-- dump date 20120504_155809 -- class Genbank::misc_feature -- table misc_feature_note -- id note 357804000001 Integrase core domain; Region: rve; cl01316 357804000002 Helix-turn-helix domains; Region: HTH; cl00088 357804000003 Winged helix-turn helix; Region: HTH_29; pfam13551 357804000004 Helix-turn-helix domains; Region: HTH; cl00088 357804000005 Winged helix-turn helix; Region: HTH_33; pfam13592 357804000006 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 357804000007 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 ABC; Region: AAA; cd00009 357804000008 Walker A motif; other site 357804000009 ATP binding site [chemical binding]; other site 357804000010 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804000011 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 357804000012 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 357804000013 Sporulation related domain; Region: SPOR; cl10051 357804000014 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; cl04104 357804000015 arginine-tRNA ligase; Region: PLN02286 357804000016 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 357804000017 active site 357804000018 HIGH motif; other site 357804000019 KMSK motif region; other site 357804000020 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 357804000021 tRNA binding surface [nucleotide binding]; other site 357804000022 anticodon binding site; other site 357804000023 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 357804000024 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804000025 Family description; Region: UvrD_C_2; cl15862 357804000026 flavin mononucleotide phosphatase; Provisional; Region: PRK10748 357804000027 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 357804000028 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 357804000029 XerD and XerC integrases, DNA breaking-rejoining enzymes, 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...; Region: INT_XerDC; cd00798 357804000030 active site 357804000031 Int/Topo IB signature motif; other site 357804000032 Protein of unknown function (DUF770); Region: DUF770; cl01402 357804000033 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3517; cl05484 357804000034 Protein of unknown function (DUF877); Region: DUF877; pfam05943 357804000035 Protein of unknown function (DUF796); Region: DUF796; cl01226 357804000036 Type VI secretion lipoprotein; Region: T6SS-SciN; cl01405 357804000037 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3522; cl01406 357804000038 Bacterial protein of unknown function (DUF876); Region: DUF876; pfam05936 357804000039 Uncharacterized protein conserved in bacteria (DUF2077); Region: DUF2077; cl01370 357804000040 Type VI protein secretion system component VasK [Intracellular trafficking, secretion, and vesicular transport]; Region: IcmF; COG3523 357804000041 ImcF-related N-terminal domain; Region: ImcF-related_N; pfam14331 357804000042 Protein of unknown function (DUF1215); Region: DUF1215; pfam06744 357804000043 Protein of unknown function (DUF770); Region: DUF770; cl01402 357804000044 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3517; cl05484 357804000045 Protein of unknown function (DUF877); Region: DUF877; pfam05943 357804000046 Protein of unknown function (DUF796); Region: DUF796; cl01226 357804000047 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 357804000048 Type VI protein secretion system component VasA [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3519 357804000049 Bacterial protein of unknown function (DUF879); Region: DUF879; cl15462 357804000050 Protein of unknown function (DUF1305); Region: DUF1305; cl01404 357804000051 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 357804000052 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 357804000053 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 357804000054 Uncharacterized protein conserved in bacteria (DUF2169); Region: DUF2169; cl02212 357804000055 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 357804000056 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 357804000057 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 357804000058 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 357804000059 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 357804000060 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 357804000061 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 357804000062 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 357804000063 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 357804000064 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 357804000065 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 357804000066 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 357804000067 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 357804000068 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 357804000069 Protein of unknown function (DUF3540); Region: DUF3540; pfam12059 357804000070 PAAR motif; Region: PAAR_motif; cl15808 357804000071 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 357804000072 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 357804000073 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 357804000074 Chitin/cellulose binding domain. Putative carbohydrate binding domain found in many different glycosyl hydrolase enzymes. May occur in tandem arrangements; Region: ChtBD3; cl00046 357804000075 Uncharacterized protein conserved in bacteria (DUF2169); Region: DUF2169; cl02212 357804000076 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 357804000077 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 357804000078 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 357804000079 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 357804000080 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 357804000081 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 357804000082 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 357804000083 hypothetical protein; Validated; Region: PRK09718 357804000084 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 357804000085 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 357804000086 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 357804000087 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 357804000088 Protein of unknown function (DUF3540); Region: DUF3540; pfam12059 357804000089 PAAR motif; Region: PAAR_motif; cl15808 357804000090 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 357804000091 Histidine kinase, Adenylyl cyclase, 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...; Region: HAMP; cd06225 357804000092 dimerization interface [polypeptide binding]; other site 357804000093 Serine phosphatase RsbU, regulator of sigma subunit [Signal transduction mechanisms / Transcription]; Region: RsbU; COG2208 357804000094 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 357804000095 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 357804000096 Major Facilitator Superfamily; Region: MFS_1; pfam07690 357804000097 putative substrate translocation pore; other site 357804000098 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 357804000099 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 357804000100 ATP-grasp domain; Region: ATP-grasp_4; cl03087 357804000101 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 357804000102 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 357804000103 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 357804000104 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 357804000105 diaminopimelate decarboxylase; Region: lysA; TIGR01048 357804000106 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 357804000107 active site 357804000108 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 357804000109 substrate binding site [chemical binding]; other site 357804000110 catalytic residues [active] 357804000111 dimer interface [polypeptide binding]; other site 357804000112 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 357804000113 putative iron binding site [ion binding]; other site 357804000114 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 357804000115 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 357804000116 active site 357804000117 (T/H)XGH motif; other site 357804000118 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 357804000119 classical (c) SDR, subgroup 5; Region: SDR_c5; cd05346 357804000120 putative NAD(P) binding site [chemical binding]; other site 357804000121 homotetramer interface [polypeptide binding]; other site 357804000122 homodimer interface [polypeptide binding]; other site 357804000123 active site 357804000124 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 357804000125 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 357804000126 DNA-binding site [nucleotide binding]; DNA binding site 357804000127 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 357804000128 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804000129 homodimer interface [polypeptide binding]; other site 357804000130 catalytic residue [active] 357804000131 ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: TauA; COG4521 357804000132 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 inorganic...; Region: PBPb; cl15306 357804000133 substrate binding pocket [chemical binding]; other site 357804000134 membrane-bound complex binding site; other site 357804000135 hinge residues; other site 357804000136 ABC-type taurine transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG4525 357804000137 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 357804000138 Walker A/P-loop; other site 357804000139 ATP binding site [chemical binding]; other site 357804000140 Q-loop/lid; other site 357804000141 ABC transporter signature motif; other site 357804000142 Walker B; other site 357804000143 D-loop; other site 357804000144 H-loop/switch region; other site 357804000145 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, and...; Region: TM_PBP2; cd06261 357804000146 dimer interface [polypeptide binding]; other site 357804000147 conserved gate region; other site 357804000148 putative PBP binding loops; other site 357804000149 ABC-ATPase subunit interface; other site 357804000150 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 357804000151 aminotransferase; Validated; Region: PRK07678 357804000152 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 357804000153 inhibitor-cofactor binding pocket; inhibition site 357804000154 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804000155 catalytic residue [active] 357804000156 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 357804000157 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 357804000158 DNA binding site [nucleotide binding] 357804000159 catalytic residue [active] 357804000160 H2TH interface [polypeptide binding]; other site 357804000161 putative catalytic residues [active] 357804000162 turnover-facilitating residue; other site 357804000163 intercalation triad [nucleotide binding]; other site 357804000164 8OG recognition residue [nucleotide binding]; other site 357804000165 putative reading head residues; other site 357804000166 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 357804000167 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 357804000168 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 357804000169 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 357804000170 hypothetical protein; Reviewed; Region: PRK00024 357804000171 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 357804000172 MPN+ (JAMM) motif; other site 357804000173 Zinc-binding site [ion binding]; other site 357804000174 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 357804000175 Flavoprotein; Region: Flavoprotein; cl08021 357804000176 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 357804000177 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 357804000178 trimer interface [polypeptide binding]; other site 357804000179 active site 357804000180 division inhibitor protein; Provisional; Region: slmA; PRK09480 357804000181 Helix-turn-helix domains; Region: HTH; cl00088 357804000182 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. MetJ...; Region: Met_repressor_MetJ; cl00010 357804000183 dimerization interface [polypeptide binding]; other site 357804000184 DNA binding site [nucleotide binding] 357804000185 corepressor binding sites; other site 357804000186 adenylate cyclase; Provisional; Region: cyaA; PRK09450 357804000187 Adenylate cyclase NT domain; Region: Adenyl_cycl_N; pfam12633 357804000188 Adenylate cyclase, class-I; Region: Adenylate_cycl; pfam01295 357804000189 putative global regulator; Reviewed; Region: PRK09559 357804000190 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 357804000191 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 357804000192 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 357804000193 L-aspartate oxidase; Provisional; Region: PRK09077 357804000194 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804000195 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 357804000196 RNA polymerase sigma factor RpoE; Provisional; Region: PRK09652 357804000197 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 357804000198 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 or...; Region: Sigma70_r4; cd06171 357804000199 DNA binding residues [nucleotide binding] 357804000200 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 357804000201 Anti sigma-E protein RseA, C-terminal domain; Region: RseA_C; pfam03873 357804000202 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 357804000203 Negative regulator of sigma E activity [Signal transduction mechanisms]; Region: RseB; COG3026 357804000204 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; cl01178 357804000205 DDE superfamily endonuclease; Region: DDE_4; cl15789 357804000206 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 357804000207 Protein of unknown function (DUF1040); Region: DUF1040; cl01176 357804000208 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 357804000209 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 357804000210 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 357804000211 NAD(P) binding site [chemical binding]; other site 357804000212 shikimate binding site; other site 357804000213 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 357804000214 AIR carboxylase; Region: AIRC; cl00310 357804000215 Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]; Region: TopA; COG0551 357804000216 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 357804000217 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 357804000218 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 357804000219 Protein of unknown function (DUF494); Region: DUF494; cl01103 357804000220 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 357804000221 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 357804000222 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 357804000223 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(II)...; Region: Pep_deformylase; cd00487 357804000224 active site 357804000225 catalytic residues [active] 357804000226 metal binding site [ion binding]; metal-binding site 357804000227 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 357804000228 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 357804000229 putative active site [active] 357804000230 substrate binding site [chemical binding]; other site 357804000231 putative cosubstrate binding site; other site 357804000232 catalytic site [active] 357804000233 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 357804000234 substrate binding site [chemical binding]; other site 357804000235 16S rRNA methyltransferase B; Provisional; Region: PRK10901 357804000236 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 357804000237 putative RNA binding site [nucleotide binding]; other site 357804000238 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 357804000239 S-adenosylmethionine binding site [chemical binding]; other site 357804000240 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 357804000241 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804000242 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; cl15357 357804000243 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804000244 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; cl15357 357804000245 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 357804000246 Cation transport protein; Region: TrkH; cl10514 357804000247 RmuC family; Region: RmuC; pfam02646 357804000248 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 357804000249 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. In...; Region: GFAT; cd00714 357804000250 glutaminase active site [active] 357804000251 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 357804000252 dimer interface [polypeptide binding]; other site 357804000253 active site 357804000254 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 357804000255 dimer interface [polypeptide binding]; other site 357804000256 active site 357804000257 transaldolase-like protein; Provisional; Region: PTZ00411 357804000258 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 357804000259 active site 357804000260 dimer interface [polypeptide binding]; other site 357804000261 catalytic residue [active] 357804000262 Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]; Region: DeoR; COG2390 357804000263 Putative sugar-binding domain; Region: Sugar-bind; pfam04198 357804000264 PTS system mannitol-specific transporter subunit IICBA; Provisional; Region: PRK15083 357804000265 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; cl00557 357804000266 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 transmembrane...; Region: PTS_IIB_mannitol; cd05567 357804000267 active site 357804000268 P-loop; other site 357804000269 phosphorylation site [posttranslational modification] 357804000270 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 357804000271 active site 357804000272 phosphorylation site [posttranslational modification] 357804000273 mannitol-1-phosphate 5-dehydrogenase; Provisional; Region: PRK02318 357804000274 Mannitol dehydrogenase Rossmann domain; Region: Mannitol_dh; pfam01232 357804000275 Mannitol dehydrogenase C-terminal domain; Region: Mannitol_dh_C; pfam08125 357804000276 Mannitol repressor; Region: MtlR; cl11450 357804000277 Transcriptional regulator [Transcription]; Region: MtlR; COG3722 357804000278 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 357804000279 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804000280 UDP-N-acetylglucosamine:LPS N-acetylglucosamine transferase [Cell envelope biogenesis, outer membrane]; Region: MurG; COG0707 357804000281 Phosphoenolpyruvate carboxykinase; Region: PEPCK_ATP; pfam01293 357804000282 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 357804000283 active site 357804000284 substrate-binding site [chemical binding]; other site 357804000285 metal-binding site [ion binding] 357804000286 ATP binding site [chemical binding]; other site 357804000287 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 357804000288 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 357804000289 dimerization interface [polypeptide binding]; other site 357804000290 domain crossover interface; other site 357804000291 redox-dependent activation switch; other site 357804000292 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 357804000293 RNA binding surface [nucleotide binding]; other site 357804000294 Type IV pilus biogenesis; Region: Pilus_PilP; cl11837 357804000295 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...; Region: PDZ_serine_protease; cd00987 357804000296 type II secretion system protein D; Region: type_II_gspD; TIGR02517 357804000297 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 357804000298 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 357804000299 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 357804000300 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 357804000301 type II secretion system protein E; Region: type_II_gspE; TIGR02533 357804000302 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 357804000303 Walker A motif; other site 357804000304 ATP binding site [chemical binding]; other site 357804000305 Walker B motif; other site 357804000306 type II secretion system protein F; Region: GspF; TIGR02120 357804000307 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 357804000308 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 357804000309 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 357804000310 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 357804000311 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 357804000312 Type II transport protein GspH; Region: GspH; pfam12019 357804000313 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 357804000314 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 357804000315 type II secretion system protein J; Region: gspJ; TIGR01711 357804000316 Type II secretion system (T2SS), protein J; Region: T2SJ; pfam11612 357804000317 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 357804000318 type II secretion system protein L; Region: typeII_sec_gspL; TIGR01709 357804000319 Type II secretion system (T2SS), protein L; Region: T2SL; pfam05134 357804000320 GspL periplasmic domain; Region: GspL_C; cl14909 357804000321 Type II secretion system (T2SS), protein M; Region: T2SM; cl01222 357804000322 Type II secretion system (T2SS), protein N; Region: T2SN; pfam01203 357804000323 LexA repressor; Validated; Region: PRK00215 357804000324 Helix-turn-helix domains; Region: HTH; cl00088 357804000325 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 (EC...; Region: S24_LexA-like; cd06529 357804000326 Catalytic site [active] 357804000327 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 357804000328 Cu(I) binding site [ion binding]; other site 357804000329 DNA-damage-inducible SOS response protein; Provisional; Region: PRK10367 357804000330 MatE; Region: MatE; cl10513 357804000331 MatE; Region: MatE; cl10513 357804000332 