Inner membrane protein CreD; Region: CreD; cl01844 998088011775 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK09451 998088011776 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 998088011777 Substrate binding site [chemical binding]; other site 998088011778 Mg++ binding site [ion binding]; other site 998088011779 N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU), C-terminal left-handed beta-helix (LbH) acetyltransferase domain: GlmU is also known as UDP-N-acetylglucosamine pyrophosphorylase. It is a bifunctional bacterial enzyme that catalyzes two...; Region: LbH_GlmU_C; cd03353 998088011780 active site 998088011781 substrate binding site [chemical binding]; other site 998088011782 CoA binding site [chemical binding]; other site 998088011783 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 998088011784 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 998088011785 ATP synthase, Delta/Epsilon chain, long alpha-helix domain; Region: ATP-synt_DE; pfam00401 998088011786 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 998088011787 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 998088011788 F1 ATP synthase beta subunit, nucleotide-binding domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a...; Region: F1-ATPase_beta; cd01133 998088011789 alpha subunit interaction interface [polypeptide binding]; other site 998088011790 Walker A motif; other site 998088011791 ATP binding site [chemical binding]; other site 998088011792 Walker B motif; other site 998088011793 inhibitor binding site; inhibition site 998088011794 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 998088011795 ATP synthase; Region: ATP-synt; cl00365 998088011796 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 998088011797 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 998088011798 F1 ATP synthase alpha, central domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to...; Region: F1_ATPase_alpha; cd01132 998088011799 beta subunit interaction interface [polypeptide binding]; other site 998088011800 Walker A motif; other site 998088011801 ATP binding site [chemical binding]; other site 998088011802 Walker B motif; other site 998088011803 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 998088011804 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 998088011805 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 998088011806 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 998088011807 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 998088011808 ATP synthase subunit C; Region: ATP-synt_C; cl00466 998088011809 ATP synthase A chain; Region: ATP-synt_A; cl00413 998088011810 ATP synthase I chain; Region: ATP_synt_I; cl09170 998088011811 ParB-like partition proteins; Region: parB_part; TIGR00180 998088011812 ParB-like nuclease domain; Region: ParBc; cl02129 998088011813 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 998088011814 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following...; Region: ParA; cd02042 998088011815 P-loop; other site 998088011816 Magnesium ion binding site [ion binding]; other site 998088011817 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following...; Region: ParA; cd02042 998088011818 Magnesium ion binding site [ion binding]; other site 998088011819 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 998088011820 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088011821 Flavin-dependent tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA [Cell cycle control, cell division, chromosome partitioning]; Region: GidA; COG0445 998088011822 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 998088011823 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 998088011824 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 998088011825 N-terminal plug; other site 998088011826 ligand-binding site [chemical binding]; other site 998088011827 multidrug transporter membrane component/ATP-binding component; Provisional; Region: PRK10522 998088011828 The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export. They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with...; Region: ABCC_MRP_Like; cd03228 998088011829 Walker A/P-loop; other site 998088011830 ATP binding site [chemical binding]; other site 998088011831 Q-loop/lid; other site 998088011832 ABC transporter signature motif; other site 998088011833 Walker B; other site 998088011834 D-loop; other site 998088011835 H-loop/switch region; other site 998088011836 iron-hydroxamate transporter ATP-binding subunit; Provisional; Region: PRK10575 998088011837 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 998088011838 Walker A/P-loop; other site 998088011839 ATP binding site [chemical binding]; other site 998088011840 Q-loop/lid; other site 998088011841 ABC transporter signature motif; other site 998088011842 Walker B; other site 998088011843 D-loop; other site 998088011844 H-loop/switch region; other site 998088011845 Fe3+-siderophore binding domain FhuD. These proteins have been shown to function as initial receptors in ABC transport of Fe3+-siderophores in many eubacterial species. They belong to the TroA-like superfamily of helical backbone metal receptor...; Region: FhuD; cd01146 998088011846 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 998088011847 siderophore binding site; other site 998088011848 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 998088011849 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist...; Region: TM_ABC_iron-siderophores_like; cd06550 998088011850 ABC-ATPase subunit interface; other site 998088011851 dimer interface [polypeptide binding]; other site 998088011852 putative PBP binding regions; other site 998088011853 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist...; Region: TM_ABC_iron-siderophores_like; cd06550 998088011854 ABC-ATPase subunit interface; other site 998088011855 dimer interface [polypeptide binding]; other site 998088011856 putative PBP binding regions; other site 998088011857 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 998088011858 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 998088011859 TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase...; Region: trmE; cd04164 998088011860 G1 box; other site 998088011861 GTP/Mg2+ binding site [chemical binding]; other site 998088011862 Switch I region; other site 998088011863 G2 box; other site 998088011864 Switch II region; other site 998088011865 G3 box; other site 998088011866 G4 box; other site 998088011867 G5 box; other site 998088011868 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 998088011869 membrane protein insertase; Provisional; Region: PRK01318 998088011870 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 998088011871 Ribonuclease P; Region: Ribonuclease_P; cl00457 998088011872 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 998088011873 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP; Region: ABC_HisP_GlnQ_permeases; cd03262 998088011874 Walker A/P-loop; other site 998088011875 ATP binding site [chemical binding]; other site 998088011876 Q-loop/lid; other site 998088011877 ABC transporter signature motif; other site 998088011878 Walker B; other site 998088011879 D-loop; other site 998088011880 H-loop/switch region; other site 998088011881 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 998088011882 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 998088011883 dimer interface [polypeptide binding]; other site 998088011884 conserved gate region; other site 998088011885 putative PBP binding loops; other site 998088011886 ABC-ATPase subunit interface; other site 998088011887 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 998088011888 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 998088011889 substrate binding pocket [chemical binding]; other site 998088011890 membrane-bound complex binding site; other site 998088011891 hinge residues; other site