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 357804000333 Coenzyme A binding pocket [chemical binding]; other site 357804000334 Homoserine O-succinyltransferase; Region: HTS; pfam04204 357804000335 Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS); Region: GATase1_HTS; cd03131 357804000336 proposed active site lysine [active] 357804000337 conserved cys residue [active] 357804000338 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 357804000339 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 357804000340 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 357804000341 substrate binding pocket [chemical binding]; other site 357804000342 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 357804000343 B12 binding site [chemical binding]; other site 357804000344 cobalt ligand [ion binding]; other site 357804000345 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 357804000346 Uncharacterized conserved protein [Function unknown]; Region: COG4715 357804000347 SWIM zinc finger; Region: SWIM; cl15408 357804000348 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 357804000349 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 357804000350 ATP binding site [chemical binding]; other site 357804000351 putative Mg++ binding site [ion binding]; other site 357804000352 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 357804000353 nucleotide binding region [chemical binding]; other site 357804000354 ATP-binding site [chemical binding]; other site 357804000355 Uncharacterized Fe-S protein [General function prediction only]; Region: COG3217 357804000356 MOSC N-terminal beta barrel domain; Region: MOSC_N; pfam03476 357804000357 MOSC domain; Region: MOSC; pfam03473 357804000358 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 357804000359 catalytic loop [active] 357804000360 iron binding site [ion binding]; other site 357804000361 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 357804000362 active site 357804000363 dimer interfaces [polypeptide binding]; other site 357804000364 catalytic residues [active] 357804000365 Protein of unknown function (DUF1422); Region: DUF1422; cl11649 357804000366 soluble pyridine nucleotide transhydrogenase; Provisional; Region: PRK05249 357804000367 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804000368 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 357804000369 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 357804000370 adenosine nucleotide hydrolase NudE; Provisional; Region: nudE; PRK11762 357804000371 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 Mg2+; Region: ADPRase_NUDT5; cd03424 357804000372 dimer interface [polypeptide binding]; other site 357804000373 ADP-ribose binding site [chemical binding]; other site 357804000374 active site 357804000375 nudix motif; other site 357804000376 metal binding site [ion binding]; metal-binding site 357804000377 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 357804000378 Ligand Binding Site [chemical binding]; other site 357804000379 Bacterial inner membrane protein; Region: Imp-YgjV; pfam10688 357804000380 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 357804000381 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 357804000382 active site 357804000383 intersubunit interface [polypeptide binding]; other site 357804000384 catalytic residue [active] 357804000385 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 357804000386 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 357804000387 substrate binding site [chemical binding]; other site 357804000388 ATP binding site [chemical binding]; other site 357804000389 Glucuronate isomerase; Region: UxaC; cl00829 357804000390 D-mannonate oxidoreductase; Provisional; Region: PRK15037 357804000391 Mannitol dehydrogenase Rossmann domain; Region: Mannitol_dh; pfam01232 357804000392 Mannitol dehydrogenase C-terminal domain; Region: Mannitol_dh_C; pfam08125 357804000393 DctM-like transporters; Region: DctM; pfam06808 357804000394 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 357804000395 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 357804000396 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 357804000397 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 357804000398 mannonate dehydratase; Provisional; Region: PRK03906 357804000399 mannonate dehydratase; Region: uxuA; TIGR00695 357804000400 DNA-binding transcriptional repressor UxuR; Provisional; Region: PRK10225 357804000401 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 357804000402 DNA-binding site [nucleotide binding]; DNA binding site 357804000403 FCD domain; Region: FCD; cl11656 357804000404 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 357804000405 Glycosyl hydrolase family 3 C-terminal domain; Region: Glyco_hydro_3_C; pfam01915 357804000406 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 357804000407 Helix-turn-helix domains; Region: HTH; cl00088 357804000408 Integrase core domain; Region: rve; cl01316 357804000409 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 357804000410 putative active site [active] 357804000411 heme pocket [chemical binding]; other site 357804000412 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804000413 metal binding site [ion binding]; metal-binding site 357804000414 active site 357804000415 I-site; other site 357804000416 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 357804000417 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 357804000418 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 357804000419 ATP binding site [chemical binding]; other site 357804000420 putative Mg++ binding site [ion binding]; other site 357804000421 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 357804000422 non-specific DNA binding site [nucleotide binding]; other site 357804000423 salt bridge; other site 357804000424 sequence-specific DNA binding site [nucleotide binding]; other site 357804000425 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 357804000426 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 357804000427 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 357804000428 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: HsdR; COG4096 357804000429 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 357804000430 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804000431 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804000432 Eukaryotic metallothionein; Region: Metallothio_Euk; pfam12749 357804000433 EcoEI R protein C-terminal; Region: EcoEI_R_C; pfam08463 357804000434 haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED; Region: HAD-SF-IA-v3; TIGR01509 357804000435 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 357804000436 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 357804000437 motif II; other site 357804000438 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 357804000439 active site 357804000440 Int/Topo IB signature motif; other site 357804000441 DNA binding site [nucleotide binding] 357804000442 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 357804000443 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 357804000444 motif II; other site 357804000445 penicillin-binding protein 1a; Provisional; Region: mrcA; PRK11636 357804000446 Transglycosylase; Region: Transgly; cl07896 357804000447 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 357804000448 Cell division protein FtsA; Region: FtsA; cl11496 357804000449 Competence protein A; Region: Competence_A; pfam11104 357804000450 Cell division protein FtsA; Region: FtsA; cl11496 357804000451 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 357804000452 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 357804000453 Pilus assembly protein, PilO; Region: PilO; cl01234 357804000454 Tfp pilus assembly protein PilP [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilP; COG3168 357804000455 Pilus assembly protein, PilP; Region: PilP; pfam04351 357804000456 AMIN domain; Region: AMIN; pfam11741 357804000457 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 357804000458 Secretin and TonB N terminus short domain; Region: STN; cl06624 357804000459 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 357804000460 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 357804000461 shikimate kinase; Reviewed; Region: aroK; PRK00131 357804000462 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 synthesis...; Region: SK; cd00464 357804000463 ADP binding site [chemical binding]; other site 357804000464 magnesium binding site [ion binding]; other site 357804000465 putative shikimate binding site; other site 357804000466 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 357804000467 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 357804000468 active site 357804000469 dimer interface [polypeptide binding]; other site 357804000470 metal binding site [ion binding]; metal-binding site 357804000471 Sporulation related domain; Region: SPOR; cl10051 357804000472 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; cl16911 357804000473 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 pentose...; Region: RPE; cd00429 357804000474 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 357804000475 substrate binding site [chemical binding]; other site 357804000476 hexamer interface [polypeptide binding]; other site 357804000477 metal binding site [ion binding]; metal-binding site 357804000478 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 357804000479 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 357804000480 active site 357804000481 HIGH motif; other site 357804000482 dimer interface [polypeptide binding]; other site 357804000483 KMSKS motif; other site 357804000484 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 357804000485 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 357804000486 dimer interface [polypeptide binding]; other site 357804000487 active site 357804000488 metal binding site [ion binding]; metal-binding site 357804000489 glutathione binding site [chemical binding]; other site 357804000490 Cytochrome c; Region: Cytochrom_C; cl11414 357804000491 Glycerol-3-phosphate acyltransferase; Region: G3P_acyltransf; cl00410 357804000492 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, and...; Region: DHNA_DHNTPE; cd00534 357804000493 homooctamer interface [polypeptide binding]; other site 357804000494 active site 357804000495 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; cl00233 357804000496 catalytic center binding site [active] 357804000497 ATP binding site [chemical binding]; other site 357804000498 Bacitracin resistance protein BacA; Region: BacA; cl00858 357804000499 Uncharacterized protein family (UPF0014); Region: UPF0014; cl00424 357804000500 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 357804000501 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 357804000502 active site 357804000503 NTP binding site [chemical binding]; other site 357804000504 metal binding triad [ion binding]; metal-binding site 357804000505 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 357804000506 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 357804000507 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 357804000508 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 ABC; Region: AAA; cd00009 357804000509 Walker A motif; other site 357804000510 ATP binding site [chemical binding]; other site 357804000511 Walker B motif; other site 357804000512 arginine finger; other site 357804000513 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 357804000514 Bacterial SH3 domain; Region: SH3_3; cl02551 357804000515 SH3 domain protein; Region: SH3_and_anchor; TIGR04211 357804000516 Protein of unknown function (DUF2031); Region: DUF2031; cl09810 357804000517 Phosphate transporter family; Region: PHO4; cl00396 357804000518 Phosphate transporter family; Region: PHO4; cl00396 357804000519 Protein of unknown function DUF47; Region: PhoU_div; pfam01865 357804000520 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 357804000521 putative active site [active] 357804000522 putative metal binding residues [ion binding]; other site 357804000523 signature motif; other site 357804000524 putative triphosphate binding site [ion binding]; other site 357804000525 CHAD domain; Region: CHAD; cl10506 357804000526 PspA/IM30 family; Region: PspA_IM30; pfam04012 357804000527 Uncharacterized protein conserved in bacteria (DUF2170); Region: DUF2170; cl01551 357804000528 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 357804000529 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 357804000530 metal binding triad; other site 357804000531 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 357804000532 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 357804000533 metal binding triad; other site 357804000534 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 357804000535 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 357804000536 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 357804000537 putative acyl-acceptor binding pocket; other site 357804000538 O-succinylbenzoic acid--CoA ligase; Provisional; Region: PRK09029 357804000539 AMP-binding enzyme; Region: AMP-binding; cl15778 357804000540 O-succinylbenzoate synthase; Provisional; Region: PRK05105 357804000541 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 357804000542 active site 357804000543 alanine racemase; Reviewed; Region: alr; PRK00053 357804000544 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 357804000545 active site 357804000546 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 357804000547 substrate binding site [chemical binding]; other site 357804000548 catalytic residues [active] 357804000549 dimer interface [polypeptide binding]; other site 357804000550 replicative DNA helicase; Region: DnaB; TIGR00665 357804000551 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 357804000552 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 357804000553 Walker A motif; other site 357804000554 ATP binding site [chemical binding]; other site 357804000555 Walker B motif; other site 357804000556 DNA binding loops [nucleotide binding] 357804000557 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; cl00526 357804000558 glycerol-3-phosphate O-acyltransferase; Region: plsB; TIGR03703 357804000559 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT-like; Region: LPLAT_DHAPAT-like; cd07993 357804000560 putative acyl-acceptor binding pocket; other site 357804000561 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 357804000562 active site residue [active] 357804000563 hypothetical protein; Provisional; Region: PRK11568 357804000564 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 357804000565 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 357804000566 Cation transport protein; Region: TrkH; cl10514 357804000567 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 357804000568 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 357804000569 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804000570 ATP-dependent DNA helicase RecQ; Provisional; Region: PRK11057 357804000571 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 357804000572 ATP binding site [chemical binding]; other site 357804000573 ATP binding site [chemical binding]; other site 357804000574 putative Mg++ binding site [ion binding]; other site 357804000575 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 357804000576 nucleotide binding region [chemical binding]; other site 357804000577 ATP-binding site [chemical binding]; other site 357804000578 RQC domain; Region: RQC; cl09632 357804000579 HRDC domain; Region: HRDC; cl02578 357804000580 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]; Region: COG3593 357804000581 Protein of unknown function (DUF2813); Region: DUF2813; pfam11398 357804000582 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 357804000583 active site 357804000584 metal binding site [ion binding]; metal-binding site 357804000585 META domain; Region: META; cl01245 357804000586 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional; Region: PRK11092 357804000587 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 357804000588 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 357804000589 synthetase active site [active] 357804000590 NTP binding site [chemical binding]; other site 357804000591 metal binding site [ion binding]; metal-binding site 357804000592 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 after...; Region: TGS_RelA_SpoT; cd01668 357804000593 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 357804000594 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 357804000595 Uncharacterized protein family (UPF0075); Region: UPF0075; cl04217 357804000596 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 357804000597 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 357804000598 FeS/SAM binding site; other site 357804000599 HemN C-terminal domain; Region: HemN_C; pfam06969 357804000600 Protein of unknown function (DUF2489); Region: DUF2489; pfam10675 357804000601 Der GTPase activator (YihI); Region: YihI; cl01172 357804000602 Cytochrome c; Region: Cytochrom_C; cl11414 357804000603 Cytochrome c; Region: Cytochrom_C; cl11414 357804000604 Predicted GTPase [General function prediction only]; Region: COG0218 357804000605 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 357804000606 G1 box; other site 357804000607 GTP/Mg2+ binding site [chemical binding]; other site 357804000608 Switch I region; other site 357804000609 G2 box; other site 357804000610 G3 box; other site 357804000611 Switch II region; other site 357804000612 G4 box; other site 357804000613 G5 box; other site 357804000614 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 357804000615 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 357804000616 active site 357804000617 Zn binding site [ion binding]; other site 357804000618 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 357804000619 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804000620 ATP binding site [chemical binding]; other site 357804000621 Walker B motif; other site 357804000622 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 357804000623 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 357804000624 2-isopropylmalate synthase; Validated; Region: PRK00915 357804000625 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 357804000626 active site 357804000627 catalytic residues [active] 357804000628 metal binding site [ion binding]; metal-binding site 357804000629 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 357804000630 methionine sulfoxide reductase B; Provisional; Region: PRK00222; cl15841 357804000631 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229 357804000632 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 357804000633 FAD binding domain; Region: FAD_binding_4; pfam01565 357804000634 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 357804000635 Helix-turn-helix domains; Region: HTH; cl00088 357804000636 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 357804000637 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 357804000638 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 357804000639 CHASE4 domain; Region: CHASE4; cl01308 357804000640 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804000641 metal binding site [ion binding]; metal-binding site 357804000642 active site 357804000643 I-site; other site 357804000644 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 357804000645 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 357804000646 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 357804000647 classical (c) SDRs; Region: SDR_c; cd05233 357804000648 NAD(P) binding site [chemical binding]; other site 357804000649 active site 357804000650 xylulokinase; Provisional; Region: PRK15027 357804000651 D-xylulose kinases, Escherichia coli xylulokinase-like subgroup; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_D-XK_EcXK-like; cd07808 357804000652 N- and C-terminal domain interface [polypeptide binding]; other site 357804000653 active site 357804000654 catalytic site [active] 357804000655 metal binding site [ion binding]; metal-binding site 357804000656 xylulose binding site [chemical binding]; other site 357804000657 putative ATP binding site [chemical binding]; other site 357804000658 homodimer interface [polypeptide binding]; other site 357804000659 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 357804000660 CPxP motif; other site 357804000661 Phosphoenolpyruvate carboxylase; Region: PEPcase; cl14656 357804000662 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 357804000663 acetylornithine deacetylase; Provisional; Region: PRK05111 357804000664 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 357804000665 metal binding site [ion binding]; metal-binding site 357804000666 putative dimer interface [polypeptide binding]; other site 357804000667 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 357804000668 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804000669 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 357804000670 AAK_NAGK-NC: N-Acetyl-L-glutamate kinase - noncyclic (NAGK-NC) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of microbial arginine biosynthesis using the acetylated, noncyclic route of...; Region: AAK_NAGK-NC; cd04249 357804000671 nucleotide binding site [chemical binding]; other site 357804000672 N-acetyl-L-glutamate binding site [chemical binding]; other site 357804000673 ornithine carbamoyltransferase; Provisional; Region: PRK14805 357804000674 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 357804000675 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804000676 Argininosuccinate synthase [Amino acid transport and metabolism]; Region: ArgG; COG0137 357804000677 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 357804000678 ANP binding site [chemical binding]; other site 357804000679 Substrate Binding Site II [chemical binding]; other site 357804000680 Substrate Binding Site I [chemical binding]; other site 357804000681 bifunctional argininosuccinate lyase/N-acetylglutamate synthase; Provisional; Region: PRK12308 357804000682 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 357804000683 active sites [active] 357804000684 tetramer interface [polypeptide binding]; other site 357804000685 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 357804000686 Coenzyme A binding pocket [chemical binding]; other site 357804000687 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 357804000688 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 357804000689 trimer interface [polypeptide binding]; other site 357804000690 putative metal binding site [ion binding]; other site 357804000691 integrase; Provisional; Region: PRK09692 357804000692 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 357804000693 active site 357804000694 Int/Topo IB signature motif; other site 357804000695 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cl00195 357804000696 Protein of unknown function (DUF511); Region: DUF511; cl01114 357804000697 Protein of unknown function (DUF2971); Region: DUF2971; pfam11185 357804000698 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 357804000699 Transposase; Region: DEDD_Tnp_IS110; pfam01548 357804000700 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 357804000701 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 357804000702 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 357804000703 Protein of unknown function (DUF3296); Region: DUF3296; pfam11726 357804000704 multiple promoter invertase; Provisional; Region: mpi; PRK13413 357804000705 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 357804000706 catalytic residues [active] 357804000707 catalytic nucleophile [active] 357804000708 Presynaptic Site I dimer interface [polypeptide binding]; other site 357804000709 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 357804000710 Synaptic Flat tetramer interface [polypeptide binding]; other site 357804000711 Synaptic Site I dimer interface [polypeptide binding]; other site 357804000712 DNA binding site [nucleotide binding] 357804000713 Helix-turn-helix domains; Region: HTH; cl00088 357804000714 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 357804000715 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 357804000716 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 357804000717 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 357804000718 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 357804000719 Interdomain contacts; other site 357804000720 Cytokine receptor motif; other site 357804000721 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 357804000722 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 357804000723 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 357804000724 catalytic core [active] 357804000725 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 357804000726 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 357804000727 Coenzyme A binding pocket [chemical binding]; other site 357804000728 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 357804000729 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 357804000730 Methyltransferase domain; Region: Methyltransf_31; pfam13847 357804000731 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 357804000732 S-adenosylmethionine binding site [chemical binding]; other site 357804000733 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 357804000734 Predicted naringenin-chalcone synthase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: BcsA; COG3424 357804000735 Chalcone and stilbene synthases; plant-specific polyketide synthases (PKS) and related enzymes, also called type III PKSs. PKS generate an array of different products, dependent on the nature of the starter molecule. They share a common chemical strategy; Region: CHS_like; cd00831 357804000736 malonyl-CoA binding site [chemical binding]; other site 357804000737 dimer interface [polypeptide binding]; other site 357804000738 active site 357804000739 product binding site; other site 357804000740 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 357804000741 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 357804000742 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804000743 metal binding site [ion binding]; metal-binding site 357804000744 active site 357804000745 I-site; other site 357804000746 Domain of unknown function (DUF4212); Region: DUF4212; cl01781 357804000747 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 357804000748 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 357804000749 Na binding site [ion binding]; other site 357804000750 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 357804000751 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 357804000752 ligand binding site [chemical binding]; other site 357804000753 flexible hinge region; other site 357804000754 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with either the CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain or the PB1 (Phox and Bem1p) domain; Region: CBS_pair_CAP-ED_DUF294_PBI_assoc2; cd04800 357804000755 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 357804000756 metal binding triad; other site 357804000757 DNA polymerase III subunit epsilon; Validated; Region: PRK09182 357804000758 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 357804000759 active site 357804000760 catalytic site [active] 357804000761 substrate binding site [chemical binding]; other site 357804000762 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 357804000763 Predicted carboxypeptidase [Amino acid transport and metabolism]; Region: COG2866 357804000764 Peptidase M14-like domain of ATP/GTP binding proteins and cytosolic carboxypeptidases; uncharacterized bacterial subgroup; Region: M14_Nna1_like_1; cd06234 357804000765 putative active site [active] 357804000766 Zn binding site [ion binding]; other site 357804000767 Domain of unknown function (DUF1840); Region: DUF1840; pfam08895 357804000768 Peptidase propeptide and YPEB domain; Region: PepSY; cl15815 357804000769 FlgD Ig-like domain; Region: FlgD_ig; cl15790 357804000770 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 357804000771 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 357804000772 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 357804000773 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_like2; cd06201 357804000774 FAD binding pocket [chemical binding]; other site 357804000775 FAD binding motif [chemical binding]; other site 357804000776 catalytic residues [active] 357804000777 NAD binding pocket [chemical binding]; other site 357804000778 phosphate binding motif [ion binding]; other site 357804000779 beta-alpha-beta structure motif; other site 357804000780 Histidine kinase, Adenylyl cyclase, 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...; Region: HAMP; cd06225 357804000781 dimerization interface [polypeptide binding]; other site 357804000782 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 357804000783 PAS fold; Region: PAS_3; pfam08447 357804000784 putative active site [active] 357804000785 heme pocket [chemical binding]; other site 357804000786 PAS domain; Region: PAS_9; pfam13426 357804000787 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 357804000788 putative active site [active] 357804000789 heme pocket [chemical binding]; other site 357804000790 PAS fold; Region: PAS_4; pfam08448 357804000791 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 357804000792 putative active site [active] 357804000793 heme pocket [chemical binding]; other site 357804000794 PAS domain S-box; Region: sensory_box; TIGR00229 357804000795 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 357804000796 putative active site [active] 357804000797 heme pocket [chemical binding]; other site 357804000798 PAS domain S-box; Region: sensory_box; TIGR00229 357804000799 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 357804000800 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804000801 metal binding site [ion binding]; metal-binding site 357804000802 active site 357804000803 I-site; other site 357804000804 Uncharacterized protein conserved in bacteria (DUF2131); Region: DUF2131; cl11547 357804000805 transcriptional regulator EutR; Provisional; Region: PRK10130 357804000806 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 357804000807 DNA binding residues [nucleotide binding] 357804000808 ethanolamine ammonia lyase large subunit; Provisional; Region: PRK15067 357804000809 Ethanolamine ammonia lyase large subunit (EutB); Region: EutB; pfam06751 357804000810 Ethanolamine ammonia-lyase light chain (EutC); Region: EutC; cl01762 357804000811 ethanolamine permease; Region: 2A0305; TIGR00908 357804000812 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 357804000813 DNA-binding site [nucleotide binding]; DNA binding site 357804000814 RNA-binding motif; other site 357804000815 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 357804000816 ligand binding site [chemical binding]; other site 357804000817 sensor protein PhoQ; Provisional; Region: PRK10815 357804000818 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 357804000819 ATP binding site [chemical binding]; other site 357804000820 Mg2+ binding site [ion binding]; other site 357804000821 G-X-G motif; other site 357804000822 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 357804000823 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 357804000824 active site 357804000825 phosphorylation site [posttranslational modification] 357804000826 intermolecular recognition site; other site 357804000827 dimerization interface [polypeptide binding]; other site 357804000828 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 and...; Region: trans_reg_C; cd00383 357804000829 DNA binding site [nucleotide binding] 357804000830 Peptidase propeptide and YPEB domain; Region: PepSY; cl15815 357804000831 selenophosphate synthetase; Provisional; Region: PRK00943 357804000832 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 357804000833 dimerization interface [polypeptide binding]; other site 357804000834 putative ATP binding site [chemical binding]; other site 357804000835 tRNA 2-selenouridine synthase; Provisional; Region: PRK11784 357804000836 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 357804000837 active site residue [active] 357804000838 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804000839 NeuB family; Region: NeuB; cl00496 357804000840 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 357804000841 bifunctional chorismate mutase/prephenate dehydrogenase; Provisional; Region: tyrA; PRK11199 357804000842 Chorismate mutase type II; Region: CM_2; cl00693 357804000843 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804000844 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 357804000845 30S subunit binding site; other site 357804000846 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 357804000847 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 357804000848 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 357804000849 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, and...; Region: TM_PBP2; cd06261 357804000850 dimer interface [polypeptide binding]; other site 357804000851 conserved gate region; other site 357804000852 putative PBP binding loops; other site 357804000853 ABC-ATPase subunit interface; other site 357804000854 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 357804000855 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, and...; Region: TM_PBP2; cd06261 357804000856 dimer interface [polypeptide binding]; other site 357804000857 conserved gate region; other site 357804000858 putative PBP binding loops; other site 357804000859 ABC-ATPase subunit interface; other site 357804000860 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 357804000861 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 357804000862 Walker A/P-loop; other site 357804000863 ATP binding site [chemical binding]; other site 357804000864 Q-loop/lid; other site 357804000865 ABC transporter signature motif; other site 357804000866 Walker B; other site 357804000867 D-loop; other site 357804000868 H-loop/switch region; other site 357804000869 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 357804000870 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 357804000871 Walker A/P-loop; other site 357804000872 ATP binding site [chemical binding]; other site 357804000873 Q-loop/lid; other site 357804000874 ABC transporter signature motif; other site 357804000875 Walker B; other site 357804000876 D-loop; other site 357804000877 H-loop/switch region; other site 357804000878 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 357804000879 lytic murein transglycosylase; Provisional; Region: PRK11619 357804000880 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 357804000881 N-acetyl-D-glucosamine binding site [chemical binding]; other site 357804000882 catalytic residue [active] 357804000883 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 357804000884 arginine repressor; Provisional; Region: PRK05066 357804000885 Arginine repressor, DNA binding domain; Region: Arg_repressor; pfam01316 357804000886 Arginine repressor, C-terminal domain; Region: Arg_repressor_C; pfam02863 357804000887 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 inorganic...; Region: PBPb; cd00134 357804000888 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 357804000889 substrate binding pocket [chemical binding]; other site 357804000890 membrane-bound complex binding site; other site 357804000891 hinge residues; other site 357804000892 malate dehydrogenase; Provisional; Region: PRK05086 357804000893 Glyoxysomal and mitochondrial malate dehydrogenases; Region: MDH_glyoxysomal_mitochondrial; cd01337 357804000894 NAD binding site [chemical binding]; other site 357804000895 dimerization interface [polypeptide binding]; other site 357804000896 Substrate binding site [chemical binding]; other site 357804000897 siroheme synthase; Provisional; Region: cysG; PRK10637 357804000898 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804000899 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 357804000900 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 357804000901 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 357804000902 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 357804000903 ligand binding site; other site 357804000904 oligomer interface; other site 357804000905 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...; Region: LbH_G1P_AT_C; cd04651 357804000906 dimer interface [polypeptide binding]; other site 357804000907 N-terminal domain interface [polypeptide binding]; other site 357804000908 sulfate 1 binding site; other site 357804000909 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11905 357804000910 Proline dehydrogenase; Region: Pro_dh; cl03282 357804000911 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 357804000912 Glutamate binding site [chemical binding]; other site 357804000913 NAD binding site [chemical binding]; other site 357804000914 catalytic residues [active] 357804000915 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 357804000916 NAD(P) binding site [chemical binding]; other site 357804000917 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 357804000918 CoenzymeA binding site [chemical binding]; other site 357804000919 subunit interaction site [polypeptide binding]; other site 357804000920 PHB binding site; other site 357804000921 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 357804000922 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 357804000923 non-specific DNA binding site [nucleotide binding]; other site 357804000924 salt bridge; other site 357804000925 sequence-specific DNA binding site [nucleotide binding]; other site 357804000926 Protein of unknown function (DUF3612); Region: DUF3612; pfam12268 357804000927 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 357804000928 active site 357804000929 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 357804000930 tetramer interface [polypeptide binding]; other site 357804000931 active site 357804000932 Mg2+/Mn2+ binding site [ion binding]; other site 357804000933 Members of the ICL/PEPM_KPHMT enzyme superfamily catalyze the formation and cleavage of either P-C or C-C bonds. Typical members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate...; Region: ICL_KPHMT; cl00435 357804000934 Alpha amylase catalytic domain found in Amylosucrase; Region: AmyAc_Amylosucrase; cd11324 357804000935 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 357804000936 active site 357804000937 catalytic site [active] 357804000938 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 357804000939 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 357804000940 Zn2+ binding site [ion binding]; other site 357804000941 Mg2+ binding site [ion binding]; other site 357804000942 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 357804000943 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 357804000944 Predicted membrane protein (DUF2061); Region: DUF2061; cl01257 357804000945 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 357804000946 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 357804000947 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 357804000948 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 357804000949 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 357804000950 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 357804000951 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 or...; Region: Sigma70_r4; cd06171 357804000952 DNA binding residues [nucleotide binding] 357804000953 DNA primase; Validated; Region: dnaG; PRK05667 357804000954 CHC2 zinc finger; Region: zf-CHC2; cl15369 357804000955 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 357804000956 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 357804000957 active site 357804000958 metal binding site [ion binding]; metal-binding site 357804000959 interdomain interaction site; other site 357804000960 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 357804000961 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; cl07879 357804000962 GatB domain; Region: GatB_Yqey; cl11497 357804000963 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 357804000964 UGMP family protein; Validated; Region: PRK09604 357804000965 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 357804000966 LPS O-antigen length regulator; Provisional; Region: PRK10381 357804000967 Chain length determinant protein; Region: Wzz; cl15801 357804000968 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 357804000969 dimer interface [polypeptide binding]; other site 357804000970 allosteric magnesium binding site [ion binding]; other site 357804000971 active site 357804000972 aspartate-rich active site metal binding site; other site 357804000973 Schiff base residues; other site 357804000974 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 357804000975 active site 357804000976 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 357804000977 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 357804000978 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 357804000979 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 357804000980 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 357804000981 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 357804000982 SCP-2 sterol transfer family; Region: SCP2; cl01225 357804000983 ubiE/COQ5 methyltransferase family; Region: Ubie_methyltran; pfam01209 357804000984 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 357804000985 S-adenosylmethionine binding site [chemical binding]; other site 357804000986 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 357804000987 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 357804000988 active site 357804000989 dimer interface [polypeptide binding]; other site 357804000990 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 357804000991 dimer interface [polypeptide binding]; other site 357804000992 active site 357804000993 Domain of unknown function (DUF1919); Region: DUF1919; cl01628 357804000994 Mannosyltransferase OCH1 and related enzymes [Cell envelope biogenesis, outer membrane]; Region: OCH1; COG3774 357804000995 Glycosyltransferase sugar-binding region containing DXD motif; Region: Gly_transf_sug; pfam04488 357804000996 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 357804000997 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 357804000998 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 357804000999 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 357804001000 putative metal binding site; other site 357804001001 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 357804001002 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 357804001003 putative active site [active] 357804001004 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 357804001005 ATP binding site [chemical binding]; other site 357804001006 N-terminal domain of Chondroitin polymerase functions as a GalNAc transferase; Region: GT2_Chondriotin_Pol_N; cd06420 357804001007 Substrate binding site; other site 357804001008 metal-binding site 357804001009 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 357804001010 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 357804001011 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 357804001012 O-Antigen ligase; Region: Wzy_C; cl04850 357804001013 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 357804001014 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 357804001015 putative active site [active] 357804001016 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 357804001017 ADP-L-glycero-D-mannoheptose-6-epimerase; Provisional; Region: rfaD; PRK11150 357804001018 NADP binding site [chemical binding]; other site 357804001019 homopentamer interface [polypeptide binding]; other site 357804001020 substrate binding site [chemical binding]; other site 357804001021 active site 357804001022 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 357804001023 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 357804001024 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 357804001025 active site residue [active] 357804001026 transketolase; Reviewed; Region: PRK12753 357804001027 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 357804001028 TPP-binding site [chemical binding]; other site 357804001029 dimer interface [polypeptide binding]; other site 357804001030 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 357804001031 PYR/PP interface [polypeptide binding]; other site 357804001032 dimer interface [polypeptide binding]; other site 357804001033 TPP binding site [chemical binding]; other site 357804001034 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 357804001035 RbsD / FucU transport protein family; Region: RbsD_FucU; cl00809 357804001036 D-ribose transporter ATP binding protein; Provisional; Region: PRK10762 357804001037 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 hexoses...; Region: ABC_Carb_Monos_I; cd03216 357804001038 Walker A/P-loop; other site 357804001039 ATP binding site [chemical binding]; other site 357804001040 Q-loop/lid; other site 357804001041 ABC transporter signature motif; other site 357804001042 Walker B; other site 357804001043 D-loop; other site 357804001044 H-loop/switch region; other site 357804001045 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 357804001046 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 357804001047 TM-ABC transporter signature motif; other site 357804001048 D-ribose transporter subunit RbsB; Provisional; Region: PRK10653 357804001049 Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs; Region: PBP1_ribose_binding; cd06323 357804001050 ligand binding site [chemical binding]; other site 357804001051 dimerization interface [polypeptide binding]; other site 357804001052 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 357804001053 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 nucleotides...; Region: ribokinase; cd01174 357804001054 substrate binding site [chemical binding]; other site 357804001055 dimer interface [polypeptide binding]; other site 357804001056 ATP binding site [chemical binding]; other site 357804001057 DNA-binding transcriptional repressor PurR; Provisional; Region: PRK10703 357804001058 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 357804001059 DNA binding site [nucleotide binding] 357804001060 domain linker motif; other site 357804001061 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 357804001062 dimerization interface [polypeptide binding]; other site 357804001063 ligand binding site [chemical binding]; other site 357804001064 Dehydratase family; Region: ILVD_EDD; cl00340 357804001065 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 357804001066 acetolactate synthase 2 catalytic subunit; Reviewed; Region: PRK08978 357804001067 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 357804001068 PYR/PP interface [polypeptide binding]; other site 357804001069 dimer interface [polypeptide binding]; other site 357804001070 TPP binding site [chemical binding]; other site 357804001071 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 357804001072 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 357804001073 TPP-binding site [chemical binding]; other site 357804001074 dimer interface [polypeptide binding]; other site 357804001075 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 357804001076 Enoyl-CoA hydratase/isomerase family; Region: ECH; pfam00378 357804001077 substrate binding site [chemical binding]; other site 357804001078 oxyanion hole (OAH) forming residues; other site 357804001079 trimer interface [polypeptide binding]; other site 357804001080 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase; Provisional; Region: PRK11126 357804001081 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 357804001082 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase; Validated; Region: PRK07449 357804001083 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 357804001084 dimer interface [polypeptide binding]; other site 357804001085 tetramer interface [polypeptide binding]; other site 357804001086 PYR/PP interface [polypeptide binding]; other site 357804001087 TPP binding site [chemical binding]; other site 357804001088 Thiamine pyrophosphate (TPP) family, SHCHC synthase subfamily, 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...; Region: TPP_SHCHC_synthase; cd02009 357804001089 TPP-binding site; other site 357804001090 Isochorismate synthase [Coenzyme metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: MenF; COG1169 357804001091 chorismate binding enzyme; Region: Chorismate_bind; cl10555 357804001092 UbiA prenyltransferase family; Region: UbiA; cl00337 357804001093 elongation factor G; Reviewed; Region: PRK00007 357804001094 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 357804001095 G1 box; other site 357804001096 putative GEF interaction site [polypeptide binding]; other site 357804001097 GTP/Mg2+ binding site [chemical binding]; other site 357804001098 Switch I region; other site 357804001099 G2 box; other site 357804001100 G3 box; other site 357804001101 Switch II region; other site 357804001102 G4 box; other site 357804001103 G5 box; other site 357804001104 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 synthesis...; Region: EFG_mtEFG_II; cd04088 357804001105 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 2...; Region: EFG_mtEFG1_IV; cd01434 357804001106 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 2...; Region: EFG_mtEFG_C; cd03713 357804001107 elongation factor G; Reviewed; Region: PRK12740 357804001108 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 357804001109 ThiC-associated domain; Region: ThiC-associated; pfam13667 357804001110 ThiC family; Region: ThiC; cl08031 357804001111 HMP-P kinase/thiamin-monophosphate pyrophosphorylase; Region: PLN02898 357804001112 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 357804001113 substrate binding site [chemical binding]; other site 357804001114 dimer interface [polypeptide binding]; other site 357804001115 ATP binding site [chemical binding]; other site 357804001116 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-; Region: TMP_TenI; cd00564 357804001117 thiamine phosphate binding site [chemical binding]; other site 357804001118 active site 357804001119 pyrophosphate binding site [ion binding]; other site 357804001120 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 357804001121 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 MoaD...; Region: ThiF_MoeB_HesA_family; cd00757 357804001122 ATP binding site [chemical binding]; other site 357804001123 substrate interface [chemical binding]; other site 357804001124 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 357804001125 thiS-thiF/thiG interaction site; other site 357804001126 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 357804001127 ThiS interaction site; other site 357804001128 putative active site [active] 357804001129 tetramer interface [polypeptide binding]; other site 357804001130 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09240 357804001131 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 357804001132 FeS/SAM binding site; other site 357804001133 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 357804001134 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 357804001135 RNA binding surface [nucleotide binding]; other site 357804001136 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 357804001137 N-acetyl-D-glucosamine binding site [chemical binding]; other site 357804001138 catalytic residue [active] 357804001139 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 357804001140 O-Antigen ligase; Region: Wzy_C; cl04850 357804001141 Domain of unknown function (DUF3366); Region: DUF3366; pfam11846 357804001142 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 357804001143 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 357804001144 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 357804001145 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 357804001146 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 357804001147 Phosphoglycerate kinase; Region: PGK; pfam00162 357804001148 substrate binding site [chemical binding]; other site 357804001149 hinge regions; other site 357804001150 ADP binding site [chemical binding]; other site 357804001151 catalytic site [active] 357804001152 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 357804001153 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 357804001154 active site 357804001155 intersubunit interface [polypeptide binding]; other site 357804001156 zinc binding site [ion binding]; other site 357804001157 Na+ binding site [ion binding]; other site 357804001158 Protein of unknown function (DUF541); Region: SIMPL; cl01077 357804001159 Adenosylmethionine decarboxylase; Region: SAM_decarbox; cl03253 357804001160 Bacterial Fe(2+) trafficking; Region: Iron_traffic; cl01104 357804001161 adenine DNA glycosylase; Provisional; Region: PRK10880 357804001162 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 357804001163 minor groove reading motif; other site 357804001164 helix-hairpin-helix signature motif; other site 357804001165 substrate binding pocket [chemical binding]; other site 357804001166 active site 357804001167 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 357804001168 DNA binding and oxoG recognition site [nucleotide binding] 357804001169 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; cl16911 357804001170 Uncharacterized proteins involved in stress response, homologs of TerZ and putative cAMP-binding protein CABP1 [Signal transduction mechanisms]; Region: TerZ; COG2310 357804001171 Uncharacterized proteins involved in stress response, similar to tellurium resistance terD; Region: TerD_like; cd06974 357804001172 putative metal binding site [ion binding]; other site 357804001173 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 357804001174 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 357804001175 Putative heavy-metal-binding; Region: YbjQ_1; cl00426 357804001176 EamA-like transporter family; Region: EamA; cl01037 357804001177 EamA-like transporter family; Region: EamA; cl01037 357804001178 ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]; Region: TbpA; COG4143 357804001179 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 357804001180 thiamine transporter membrane protein; Reviewed; Region: thiP; PRK09433 357804001181 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, and...; Region: TM_PBP2; cl00427 357804001182 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, and...; Region: TM_PBP2; cd06261 357804001183 dimer interface [polypeptide binding]; other site 357804001184 conserved gate region; other site 357804001185 putative PBP binding loops; other site 357804001186 ABC-ATPase subunit interface; other site 357804001187 ABC-type thiamine transport system, ATPase component [Coenzyme metabolism]; Region: ThiQ; COG3840 357804001188 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804001189 Walker A/P-loop; other site 357804001190 ATP binding site [chemical binding]; other site 357804001191 Q-loop/lid; other site 357804001192 ABC transporter signature motif; other site 357804001193 Walker B; other site 357804001194 D-loop; other site 357804001195 H-loop/switch region; other site 357804001196 DNA-binding transcriptional dual regulator Crp; Provisional; Region: PRK11753 357804001197 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 357804001198 ligand binding site [chemical binding]; other site 357804001199 flexible hinge region; other site 357804001200 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 357804001201 putative switch regulator; other site 357804001202 non-specific DNA interactions [nucleotide binding]; other site 357804001203 DNA binding site [nucleotide binding] 357804001204 sequence specific DNA binding site [nucleotide binding]; other site 357804001205 putative cAMP binding site [chemical binding]; other site 357804001206 Uncharacterized protein family (UPF0270); Region: UPF0270; cl01180 357804001207 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 357804001208 active site clefts [active] 357804001209 zinc binding site [ion binding]; other site 357804001210 dimer interface [polypeptide binding]; other site 357804001211 Cytochrome c; Region: Cytochrom_C; cl11414 357804001212 Mg chelatase-related protein; Region: TIGR00368 357804001213 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 357804001214 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 ABC; Region: AAA; cd00009 357804001215 Walker A motif; other site 357804001216 ATP binding site [chemical binding]; other site 357804001217 Walker B motif; other site 357804001218 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 357804001219 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 357804001220 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 357804001221 HIGH motif; other site 357804001222 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 357804001223 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 357804001224 active site 357804001225 KMSKS motif; other site 357804001226 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 357804001227 tRNA binding surface [nucleotide binding]; other site 357804001228 anticodon binding site; other site 357804001229 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 357804001230 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; cl01106 357804001231 multifunctional aminopeptidase A; Provisional; Region: PRK00913 357804001232 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 and...; Region: Peptidase_M17; cd00433 357804001233 interface (dimer of trimers) [polypeptide binding]; other site 357804001234 Substrate-binding/catalytic site; other site 357804001235 Zn-binding sites [ion binding]; other site 357804001236 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 357804001237 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 357804001238 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 357804001239 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 357804001240 RDD family; Region: RDD; cl00746 357804001241 integrase; Provisional; Region: int; PHA02601 357804001242 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 357804001243 active site 357804001244 DNA binding site [nucleotide binding] 357804001245 Int/Topo IB signature motif; other site 357804001246 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 357804001247 Virulence-associated protein E; Region: VirE; pfam05272 357804001248 Helix-turn-helix domains; Region: HTH; cl00088 357804001249 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 357804001250 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 357804001251 active site 357804001252 DNA binding site [nucleotide binding] 357804001253 Int/Topo IB signature motif; other site 357804001254 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 357804001255 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 357804001256 Predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold [General function prediction only]; Region: LipA; COG1075 357804001257 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 357804001258 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. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 357804001259 Walker A/P-loop; other site 357804001260 ATP binding site [chemical binding]; other site 357804001261 Q-loop/lid; other site 357804001262 ABC transporter signature motif; other site 357804001263 Walker B; other site 357804001264 D-loop; other site 357804001265 H-loop/switch region; other site 357804001266 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 357804001267 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, and...; Region: TM_PBP2; cd06261 357804001268 dimer interface [polypeptide binding]; other site 357804001269 conserved gate region; other site 357804001270 putative PBP binding loops; other site 357804001271 ABC-ATPase subunit interface; other site 357804001272 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 357804001273 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, and...; Region: TM_PBP2; cd06261 357804001274 dimer interface [polypeptide binding]; other site 357804001275 conserved gate region; other site 357804001276 putative PBP binding loops; other site 357804001277 ABC-ATPase subunit interface; other site 357804001278 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 inorganic...; Region: PBPb; cd00134 357804001279 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 357804001280 substrate binding pocket [chemical binding]; other site 357804001281 membrane-bound complex binding site; other site 357804001282 hinge residues; other site 357804001283 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 357804001284 homotrimer interaction site [polypeptide binding]; other site 357804001285 putative active site [active] 357804001286 Amidase; Region: Amidase; cl11426 357804001287 Helix-turn-helix domains; Region: HTH; cl00088 357804001288 DNA-binding transcriptional regulator IlvY; Provisional; Region: PRK11716 357804001289 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 357804001290 Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily; Region: CE4_u8; cd10932 357804001291 NodB motif; other site 357804001292 putative active site [active] 357804001293 putative catalytic site [active] 357804001294 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 357804001295 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 357804001296 binding surface 357804001297 TPR motif; other site 357804001298 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 357804001299 binding surface 357804001300 TPR motif; other site 357804001301 PEP-CTERM-box response regulator transcription factor; Region: PEP_resp_reg; TIGR02915 357804001302 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 357804001303 active site 357804001304 phosphorylation site [posttranslational modification] 357804001305 intermolecular recognition site; other site 357804001306 dimerization interface [polypeptide binding]; other site 357804001307 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 ABC; Region: AAA; cd00009 357804001308 Walker A motif; other site 357804001309 ATP binding site [chemical binding]; other site 357804001310 Walker B motif; other site 357804001311 arginine finger; other site 357804001312 Helix-turn-helix domains; Region: HTH; cl00088 357804001313 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl01155 357804001314 exopolysaccharide/PEPCTERM locus tyrosine autokinase; Region: pepcterm_TyrKin; TIGR03018 357804001315 polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Region: pepcterm_ChnLen; TIGR03007 357804001316 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 357804001317 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 357804001318 SLBB domain; Region: SLBB; pfam10531 357804001319 putative PEP-CTERM system histidine kinase; Region: PEP_his_kin; TIGR02916 357804001320 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 357804001321 ATP binding site [chemical binding]; other site 357804001322 Mg2+ binding site [ion binding]; other site 357804001323 G-X-G motif; other site 357804001324 UDP-N-acetyl-D-mannosamine dehydrogenase; Provisional; Region: wecC; PRK11064 357804001325 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 357804001326 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804001327 UDP-N-acetylglucosamine 2-epimerase; Region: wecB; TIGR00236 357804001328 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 357804001329 active site 357804001330 homodimer interface [polypeptide binding]; other site 357804001331 Protein involved in cellulose biosynthesis (CelD) [Cell envelope biogenesis, outer membrane]; Region: COG5653 357804001332 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 357804001333 Heparinase II/III-like protein; Region: Hepar_II_III; cl15421 357804001334 Transmembrane exosortase (Exosortase_EpsH); Region: Exosortase_EpsH; pfam09721 357804001335 Predicted membrane protein [Function unknown]; Region: COG4083; cl15694 357804001336 Protein of unknown function (DUF3485); Region: DUF3485; cl11827 357804001337 The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common...; Region: Glyco_transf_WecG_TagA; cd06533 357804001338 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 357804001339 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 357804001340 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 357804001341 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 357804001342 AMP-binding enzyme; Region: AMP-binding; cl15778 357804001343 O-Antigen ligase; Region: Wzy_C; cl04850 357804001344 OpgC protein; Region: OpgC_C; cl00792 357804001345 Acyltransferase family; Region: Acyl_transf_3; pfam01757 357804001346 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 357804001347 Ligand binding site; other site 357804001348 Putative Catalytic site; other site 357804001349 DXD motif; other site 357804001350 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 357804001351 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 357804001352 FAD dependent oxidoreductase; Region: DAO; pfam01266 357804001353 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 357804001354 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804001355 NAD(P) binding site [chemical binding]; other site 357804001356 active site 357804001357 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 357804001358 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 357804001359 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 357804001360 Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a deformed (beta/alpha)8 barrel fold with 5- or 6-strands; Region: CE4_NodB_like_5s_6s; cd10918 357804001361 Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a deformed (beta/alpha)8 barrel fold with 5- or 6-strands; Region: CE4_NodB_like_5s_6s; cd10918 357804001362 putative active site [active] 357804001363 putative metal binding site [ion binding]; other site 357804001364 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 357804001365 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 357804001366 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 357804001367 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 357804001368 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 357804001369 Interdomain contacts; other site 357804001370 Undecaprenyl-phosphate glucose phosphotransferase; Region: WcaJ_sugtrans; TIGR03023 357804001371 Bacterial sugar transferase; Region: Bac_transf; cl00939 357804001372 alternate F1F0 ATPase, F1 subunit beta; Region: alt_F1F0_F1_bet; TIGR03305 357804001373 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 357804001374 alpha subunit interaction interface [polypeptide binding]; other site 357804001375 Walker A motif; other site 357804001376 ATP binding site [chemical binding]; other site 357804001377 Walker B motif; other site 357804001378 inhibitor binding site; inhibition site 357804001379 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 357804001380 F0F1 ATP synthase subunit epsilon; Validated; Region: PRK06228 357804001381 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 357804001382 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; cl09754 357804001383 N-ATPase, AtpR subunit; Region: AtpR; cl11871 357804001384 ATP synthase A chain; Region: ATP-synt_A; cl00413 357804001385 ATP synthase subunit C; Region: ATP-synt_C; cl00466 357804001386 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 357804001387 alternate F1F0 ATPase, F0 subunit B; Region: alt_F1F0_F0_B; TIGR03321 357804001388 alternate F1F0 ATPase, F1 subunit alpha; Region: alt_F1F0_F1_al; TIGR03324 357804001389 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 357804001390 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804001391 Walker A motif; other site 357804001392 ATP binding site [chemical binding]; other site 357804001393 Walker B motif; other site 357804001394 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 357804001395 ATP synthase; Region: ATP-synt; cl00365 357804001396 F0F1 ATP synthase subunit gamma; Provisional; Region: PRK13422 357804001397 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 357804001398 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, acyl; Region: Biotinyl_lipoyl_domains; cl11404 357804001399 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, acyl; Region: Biotinyl_lipoyl_domains; cl11404 357804001400 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 357804001401 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 357804001402 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; cl15357 357804001403 transmembrane helices; other site 357804001404 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 357804001405 Pilin (bacterial filament); Region: Pilin; pfam00114 357804001406 putative major pilin subunit; Provisional; Region: PRK10574 357804001407 putative major pilin subunit; Provisional; Region: PRK10574 357804001408 putative major pilin subunit; Provisional; Region: PRK10574 357804001409 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 357804001410 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 357804001411 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 357804001412 Walker A motif; other site 357804001413 ATP binding site [chemical binding]; other site 357804001414 Walker B motif; other site 357804001415 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 357804001416 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 357804001417 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 357804001418 Response regulator receiver domain; Region: Response_reg; pfam00072 357804001419 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 357804001420 active site 357804001421 phosphorylation site [posttranslational modification] 357804001422 intermolecular recognition site; other site 357804001423 dimerization interface [polypeptide binding]; other site 357804001424 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 357804001425 CHASE domain; Region: CHASE; cl01369 357804001426 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 357804001427 PAS fold; Region: PAS_3; pfam08447 357804001428 putative active site [active] 357804001429 heme pocket [chemical binding]; other site 357804001430 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 357804001431 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 357804001432 putative active site [active] 357804001433 heme pocket [chemical binding]; other site 357804001434 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...; Region: HisKA; cd00082 357804001435 dimer interface [polypeptide binding]; other site 357804001436 phosphorylation site [posttranslational modification] 357804001437 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 357804001438 ATP binding site [chemical binding]; other site 357804001439 Mg2+ binding site [ion binding]; other site 357804001440 G-X-G motif; other site 357804001441 Response regulator receiver domain; Region: Response_reg; pfam00072 357804001442 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 357804001443 active site 357804001444 phosphorylation site [posttranslational modification] 357804001445 intermolecular recognition site; other site 357804001446 dimerization interface [polypeptide binding]; other site 357804001447 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 357804001448 putative binding surface; other site 357804001449 active site 357804001450 Protein of unknown function (DUF3297); Region: DUF3297; pfam11730 357804001451 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 357804001452 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 357804001453 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 357804001454 N-acetylglucosamine-6-phosphate deacetylase; Region: nagA; TIGR00221 357804001455 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 357804001456 active site 357804001457 dimer interface [polypeptide binding]; other site 357804001458 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 or...; Region: GlcN6P_deaminase; cd01399 357804001459 active site 357804001460 trimer interface [polypeptide binding]; other site 357804001461 allosteric site; other site 357804001462 active site lid [active] 357804001463 hexamer (dimer of trimers) interface [polypeptide binding]; other site 357804001464 PTS system, N-acetylglucosamine-specific IIBC component; Region: PTS-II-BC-nag; TIGR01998 357804001465 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; cl00557 357804001466 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 family...; Region: PTS_IIB_glc; cd00212 357804001467 active site turn [active] 357804001468 phosphorylation site [posttranslational modification] 357804001469 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 357804001470 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 357804001471 active site 357804001472 HIGH motif; other site 357804001473 nucleotide binding site [chemical binding]; other site 357804001474 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 357804001475 KMSKS motif; other site 357804001476 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 357804001477 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 357804001478 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804001479 Walker A motif; other site 357804001480 ATP binding site [chemical binding]; other site 357804001481 Walker B motif; other site 357804001482 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 357804001483 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 357804001484 active site 357804001485 catalytic site [active] 357804001486 substrate binding site [chemical binding]; other site 357804001487 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 357804001488 RNA/DNA hybrid binding site [nucleotide binding]; other site 357804001489 active site 357804001490 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; cl16911 357804001491 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 357804001492 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 357804001493 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 357804001494 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 357804001495 N-acetyl-D-glucosamine binding site [chemical binding]; other site 357804001496 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 357804001497 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 357804001498 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 357804001499 Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; Region: E_set; cl09101 357804001500 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. MutH...; Region: MutH_Sau3AI; cd00583 357804001501 putative DNA-binding cleft [nucleotide binding]; other site 357804001502 putative DNA clevage site; other site 357804001503 molecular lever; other site 357804001504 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 plant...; Region: Ap4A_hydrolase_plant_like; cd03671 357804001505 putative active site [active] 357804001506 Ap4A binding site [chemical binding]; other site 357804001507 nudix motif; other site 357804001508 putative metal binding site [ion binding]; other site 357804001509 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional; Region: PRK11061 357804001510 GAF domain; Region: GAF; cl15785 357804001511 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 357804001512 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 357804001513 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 357804001514 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 357804001515 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 357804001516 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 357804001517 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 357804001518 dimerization interface [polypeptide binding]; other site 357804001519 active site 357804001520 glutathione reductase; Validated; Region: PRK06116 357804001521 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 357804001522 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 357804001523 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 357804001524 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; cd01494 357804001525 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 357804001526 catalytic residue [active] 357804001527 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 357804001528 PAS domain; Region: PAS_9; pfam13426 357804001529 putative active site [active] 357804001530 heme pocket [chemical binding]; other site 357804001531 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804001532 metal binding site [ion binding]; metal-binding site 357804001533 active site 357804001534 I-site; other site 357804001535 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 357804001536 FG-GAP repeat; Region: FG-GAP; cl15299 357804001537 FG-GAP repeat; Region: FG-GAP; cl15299 357804001538 FG-GAP repeat; Region: FG-GAP; cl15299 357804001539 FG-GAP repeat; Region: FG-GAP; cl15299 357804001540 FG-GAP repeat; Region: FG-GAP; cl15299 357804001541 FG-GAP repeat; Region: FG-GAP; cl15299 357804001542 FG-GAP repeat; Region: FG-GAP; cl15299 357804001543 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 357804001544 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 357804001545 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 357804001546 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 357804001547 putative active site [active] 357804001548 putative metal binding site [ion binding]; other site 357804001549 putative chaperone; Provisional; Region: PRK11678 357804001550 hypothetical protein; Provisional; Region: PRK13560 357804001551 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 357804001552 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 357804001553 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804001554 metal binding site [ion binding]; metal-binding site 357804001555 active site 357804001556 I-site; other site 357804001557 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 357804001558 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 357804001559 dimerization interface [polypeptide binding]; other site 357804001560 GTP cyclohydrolase II [Coenzyme metabolism]; Region: RibA; COG0807 357804001561 active site 357804001562 Pirin-related protein [General function prediction only]; Region: COG1741 357804001563 Cupin domain; Region: Cupin_2; cl09118 357804001564 Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: ECM4; COG0435 357804001565 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 357804001566 C-terminal, alpha helical domain of Class Omega-like Glutathione S-transferases; Region: GST_C_Omega_like; cd03190 357804001567 putative dimer interface [polypeptide binding]; other site 357804001568 N-terminal domain interface [polypeptide binding]; other site 357804001569 putative substrate binding pocket (H-site) [chemical binding]; other site 357804001570 PTS system trehalose(maltose)-specific transporter subunits IIBC; Provisional; Region: PRK11007 357804001571 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 family...; Region: PTS_IIB_glc; cd00212 357804001572 active site turn [active] 357804001573 phosphorylation site [posttranslational modification] 357804001574 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; cl00557 357804001575 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 357804001576 Alpha amylase catalytic domain found in Sucrose isomerases, oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase), dextran glucosidase (also called glucan 1,6-alpha-glucosidase), and related proteins; Region: AmyAc_SI_OligoGlu_DGase; cd11333 357804001577 Ca binding site [ion binding]; other site 357804001578 active site 357804001579 catalytic site [active] 357804001580 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 357804001581 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 357804001582 substrate binding pocket [chemical binding]; other site 357804001583 chain length determination region; other site 357804001584 substrate-Mg2+ binding site; other site 357804001585 catalytic residues [active] 357804001586 aspartate-rich region 1; other site 357804001587 active site lid residues [active] 357804001588 aspartate-rich region 2; other site 357804001589 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 357804001590 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 357804001591 GTPase CgtA; Reviewed; Region: obgE; PRK12298 357804001592 GTP1/OBG; Region: GTP1_OBG; pfam01018 357804001593 Obg GTPase; Region: Obg; cd01898 357804001594 G1 box; other site 357804001595 GTP/Mg2+ binding site [chemical binding]; other site 357804001596 Switch I region; other site 357804001597 G2 box; other site 357804001598 G3 box; other site 357804001599 Switch II region; other site 357804001600 G4 box; other site 357804001601 G5 box; other site 357804001602 hybrid sensory histidine kinase BarA; Provisional; Region: PRK11107 357804001603 Uncharacterized signal transduction histidine kinase domain (DUF2222); Region: DUF2222; pfam09984 357804001604 Histidine kinase, Adenylyl cyclase, 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...; Region: HAMP; cl01054 357804001605 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...; Region: HisKA; cd00082 357804001606 dimer interface [polypeptide binding]; other site 357804001607 phosphorylation site [posttranslational modification] 357804001608 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 357804001609 ATP binding site [chemical binding]; other site 357804001610 Mg2+ binding site [ion binding]; other site 357804001611 G-X-G motif; other site 357804001612 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 357804001613 active site 357804001614 phosphorylation site [posttranslational modification] 357804001615 intermolecular recognition site; other site 357804001616 dimerization interface [polypeptide binding]; other site 357804001617 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 357804001618 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 357804001619 TRAM domain; Region: TRAM; cl01282 357804001620 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; cl16911 357804001621 (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional; Region: relA; PRK10872 357804001622 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 357804001623 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 357804001624 synthetase active site [active] 357804001625 NTP binding site [chemical binding]; other site 357804001626 metal binding site [ion binding]; metal-binding site 357804001627 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 after...; Region: TGS_RelA_SpoT; cd01668 357804001628 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 357804001629 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 357804001630 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 357804001631 putative active site [active] 357804001632 catalytic triad [active] 357804001633 putative dimer interface [polypeptide binding]; other site 357804001634 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 357804001635 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 357804001636 Transporter associated domain; Region: CorC_HlyC; cl08393 357804001637 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 357804001638 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 357804001639 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804001640 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 357804001641 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 357804001642 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 357804001643 FeS/SAM binding site; other site 357804001644 TRAM domain; Region: TRAM; cl01282 357804001645 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804001646 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Provisional; Region: PRK08849 357804001647 malate dehydrogenase; Provisional; Region: PRK13529 357804001648 Malic enzyme, N-terminal domain; Region: malic; pfam00390 357804001649 NAD(P) binding domain of malic enzyme (ME), subgroup 1; Region: NAD_bind_1_malic_enz; cd05312 357804001650 NAD(P) binding site [chemical binding]; other site 357804001651 DctM-like transporters; Region: DctM; pfam06808 357804001652 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 357804001653 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 357804001654 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 357804001655 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 357804001656 Conserved TM helix; Region: TM_helix; pfam05552 357804001657 Mechanosensitive ion channel; Region: MS_channel; pfam00924 357804001658 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG3571 357804001659 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 357804001660 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 357804001661 putative substrate translocation pore; other site 357804001662 Transcriptional regulator [Transcription]; Region: LysR; COG0583 357804001663 Helix-turn-helix domains; Region: HTH; cl00088 357804001664 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 357804001665 substrate binding pocket [chemical binding]; other site 357804001666 dimerization interface [polypeptide binding]; other site 357804001667 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 357804001668 substrate binding site [chemical binding]; other site 357804001669 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 357804001670 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 357804001671 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, and...; Region: TM_PBP2; cd06261 357804001672 dimer interface [polypeptide binding]; other site 357804001673 conserved gate region; other site 357804001674 putative PBP binding loops; other site 357804001675 ABC-ATPase subunit interface; other site 357804001676 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 357804001677 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 357804001678 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, and...; Region: TM_PBP2; cd06261 357804001679 dimer interface [polypeptide binding]; other site 357804001680 conserved gate region; other site 357804001681 putative PBP binding loops; other site 357804001682 ABC-ATPase subunit interface; other site 357804001683 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 357804001684 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 357804001685 Walker A/P-loop; other site 357804001686 ATP binding site [chemical binding]; other site 357804001687 Q-loop/lid; other site 357804001688 ABC transporter signature motif; other site 357804001689 Walker B; other site 357804001690 D-loop; other site 357804001691 H-loop/switch region; other site 357804001692 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 357804001693 ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]; Region: AppF; COG4608 357804001694 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 357804001695 Walker A/P-loop; other site 357804001696 ATP binding site [chemical binding]; other site 357804001697 Q-loop/lid; other site 357804001698 ABC transporter signature motif; other site 357804001699 Walker B; other site 357804001700 D-loop; other site 357804001701 H-loop/switch region; other site 357804001702 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 357804001703 Transcriptional regulators [Transcription]; Region: PurR; COG1609 357804001704 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 357804001705 DNA binding site [nucleotide binding] 357804001706 domain linker motif; other site 357804001707 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 357804001708 dimerization interface (closed form) [polypeptide binding]; other site 357804001709 ligand binding site [chemical binding]; other site 357804001710 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl01155 357804001711 Laminarinase, member of the glycosyl hydrolase family 16; Region: GH16_laminarinase_like; cd08023 357804001712 active site 357804001713 catalytic residues [active] 357804001714 Glycosyl hydrolases family 17; Region: Glyco_hydro_17; cl02191 357804001715 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 357804001716 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 357804001717 catalytic residues [active] 357804001718 hinge region; other site 357804001719 alpha helical domain; other site 357804001720 Laminarinase, member of the glycosyl hydrolase family 16; Region: GH16_laminarinase_like; cd08023 357804001721 active site 357804001722 catalytic residues [active] 357804001723 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 357804001724 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 357804001725 Maltose operon periplasmic protein precursor (MalM); Region: MalM; cl11647 357804001726 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 357804001727 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 357804001728 Walker A/P-loop; other site 357804001729 ATP binding site [chemical binding]; other site 357804001730 Q-loop/lid; other site 357804001731 ABC transporter signature motif; other site 357804001732 Walker B; other site 357804001733 D-loop; other site 357804001734 H-loop/switch region; other site 357804001735 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 357804001736 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 357804001737 Walker A/P-loop; other site 357804001738 ATP binding site [chemical binding]; other site 357804001739 Q-loop/lid; other site 357804001740 ABC transporter signature motif; other site 357804001741 Walker B; other site 357804001742 D-loop; other site 357804001743 H-loop/switch region; other site 357804001744 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 357804001745 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 357804001746 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 357804001747 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 357804001748 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, and...; Region: TM_PBP2; cd06261 357804001749 dimer interface [polypeptide binding]; other site 357804001750 conserved gate region; other site 357804001751 putative PBP binding loops; other site 357804001752 ABC-ATPase subunit interface; other site 357804001753 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 357804001754 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 357804001755 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, and...; Region: TM_PBP2; cd06261 357804001756 dimer interface [polypeptide binding]; other site 357804001757 conserved gate region; other site 357804001758 putative PBP binding loops; other site 357804001759 ABC-ATPase subunit interface; other site 357804001760 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; cl00566 357804001761 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 357804001762 NAD(P) transhydrogenase subunit alpha; Provisional; Region: pntA; PRK09424 357804001763 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; cl15379 357804001764 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804001765 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 357804001766 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 357804001767 active site 357804001768 ATP-dependent helicase HepA; Validated; Region: PRK04914 357804001769 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 357804001770 ATP binding site [chemical binding]; other site 357804001771 putative Mg++ binding site [ion binding]; other site 357804001772 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 357804001773 nucleotide binding region [chemical binding]; other site 357804001774 ATP-binding site [chemical binding]; other site 357804001775 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 357804001776 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 357804001777 DNA-binding site [nucleotide binding]; DNA binding site 357804001778 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 357804001779 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804001780 homodimer interface [polypeptide binding]; other site 357804001781 catalytic residue [active] 357804001782 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 357804001783 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 357804001784 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 357804001785 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 357804001786 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 357804001787 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804001788 Walker A/P-loop; other site 357804001789 ATP binding site [chemical binding]; other site 357804001790 Q-loop/lid; other site 357804001791 ABC transporter signature motif; other site 357804001792 Walker B; other site 357804001793 D-loop; other site 357804001794 H-loop/switch region; other site 357804001795 ABC-2 type transporter; Region: ABC2_membrane; cl11417 357804001796 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; cl16911 357804001797 TMAO/DMSO reductase; Reviewed; Region: PRK05363 357804001798 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 357804001799 Moco binding site; other site 357804001800 metal coordination site [ion binding]; other site 357804001801 Ferric reductase like transmembrane component; Region: Ferric_reduct; cl01043 357804001802 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 357804001803 tetramerization interface [polypeptide binding]; other site 357804001804 active site 357804001805 pantoate--beta-alanine ligase; Region: panC; TIGR00018 357804001806 Pantoate-beta-alanine ligase; Region: PanC; cd00560 357804001807 active site 357804001808 ATP-binding site [chemical binding]; other site 357804001809 pantoate-binding site; other site 357804001810 HXXH motif; other site 357804001811 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 357804001812 oligomerization interface [polypeptide binding]; other site 357804001813 active site 357804001814 metal binding site [ion binding]; metal-binding site 357804001815 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 357804001816 catalytic center binding site [active] 357804001817 ATP binding site [chemical binding]; other site 357804001818 poly(A) polymerase; Region: pcnB; TIGR01942 357804001819 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 357804001820 active site 357804001821 NTP binding site [chemical binding]; other site 357804001822 metal binding triad [ion binding]; metal-binding site 357804001823 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 357804001824 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 357804001825 tRNA synthetases class I (E and Q), catalytic domain; Region: tRNA-synt_1c; pfam00749 357804001826 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 357804001827 active site 357804001828 nucleotide binding site [chemical binding]; other site 357804001829 HIGH motif; other site 357804001830 KMSKS motif; other site 357804001831 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 357804001832 ATP-dependent helicase HrpB; Region: DEAH_box_HrpB; TIGR01970 357804001833 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 357804001834 ATP binding site [chemical binding]; other site 357804001835 putative Mg++ binding site [ion binding]; other site 357804001836 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804001837 Helicase associated domain (HA2); Region: HA2; cl04503 357804001838 ATP-dependent helicase C-terminal; Region: HrpB_C; pfam08482 357804001839 Domain of unknown function (DUF4126); Region: DUF4126; pfam13548 357804001840 Short C-terminal domain; Region: SHOCT; cl01373 357804001841 Uncharacterized BCR, YnfA/UPF0060 family; Region: UPF0060; cl00757 357804001842 PilX N-terminal; Region: PilX_N; pfam14341 357804001843 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 357804001844 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 357804001845 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 357804001846 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 357804001847 active site 357804001848 ADP/pyrophosphate binding site [chemical binding]; other site 357804001849 dimerization interface [polypeptide binding]; other site 357804001850 allosteric effector site; other site 357804001851 fructose-1,6-bisphosphate binding site; other site 357804001852 Protein of unknown function (DUF3465); Region: DUF3465; pfam11948 357804001853 LysE type translocator; Region: LysE; cl00565 357804001854 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 as...; Region: ASCH_yqfb_like; cd06552 357804001855 penicillin-binding protein 1B; Region: PBP_1b; TIGR02071 357804001856 Transglycosylase; Region: Transgly; cl07896 357804001857 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 357804001858 Fe-S metabolism associated domain; Region: SufE; cl00951 357804001859 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 357804001860 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; cl16911 357804001861 Protein of unknown function (DUF890); Region: Methyltransf_10; pfam05971 357804001862 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 357804001863 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804001864 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 357804001865 L-serine binding site [chemical binding]; other site 357804001866 ACT domain interface; other site 357804001867 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 357804001868 tetramer (dimer of dimers) interface [polypeptide binding]; other site 357804001869 active site 357804001870 dimer interface [polypeptide binding]; other site 357804001871 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 357804001872 Putative integral membrane protein (DUF2391); Region: DUF2391; cl01935 357804001873 Cell division protein ZapA; Region: ZapA; cl01146 357804001874 Uncharacterized protein family (UPF0149); Region: UPF0149; cl01173 357804001875 proline aminopeptidase P II; Provisional; Region: PRK10879 357804001876 Aminopeptidase P, N-terminal domain; Region: AMP_N; cl08433 357804001877 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 on...; Region: Prolidase; cd01087 357804001878 active site 357804001879 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804001880 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 357804001881 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804001882 hypothetical protein; Provisional; Region: PRK06753 357804001883 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804001884 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 357804001885 trans-2-enoyl-CoA reductase; Provisional; Region: PRK13656 357804001886 NAD(P)H binding domain of trans-2-enoyl-CoA reductase; Region: Eno-Rase_NADH_b; pfam12242 357804001887 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804001888 Enoyl reductase FAD binding domain; Region: Eno-Rase_FAD_bd; pfam07055 357804001889 Transcriptional regulators [Transcription]; Region: MarR; COG1846 357804001890 Helix-turn-helix domains; Region: HTH; cl00088 357804001891 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 357804001892 Helix-turn-helix domains; Region: HTH; cl00088 357804001893 NMT1-like family; Region: NMT1_2; cl15260 357804001894 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 357804001895 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, and...; Region: TM_PBP2; cd06261 357804001896 dimer interface [polypeptide binding]; other site 357804001897 conserved gate region; other site 357804001898 putative PBP binding loops; other site 357804001899 ABC-ATPase subunit interface; other site 357804001900 glycine betaine transporter ATP-binding subunit; Provisional; Region: PRK10070 357804001901 This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these...; Region: ABC_Pro_Gly_Bertaine; cd03294 357804001902 Walker A/P-loop; other site 357804001903 ATP binding site [chemical binding]; other site 357804001904 Q-loop/lid; other site 357804001905 ABC transporter signature motif; other site 357804001906 Walker B; other site 357804001907 D-loop; other site 357804001908 H-loop/switch region; other site 357804001909 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the ABC transporter OpuCA. OpuCA is the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing...; Region: CBS_pair_ABC_OpuCA_assoc2; cd04583 357804001910 KpsF/GutQ family protein; Region: kpsF; TIGR00393 357804001911 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...; Region: SIS_Kpsf; cd05014 357804001912 putative active site [active] 357804001913 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 357804001914 Dicarboxylate transport; Region: DctA-YdbH; cl14674 357804001915 YnbE-like lipoprotein; Region: Lipoprotein_19; pfam13617 357804001916 Protein of unknown function (DUF1318); Region: DUF1318; cl01547 357804001917 Protein of unknown function (DUF1145); Region: DUF1145; cl11481 357804001918 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 357804001919 S-adenosylmethionine binding site [chemical binding]; other site 357804001920 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 357804001921 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 357804001922 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 357804001923 P loop; other site 357804001924 GTP binding site [chemical binding]; other site 357804001925 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 357804001926 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804001927 Walker A/P-loop; other site 357804001928 ATP binding site [chemical binding]; other site 357804001929 Q-loop/lid; other site 357804001930 ABC transporter signature motif; other site 357804001931 Walker B; other site 357804001932 D-loop; other site 357804001933 H-loop/switch region; other site 357804001934 putative protein insertion permease FtsX; Region: ftsX; TIGR00439 357804001935 FtsX-like permease family; Region: FtsX; cl15850 357804001936 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 357804001937 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 357804001938 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 357804001939 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 or...; Region: Sigma70_r4; cd06171 357804001940 DNA binding residues [nucleotide binding] 357804001941 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 357804001942 Prephenate dehydratase; Region: PDT; pfam00800 357804001943 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 357804001944 putative L-Phe binding site [chemical binding]; other site 357804001945 tRNA (uracil-5-)-methyltransferase; Region: trmA_only; TIGR02143 357804001946 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 357804001947 S-adenosylmethionine binding site [chemical binding]; other site 357804001948 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 357804001949 NnrS protein; Region: NnrS; cl01258 357804001950 Predicted transcriptional regulator [Transcription]; Region: COG1959 357804001951 Helix-turn-helix domains; Region: HTH; cl00088 357804001952 HPP family; Region: HPP; pfam04982 357804001953 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 357804001954 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 357804001955 Domain of unknown function (DUF4202); Region: DUF4202; pfam13875 357804001956 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 357804001957 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 357804001958 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 357804001959 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; cl00047 357804001960 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 357804001961 RNA/DNA binding site [nucleotide binding]; other site 357804001962 RRM dimerization site [polypeptide binding]; other site 357804001963 GTP-binding protein LepA; Provisional; Region: PRK05433 357804001964 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 357804001965 G1 box; other site 357804001966 putative GEF interaction site [polypeptide binding]; other site 357804001967 GTP/Mg2+ binding site [chemical binding]; other site 357804001968 Switch I region; other site 357804001969 G2 box; other site 357804001970 G3 box; other site 357804001971 Switch II region; other site 357804001972 G4 box; other site 357804001973 G5 box; other site 357804001974 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-Tu...; Region: lepA_II; cd03699 357804001975 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 357804001976 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 357804001977 signal peptidase I; Provisional; Region: PRK10861 357804001978 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 357804001979 Catalytic site [active] 357804001980 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 357804001981 ribonuclease III; Reviewed; Region: rnc; PRK00102 357804001982 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...; Region: RIBOc; cd00593 357804001983 dimerization interface [polypeptide binding]; other site 357804001984 active site 357804001985 metal binding site [ion binding]; metal-binding site 357804001986 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 III; Region: DSRM; cd00048 357804001987 dsRNA binding site [nucleotide binding]; other site 357804001988 GTPase Era; Reviewed; Region: era; PRK00089 357804001989 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 357804001990 G1 box; other site 357804001991 GTP/Mg2+ binding site [chemical binding]; other site 357804001992 Switch I region; other site 357804001993 G2 box; other site 357804001994 Switch II region; other site 357804001995 G3 box; other site 357804001996 G4 box; other site 357804001997 G5 box; other site 357804001998 KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional...; Region: KH-II; cl00098 357804001999 Recombination protein O N terminal; Region: RecO_N; cl15812 357804002000 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 357804002001 Recombination protein O C terminal; Region: RecO_C; pfam02565 357804002002 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 357804002003 active site 357804002004 hydrophilic channel; other site 357804002005 dimerization interface [polypeptide binding]; other site 357804002006 catalytic residues [active] 357804002007 active site lid [active] 357804002008 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 357804002009 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 357804002010 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 357804002011 catalytic residue [active] 357804002012 Glycerate kinase family; Region: Gly_kinase; cl00841 357804002013 DctM-like transporters; Region: DctM; pfam06808 357804002014 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 357804002015 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 357804002016 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 357804002017 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 357804002018 bifunctional aldehyde dehydrogenase/enoyl-CoA hydratase; Provisional; Region: PRK11563 357804002019 N-terminal domain of the monoamine oxidase C dehydratase; Region: ALDH_MaoC-N; cd07128 357804002020 substrate binding site [chemical binding]; other site 357804002021 dimer interface [polypeptide binding]; other site 357804002022 NADP binding site [chemical binding]; other site 357804002023 catalytic residues [active] 357804002024 MaoC_C The C-terminal hot dog fold of the MaoC (monoamine oxidase C) dehydratase regulatory protein. Orthologs of MaoC include PaaZ [Escherichia coli] and PaaN [Pseudomonas putida], which are putative ring-opening enzymes involved in phenylacetic acid...; Region: MaoC_C; cd03452 357804002025 substrate binding site [chemical binding]; other site 357804002026 Phenylacetic acid catabolic protein; Region: PaaA_PaaC; cl01346 357804002027 phenylacetate-CoA oxygenase, PaaG subunit; Region: PA_CoA_Oxy1; TIGR02156 357804002028 Phenylacetic acid degradation B; Region: PaaB; cl01371 357804002029 Phenylacetic acid catabolic protein; Region: PaaA_PaaC; cl01346 357804002030 Domain of unknown function DUF59; Region: DUF59; cl00941 357804002031 phenylacetate-CoA oxygenase, PaaJ subunit; Region: PA_CoA_Oxy4; TIGR02159 357804002032 phenylacetate-CoA oxygenase/reductase, PaaK subunit; Region: PA_CoA_Oxy5; TIGR02160 357804002033 NAD(P) binding domain of ferredoxin reductase like phenylacetic acid (PA) degradation oxidoreductase. PA oxidoreductases of E. coli hydroxylate PA-CoA in the second step of PA degradation. Members of this group typically fuse a ferredoxin reductase-like...; Region: PA_degradation_oxidoreductase_like; cd06214 357804002034 FAD binding pocket [chemical binding]; other site 357804002035 FAD binding motif [chemical binding]; other site 357804002036 phosphate binding motif [ion binding]; other site 357804002037 beta-alpha-beta structure motif; other site 357804002038 NAD(p) ribose binding residues [chemical binding]; other site 357804002039 NAD binding pocket [chemical binding]; other site 357804002040 NAD(P)-pyrophosphate-nicotinamide binding residues [chemical binding]; other site 357804002041 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 357804002042 catalytic loop [active] 357804002043 iron binding site [ion binding]; other site 357804002044 enoyl-CoA hydratase-isomerase; Provisional; Region: PRK09674 357804002045 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 357804002046 substrate binding site [chemical binding]; other site 357804002047 oxyanion hole (OAH) forming residues; other site 357804002048 trimer interface [polypeptide binding]; other site 357804002049 enoyl-CoA hydratase; Provisional; Region: PRK08140 357804002050 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 357804002051 substrate binding site [chemical binding]; other site 357804002052 oxyanion hole (OAH) forming residues; other site 357804002053 trimer interface [polypeptide binding]; other site 357804002054 3-hydroxy-acyl-CoA dehydrogenase; Validated; Region: PRK08268 357804002055 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804002056 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 357804002057 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 357804002058 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 357804002059 CoenzymeA binding site [chemical binding]; other site 357804002060 subunit interaction site [polypeptide binding]; other site 357804002061 PHB binding site; other site 357804002062 beta-ketoadipyl CoA thiolase; Validated; Region: PRK09050 357804002063 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 357804002064 dimer interface [polypeptide binding]; other site 357804002065 active site 357804002066 AMP-binding enzyme; Region: AMP-binding; cl15778 357804002067 phenylacetate-CoA ligase; Region: PA_CoA_ligase; TIGR02155 357804002068 phenylacetic acid degradation operon negative regulatory protein PaaX; Region: PaaX_trns_reg; TIGR02277 357804002069 PaaX-like protein; Region: PaaX; pfam07848 357804002070 PaaX-like protein C-terminal domain; Region: PaaX_C; pfam08223 357804002071 phenylacetic acid degradation protein PaaY; Region: PaaY; TIGR02287 357804002072 paaY-like: This group is composed by uncharacterized proteins with similarity to the protein product of the E. coli paaY gene, which is part of the paa gene cluster responsible for phenylacetic acid degradation. Proteins in this group are expected to...; Region: LbH_paaY_like; cd04745 357804002073 putative trimer interface [polypeptide binding]; other site 357804002074 putative metal binding site [ion binding]; other site 357804002075 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 357804002076 Protein export membrane protein; Region: SecD_SecF; cl14618 357804002077 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 357804002078 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, acyl; Region: Biotinyl_lipoyl_domains; cl11404 357804002079 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, acyl; Region: Biotinyl_lipoyl_domains; cl11404 357804002080 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 357804002081 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) N-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs; Region: NTP-PPase_MazG_Nterm; cd11528 357804002082 homodimer interface [polypeptide binding]; other site 357804002083 metal binding site [ion binding]; metal-binding site 357804002084 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs'; Region: NTP-PPase_MazG_Cterm; cd11529 357804002085 homodimer interface [polypeptide binding]; other site 357804002086 active site 357804002087 putative chemical substrate binding site [chemical binding]; other site 357804002088 metal binding site [ion binding]; metal-binding site 357804002089 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. Trimers...; Region: gram_neg_porins; cd00342 357804002090 eyelet of channel; other site 357804002091 trimer interface [polypeptide binding]; other site 357804002092 CTP synthetase; Validated; Region: pyrG; PRK05380 357804002093 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 nascent...; Region: CTGs; cd03113 357804002094 Catalytic site [active] 357804002095 active site 357804002096 UTP binding site [chemical binding]; other site 357804002097 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 357804002098 active site 357804002099 putative oxyanion hole; other site 357804002100 catalytic triad [active] 357804002101 enolase; Provisional; Region: eno; PRK00077 357804002102 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 357804002103 dimer interface [polypeptide binding]; other site 357804002104 metal binding site [ion binding]; metal-binding site 357804002105 substrate binding pocket [chemical binding]; other site 357804002106 Septum formation initiator; Region: DivIC; cl11433 357804002107 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 357804002108 substrate binding site; other site 357804002109 dimer interface; other site 357804002110 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 biosynthesis; Region: MECDP_synthase; cd00554 357804002111 homotrimer interaction site [polypeptide binding]; other site 357804002112 zinc binding site [ion binding]; other site 357804002113 CDP-binding sites; other site 357804002114 tRNA pseudouridine synthase D (TruD); Region: TruD; pfam01142 357804002115 Pseudouridine synthase, similar to Escherichia coli TruD; Region: PseudoU_synth_EcTruD; cd02575 357804002116 Permutation of conserved domain; other site 357804002117 active site 357804002118 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 357804002119 Survival protein SurE; Region: SurE; cl00448 357804002120 Protein of unknown function (DUF1471); Region: DUF1471; cl11507 357804002121 lipoprotein NlpD; Provisional; Region: nlpD; PRK10871 357804002122 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 357804002123 RNA polymerase sigma factor RpoS; Region: rpoS_proteo; TIGR02394 357804002124 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 357804002125 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 357804002126 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 357804002127 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 or...; Region: Sigma70_r4; cd06171 357804002128 DNA binding residues [nucleotide binding] 357804002129 Protein of unknown function (DUF3545); Region: DUF3545; pfam12065 357804002130 hypothetical protein; Provisional; Region: PRK10506 357804002131 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 357804002132 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3323 357804002133 YcxB-like protein; Region: YcxB; pfam14317 357804002134 cystathionine beta-lyase; Provisional; Region: PRK09028 357804002135 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 357804002136 homodimer interface [polypeptide binding]; other site 357804002137 substrate-cofactor binding pocket; other site 357804002138 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804002139 catalytic residue [active] 357804002140 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 357804002141 thymidine kinase; Provisional; Region: PRK04296 357804002142 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the...; Region: S2P-M50_like_2; cd06160 357804002143 active site 357804002144 putative substrate binding region [chemical binding]; other site 357804002145 Predicted thiol oxidoreductase [Energy production and conversion]; Region: COG3488 357804002146 Imelysin; Region: Peptidase_M75; cl09159 357804002147 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 357804002148 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; cl01132 357804002149 outer membrane protein A; Reviewed; Region: PRK10808 357804002150 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl01155 357804002151 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 357804002152 ligand binding site [chemical binding]; other site 357804002153 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 357804002154 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 357804002155 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 357804002156 Walker A/P-loop; other site 357804002157 ATP binding site [chemical binding]; other site 357804002158 Q-loop/lid; other site 357804002159 ABC transporter signature motif; other site 357804002160 Walker B; other site 357804002161 D-loop; other site 357804002162 H-loop/switch region; other site 357804002163 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 357804002164 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 357804002165 active site 357804002166 purine riboside binding site [chemical binding]; other site 357804002167 Domain of unknown function (DUF368); Region: DUF368; cl00893 357804002168 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; cl15357 357804002169 Citrate transporter; Region: CitMHS; pfam03600 357804002170 transmembrane helices; other site 357804002171 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 357804002172 putative active site [active] 357804002173 putative CoA binding site [chemical binding]; other site 357804002174 nudix motif; other site 357804002175 metal binding site [ion binding]; metal-binding site 357804002176 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 357804002177 S-adenosylmethionine binding site [chemical binding]; other site 357804002178 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 357804002179 S-adenosylmethionine binding site [chemical binding]; other site 357804002180 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 357804002181 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 357804002182 dimer interface [polypeptide binding]; other site 357804002183 anticodon binding site; other site 357804002184 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 357804002185 homodimer interface [polypeptide binding]; other site 357804002186 motif 1; other site 357804002187 active site 357804002188 motif 2; other site 357804002189 GAD domain; Region: GAD; pfam02938 357804002190 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 attaches...; Region: class_II_aaRS-like_core; cl00268 357804002191 active site 357804002192 motif 3; other site 357804002193 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl01155 357804002194 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 357804002195 dinuclear metal binding motif [ion binding]; other site 357804002196 cyanate hydratase; Validated; Region: PRK02866 357804002197 Cyanase C-terminal domain. Cyanase (Cyanate lyase) is responsible for the hydrolysis of cyanate. It catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. This allows organisms that possess the enzyme to overcome the...; Region: Cyanase_C; cd00559 357804002198 oligomer interface [polypeptide binding]; other site 357804002199 active site 357804002200 Formate/nitrite transporter; Region: Form_Nir_trans; cl00927 357804002201 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 357804002202 active site 357804002203 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 357804002204 Catalytic domain of Protein Kinases; Region: PKc; cd00180 357804002205 active site 357804002206 ATP binding site [chemical binding]; other site 357804002207 substrate binding site [chemical binding]; other site 357804002208 activation loop (A-loop); other site 357804002209 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; cl16911 357804002210 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_b; cd00914 357804002211 aromatic arch; other site 357804002212 DCoH dimer interaction site [polypeptide binding]; other site 357804002213 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 357804002214 DCoH tetramer interaction site [polypeptide binding]; other site 357804002215 substrate binding site [chemical binding]; other site 357804002216 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 357804002217 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804002218 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 357804002219 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 357804002220 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 357804002221 DctM-like transporters; Region: DctM; pfam06808 357804002222 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 357804002223 Sugar fermentation stimulation protein; Region: SfsA; cl00647 357804002224 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 357804002225 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 357804002226 active site 357804002227 phosphorylation site [posttranslational modification] 357804002228 intermolecular recognition site; other site 357804002229 dimerization interface [polypeptide binding]; other site 357804002230 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 ABC; Region: AAA; cd00009 357804002231 Walker A motif; other site 357804002232 ATP binding site [chemical binding]; other site 357804002233 Walker B motif; other site 357804002234 arginine finger; other site 357804002235 Helix-turn-helix domains; Region: HTH; cl00088 357804002236 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 357804002237 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...; Region: HisKA; cd00082 357804002238 dimer interface [polypeptide binding]; other site 357804002239 phosphorylation site [posttranslational modification] 357804002240 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 357804002241 ATP binding site [chemical binding]; other site 357804002242 Mg2+ binding site [ion binding]; other site 357804002243 G-X-G motif; other site 357804002244 Protein of unknown function (DUF3461); Region: DUF3461; cl10125 357804002245 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 357804002246 active site 357804002247 putative DNA-binding cleft [nucleotide binding]; other site 357804002248 dimer interface [polypeptide binding]; other site 357804002249 putative chloramphenical resistance permease RarD; Provisional; Region: PRK15430 357804002250 EamA-like transporter family; Region: EamA; cl01037 357804002251 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 357804002252 RuvA N terminal domain; Region: RuvA_N; pfam01330 357804002253 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 357804002254 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 357804002255 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 ABC; Region: AAA; cd00009 357804002256 Walker A motif; other site 357804002257 ATP binding site [chemical binding]; other site 357804002258 Walker B motif; other site 357804002259 arginine finger; other site 357804002260 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 357804002261 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 357804002262 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 357804002263 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 357804002264 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 357804002265 Membrane bound YbgT-like protein; Region: YbgT_YccB; cl02039 357804002266 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 sites; Region: 4HBT; cd00586 357804002267 active site 357804002268 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 357804002269 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 357804002270 TolA protein; Region: tolA_full; TIGR02794 357804002271 Gram-negative bacterial tonB protein; Region: TonB; cl10048 357804002272 translocation protein TolB; Provisional; Region: tolB; PRK04792 357804002273 TolB amino-terminal domain; Region: TolB_N; cl00639 357804002274 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 357804002275 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 357804002276 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 357804002277 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 357804002278 ligand binding site [chemical binding]; other site 357804002279 tol-pal system protein YbgF; Provisional; Region: PRK10803 357804002280 Tetratricopeptide repeat; Region: TPR_6; pfam13174 357804002281 Quinolinate synthetase A protein; Region: NadA; cl00420 357804002282 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4807 357804002283 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 357804002284 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 357804002285 endonuclease III; Provisional; Region: PRK10702 357804002286 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 357804002287 minor groove reading motif; other site 357804002288 helix-hairpin-helix signature motif; other site 357804002289 substrate binding pocket [chemical binding]; other site 357804002290 active site 357804002291 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 357804002292 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 357804002293 FMN-binding domain; Region: FMN_bind; cl01081 357804002294 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 357804002295 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 357804002296 RnfC Barrel sandwich hybrid domain; Region: RnfC_N; pfam13375 357804002297 SLBB domain; Region: SLBB; pfam10531 357804002298 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...; Region: HCP_like; cl14655 357804002299 Protein of unknown function (DUF2968); Region: DUF2968; pfam11180 357804002300 electron transport complex protein RnfC; Provisional; Region: PRK05035 357804002301 electron transport complex protein RnfB; Provisional; Region: PRK05113 357804002302 Putative Fe-S cluster; Region: FeS; pfam04060 357804002303 4Fe-4S binding domain; Region: Fer4; cl02805 357804002304 4Fe-4S binding domain; Region: Fer4; cl02805 357804002305 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 357804002306 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK09263 357804002307 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK09263 357804002308 ATP cone domain; Region: ATP-cone; pfam03477 357804002309 Class III ribonucleotide reductase; Region: RNR_III; cd01675 357804002310 effector binding site; other site 357804002311 active site 357804002312 Zn binding site [ion binding]; other site 357804002313 glycine loop; other site 357804002314 anaerobic ribonucleotide reductase-activating protein; Provisional; Region: nrdG; cl15804 357804002315 4Fe-4S single cluster domain; Region: Fer4_12; pfam13353 357804002316 ATP-dependent Clp protease adaptor protein ClpS; Region: ClpS; cl00933 357804002317 ATP-dependent Clp protease ATP-binding subunit; Provisional; Region: clpA; PRK11034 357804002318 Clp amino terminal domain; Region: Clp_N; pfam02861 357804002319 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 ABC; Region: AAA; cd00009 357804002320 Walker A motif; other site 357804002321 ATP binding site [chemical binding]; other site 357804002322 Walker B motif; other site 357804002323 arginine finger; other site 357804002324 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 ABC; Region: AAA; cd00009 357804002325 Walker A motif; other site 357804002326 ATP binding site [chemical binding]; other site 357804002327 Walker B motif; other site 357804002328 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 357804002329 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 357804002330 rRNA binding site [nucleotide binding]; other site 357804002331 predicted 30S ribosome binding site; other site 357804002332 BolA-like protein; Region: BolA; cl00386 357804002333 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 357804002334 RnfC Barrel sandwich hybrid domain; Region: RnfC_N; pfam13375 357804002335 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 357804002336 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 357804002337 FMN-binding domain; Region: FMN_bind; cl01081 357804002338 Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrC [Energy production and conversion]; Region: NqrC; COG2869 357804002339 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 357804002340 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 357804002341 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 357804002342 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 357804002343 catalytic loop [active] 357804002344 iron binding site [ion binding]; other site 357804002345 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+ oxidoreductase; Region: NADH_quinone_reductase; cd06188 357804002346 FAD binding pocket [chemical binding]; other site 357804002347 FAD binding motif [chemical binding]; other site 357804002348 phosphate binding motif [ion binding]; other site 357804002349 beta-alpha-beta structure motif; other site 357804002350 NAD binding pocket [chemical binding]; other site 357804002351 ApbE family; Region: ApbE; cl00643 357804002352 Protein of unknown function (DUF539); Region: DUF539; cl01129 357804002353 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; cl00727 357804002354 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 357804002355 DNA-binding site [nucleotide binding]; DNA binding site 357804002356 RNA-binding motif; other site 357804002357 2'-deoxycytidine 5'-triphosphate deaminase (DCD); Region: DCD; pfam06559 357804002358 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 357804002359 trimer interface [polypeptide binding]; other site 357804002360 active site 357804002361 hypothetical protein; Provisional; Region: PRK05939 357804002362 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 357804002363 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 357804002364 catalytic residue [active] 357804002365 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 357804002366 active site 357804002367 NTP binding site [chemical binding]; other site 357804002368 metal binding triad [ion binding]; metal-binding site 357804002369 antibiotic binding site [chemical binding]; other site 357804002370 Protein of unknown function DUF86; Region: DUF86; cl01031 357804002371 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 357804002372 active site 357804002373 NTP binding site [chemical binding]; other site 357804002374 metal binding triad [ion binding]; metal-binding site 357804002375 antibiotic binding site [chemical binding]; other site 357804002376 Protein of unknown function DUF86; Region: DUF86; cl01031 357804002377 Capsule assembly protein Wzi; Region: Caps_assemb_Wzi; pfam14052 357804002378 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 357804002379 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 357804002380 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 357804002381 Capsule biosynthesis GfcC; Region: Caps_synth_GfcC; pfam06251 357804002382 SLBB domain; Region: SLBB; pfam10531 357804002383 Chain length determinant protein [Cell envelope biogenesis, outer membrane]; Region: WzzB; COG3765 357804002384 Chain length determinant protein; Region: Wzz; cl15801 357804002385 Chain length determinant protein; Region: Wzz; cl15801 357804002386 GDP-mannose glycosyl hydrolase (AKA GDP-mannose mannosyl hydrolase (GDPMH)) is a member of the Nudix hydrolase superfamily. This class of enzymes is unique from other members of the superfamily in two aspects. First, it contains a modified Nudix...; Region: GDPMH; cd03430 357804002387 active site 357804002388 GDP-Mannose binding site [chemical binding]; other site 357804002389 dimer interface [polypeptide binding]; other site 357804002390 modified nudix motif 357804002391 metal binding site [ion binding]; metal-binding site 357804002392 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 357804002393 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 357804002394 Substrate binding site; other site 357804002395 Cupin domain; Region: Cupin_2; cl09118 357804002396 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 357804002397 Transposase [DNA replication, recombination, and repair]; Region: COG5433 357804002398 Transposase [DNA replication, recombination, and repair]; Region: COG5433 357804002399 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 357804002400 ManB is a bacterial phosphomannomutase (PMM) that catalyzes the conversion of mannose 6-phosphate to mannose-1-phosphate in the second of three steps in the GDP-mannose pathway, in which GDP-D-mannose is synthesized from fructose-6-phosphate. In...; Region: ManB; cd03088 357804002401 active site 357804002402 substrate binding site [chemical binding]; other site 357804002403 metal binding site [ion binding]; metal-binding site 357804002404 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 357804002405 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 357804002406 NADP-binding site; other site 357804002407 homotetramer interface [polypeptide binding]; other site 357804002408 substrate binding site [chemical binding]; other site 357804002409 homodimer interface [polypeptide binding]; other site 357804002410 active site 357804002411 GDP-fucose synthetase, extended (e) SDRs; Region: GDP_FS_SDR_e; cd05239 357804002412 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 357804002413 NADP binding site [chemical binding]; other site 357804002414 active site 357804002415 putative substrate binding site [chemical binding]; other site 357804002416 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 357804002417 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 357804002418 catalytic loop [active] 357804002419 iron binding site [ion binding]; other site 357804002420 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, FMN; Region: flavin_oxioreductase; cd06189 357804002421 FAD binding pocket [chemical binding]; other site 357804002422 FAD binding motif [chemical binding]; other site 357804002423 phosphate binding motif [ion binding]; other site 357804002424 beta-alpha-beta structure motif; other site 357804002425 NAD binding pocket [chemical binding]; other site 357804002426 G1P_cytidylyltransferase catalyzes the production of CDP-D-Glucose; Region: G1P_cytidylyltransferase; cd02524 357804002427 substrate binding site; other site 357804002428 CDP-glucose 4,6-dehydratase; Region: CDP_4_6_dhtase; TIGR02622 357804002429 CDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: CDP_GD_SDR_e; cd05252 357804002430 NAD binding site [chemical binding]; other site 357804002431 homotetramer interface [polypeptide binding]; other site 357804002432 homodimer interface [polypeptide binding]; other site 357804002433 substrate binding site [chemical binding]; other site 357804002434 active site 357804002435 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 357804002436 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 357804002437 inhibitor-cofactor binding pocket; inhibition site 357804002438 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804002439 catalytic residue [active] 357804002440 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804002441 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 357804002442 NAD(P) binding site [chemical binding]; other site 357804002443 active site 357804002444 CDP-tyvelose 2-epimerase, extended (e) SDRs; Region: CDP_TE_SDR_e; cd05258 357804002445 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 357804002446 NAD binding site [chemical binding]; other site 357804002447 homotetramer interface [polypeptide binding]; other site 357804002448 homodimer interface [polypeptide binding]; other site 357804002449 active site 357804002450 substrate binding site [chemical binding]; other site 357804002451 MatE; Region: MatE; cl10513 357804002452 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 357804002453 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 357804002454 active site 357804002455 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 357804002456 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 357804002457 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 357804002458 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 357804002459 Transposase [DNA replication, recombination, and repair]; Region: COG5433 357804002460 Transposase [DNA replication, recombination, and repair]; Region: COG5433 357804002461 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 357804002462 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 357804002463 NAD(P) binding site [chemical binding]; other site 357804002464 homodimer interface [polypeptide binding]; other site 357804002465 substrate binding site [chemical binding]; other site 357804002466 active site 357804002467 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 357804002468 dTDP-4-dehydrorhamnose reductase [Cell envelope biogenesis, outer membrane]; Region: RfbD; COG1091 357804002469 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 357804002470 NADP binding site [chemical binding]; other site 357804002471 active site 357804002472 putative substrate binding site [chemical binding]; other site 357804002473 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 357804002474 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 357804002475 active site 357804002476 homodimer interface [polypeptide binding]; other site 357804002477 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 357804002478 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 357804002479 Transposase [DNA replication, recombination, and repair]; Region: COG5433 357804002480 Transposase [DNA replication, recombination, and repair]; Region: COG5433 357804002481 DDE superfamily endonuclease; Region: DDE_4; cl15789 357804002482 undecaprenyl-phosphate alpha-N-acetylglucosaminyl 1-phosphatetransferase; Region: ECA_wecA; TIGR02380 357804002483 This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins. WecA is an UDP-N-acetylglucosamine (GlcNAc):undecaprenyl-phosphate (Und-P) GlcNAc-1-phosphate transferase that catalyzes the formation of a phosphodiester bond...; Region: GT_WecA_like; cd06853 357804002484 Mg++ binding site [ion binding]; other site 357804002485 putative catalytic motif [active] 357804002486 substrate binding site [chemical binding]; other site 357804002487 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 357804002488 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 357804002489 Active Sites [active] 357804002490 S23 ribosomal protein; Region: Ribosomal_S23p; cl05287 357804002491 sulfate adenylyltransferase subunit 1; Provisional; Region: cysN; PRK05124 357804002492 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 357804002493 CysD dimerization site [polypeptide binding]; other site 357804002494 G1 box; other site 357804002495 putative GEF interaction site [polypeptide binding]; other site 357804002496 GTP/Mg2+ binding site [chemical binding]; other site 357804002497 Switch I region; other site 357804002498 G2 box; other site 357804002499 G3 box; other site 357804002500 Switch II region; other site 357804002501 G4 box; other site 357804002502 G5 box; other site 357804002503 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 CysN...; Region: CysN_NodQ_II; cd03695 357804002504 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 CysN...; Region: CysN_NoDQ_III; cd04095 357804002505 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; cl15357 357804002506 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; cl15357 357804002507 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; cl15357 357804002508 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; cl15357 357804002509 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 of...; Region: APSK; cd02027 357804002510 Gluconate kinase [Carbohydrate transport and metabolism]; Region: GntK; COG3265 357804002511 ligand-binding site [chemical binding]; other site 357804002512 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 357804002513 RNA/DNA binding site [nucleotide binding]; other site 357804002514 RRM dimerization site [polypeptide binding]; other site 357804002515 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 357804002516 Transposase [DNA replication, recombination, and repair]; Region: COG5433 357804002517 Transposase [DNA replication, recombination, and repair]; Region: COG5433 357804002518 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 357804002519 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 357804002520 G1 box; other site 357804002521 putative GEF interaction site [polypeptide binding]; other site 357804002522 GTP/Mg2+ binding site [chemical binding]; other site 357804002523 Switch I region; other site 357804002524 G2 box; other site 357804002525 G3 box; other site 357804002526 Switch II region; other site 357804002527 G4 box; other site 357804002528 G5 box; other site 357804002529 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 357804002530 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 357804002531 active site 357804002532 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 357804002533 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 357804002534 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 357804002535 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; cl00663 357804002536 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 357804002537 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 357804002538 S-adenosylmethionine binding site [chemical binding]; other site 357804002539 ATP-dependent metalloprotease; Reviewed; Region: hflB; PRK10733 357804002540 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 ABC; Region: AAA; cd00009 357804002541 Walker A motif; other site 357804002542 ATP binding site [chemical binding]; other site 357804002543 Walker B motif; other site 357804002544 arginine finger; other site 357804002545 Peptidase family M41; Region: Peptidase_M41; pfam01434 357804002546 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 357804002547 dihydropteroate synthase; Region: DHPS; TIGR01496 357804002548 substrate binding pocket [chemical binding]; other site 357804002549 dimer interface [polypeptide binding]; other site 357804002550 inhibitor binding site; inhibition site 357804002551 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 357804002552 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...; Region: GlmM; cd05802 357804002553 active site 357804002554 substrate binding site [chemical binding]; other site 357804002555 metal binding site [ion binding]; metal-binding site 357804002556 Preprotein translocase SecG subunit; Region: SecG; cl09123 357804002557 ribosome maturation protein RimP; Reviewed; Region: PRK00092 357804002558 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 of...; Region: Sm_like; cl00259 357804002559 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 357804002560 Sm1 motif; other site 357804002561 predicted subunit interaction site [polypeptide binding]; other site 357804002562 RNA binding pocket [nucleotide binding]; other site 357804002563 Sm2 motif; other site 357804002564 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 357804002565 NusA N-terminal domain; Region: NusA_N; pfam08529 357804002566 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 three...; Region: S1_NusA; cd04455 357804002567 RNA binding site [nucleotide binding]; other site 357804002568 homodimer interface [polypeptide binding]; other site 357804002569 KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional...; Region: KH-II; cl00098 357804002570 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 357804002571 G-X-X-G motif; other site 357804002572 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 357804002573 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 357804002574 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 357804002575 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 357804002576 translation initiation factor IF-2; Region: IF-2; TIGR00487 357804002577 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 357804002578 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 357804002579 G1 box; other site 357804002580 putative GEF interaction site [polypeptide binding]; other site 357804002581 GTP/Mg2+ binding site [chemical binding]; other site 357804002582 Switch I region; other site 357804002583 G2 box; other site 357804002584 G3 box; other site 357804002585 Switch II region; other site 357804002586 G4 box; other site 357804002587 G5 box; other site 357804002588 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 cell; Region: IF2_mtIF2_II; cd03702 357804002589 Translation-initiation factor 2; Region: IF-2; pfam11987 357804002590 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 factor...; Region: mtIF2_IVc; cd03692 357804002591 Ribosome-binding factor A; Region: RBFA; cl00542 357804002592 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 357804002593 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 357804002594 RNA binding site [nucleotide binding]; other site 357804002595 active site 357804002596 Pseudouridine synthase II TruB, C-terminal; Region: TruB-C_2; pfam09157 357804002597 Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_uncharacterized_transporter; cd06325 357804002598 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 357804002599 zinc binding site [ion binding]; other site 357804002600 putative ligand binding site [chemical binding]; other site 357804002601 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cd06574 357804002602 TM-ABC transporter signature motif; other site 357804002603 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 357804002604 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804002605 Walker A/P-loop; other site 357804002606 ATP binding site [chemical binding]; other site 357804002607 Q-loop/lid; other site 357804002608 ABC transporter signature motif; other site 357804002609 Walker B; other site 357804002610 D-loop; other site 357804002611 H-loop/switch region; other site 357804002612 Ping_R0041; ribosomal S15 leader as predicted by Rfam (RF00114), score 27.47 357804002613 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 ribosome; Region: Ribosomal_S15p_S13e; cd00353 357804002614 16S/18S rRNA binding site [nucleotide binding]; other site 357804002615 S13e-L30e interaction site [polypeptide binding]; other site 357804002616 25S rRNA binding site [nucleotide binding]; other site 357804002617 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 357804002618 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 357804002619 RNase E interface [polypeptide binding]; other site 357804002620 trimer interface [polypeptide binding]; other site 357804002621 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 357804002622 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 357804002623 RNase E interface [polypeptide binding]; other site 357804002624 trimer interface [polypeptide binding]; other site 357804002625 active site 357804002626 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 357804002627 putative nucleic acid binding region [nucleotide binding]; other site 357804002628 G-X-X-G motif; other site 357804002629 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 357804002630 RNA binding site [nucleotide binding]; other site 357804002631 domain interface; other site 357804002632 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 357804002633 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 357804002634 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 357804002635 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 357804002636 aromatic acid decarboxylase; Validated; Region: PRK05920 357804002637 Flavoprotein; Region: Flavoprotein; cl08021 357804002638 5S ribosomal RNA region; shows weak similarity to 5S central region 357804002639 Protein of unknown function (DUF2982); Region: DUF2982; pfam11201 357804002640 CreA protein; Region: CreA; pfam05981 357804002641 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); Region: DUF2310; cl02380 357804002642 Protein of unknown function (DUF3301); Region: DUF3301; pfam11743 357804002643 Protein of unknown function (DUF3549); Region: DUF3549; pfam12069 357804002644 tRNA pseudouridine synthase C; Region: DUF446; cl01187 357804002645 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: VicK; COG5002 357804002646 Histidine kinase, Adenylyl cyclase, 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...; Region: HAMP; cd06225 357804002647 dimerization interface [polypeptide binding]; other site 357804002648 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 357804002649 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...; Region: HisKA; cd00082 357804002650 dimer interface [polypeptide binding]; other site 357804002651 phosphorylation site [posttranslational modification] 357804002652 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 357804002653 ATP binding site [chemical binding]; other site 357804002654 Mg2+ binding site [ion binding]; other site 357804002655 G-X-G motif; other site 357804002656 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 357804002657 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 357804002658 ATP binding site [chemical binding]; other site 357804002659 Mg++ binding site [ion binding]; other site 357804002660 motif III; other site 357804002661 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 357804002662 nucleotide binding region [chemical binding]; other site 357804002663 ATP-binding site [chemical binding]; other site 357804002664 Protein of unknown function (DUF2914); Region: DUF2914; pfam11141 357804002665 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 357804002666 FxsA cytoplasmic membrane protein; Region: FxsA; cl01148 357804002667 Protein of unknown function (DUF1107); Region: DUF1107; pfam06526 357804002668 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. It...; Region: cpn10; cd00320 357804002669 oligomerisation interface [polypeptide binding]; other site 357804002670 mobile loop; other site 357804002671 roof hairpin; other site 357804002672 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 357804002673 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 357804002674 ring oligomerisation interface [polypeptide binding]; other site 357804002675 ATP/Mg binding site [chemical binding]; other site 357804002676 stacking interactions; other site 357804002677 hinge regions; other site 357804002678 Protein of unknown function (DUF3494); Region: DUF3494; pfam11999 357804002679 Protein of unknown function (DUF3494); Region: DUF3494; pfam11999 357804002680 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804002681 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804002682 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 357804002683 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 357804002684 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804002685 sulfur acceptor protein CsdL; Provisional; Region: PRK15116 357804002686 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-like...; Region: YgdL_like; cd00755 357804002687 putative ATP binding site [chemical binding]; other site 357804002688 putative substrate interface [chemical binding]; other site 357804002689 ketol-acid reductoisomerase; Validated; Region: PRK05225 357804002690 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804002691 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 357804002692 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 357804002693 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 357804002694 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it...; Region: TST_Repeat_1; cd01448 357804002695 active site residue [active] 357804002696 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 357804002697 active site residue [active] 357804002698 Helix-turn-helix domains; Region: HTH; cl00088 357804002699 DNA-binding transcriptional regulator IlvY; Provisional; Region: PRK11716 357804002700 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 357804002701 putative dimerization interface [polypeptide binding]; other site 357804002702 Flagellin N-methylase; Region: FliB; cl00497 357804002703 Transcriptional activator HlyU; Region: HlyU; cl02273 357804002704 Membrane fusogenic activity; Region: BMFP; cl01115 357804002705 Protein of unknown function (DUF2750); Region: DUF2750; pfam11042 357804002706 Arginase family; Region: Arginase; cl00306 357804002707 arginine decarboxylase; Provisional; Region: PRK05354 357804002708 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 357804002709 dimer interface [polypeptide binding]; other site 357804002710 active site 357804002711 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 357804002712 catalytic residues [active] 357804002713 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 357804002714 RNase E inhibitor protein; Provisional; Region: PRK11191 357804002715 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 357804002716 putative acyl-acceptor binding pocket; other site 357804002717 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 357804002718 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 DNA...; Region: TOP4c; cd00187 357804002719 CAP-like domain; other site 357804002720 active site 357804002721 primary dimer interface [polypeptide binding]; other site 357804002722 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 357804002723 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 357804002724 inhibitor-cofactor binding pocket; inhibition site 357804002725 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804002726 catalytic residue [active] 357804002727 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-linked...; Region: EriC; cd01031 357804002728 Voltage gated chloride channel; Region: Voltage_CLC; pfam00654 357804002729 Cl- selectivity filter; other site 357804002730 Cl- binding residues [ion binding]; other site 357804002731 pore gating glutamate residue; other site 357804002732 dimer interface [polypeptide binding]; other site 357804002733 H+/Cl- coupling transport residue; other site 357804002734 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 357804002735 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 357804002736 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, acyl; Region: Biotinyl_lipoyl_domains; cl11404 357804002737 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 357804002738 Predicted membrane protein [Function unknown]; Region: COG2860 357804002739 UPF0126 domain; Region: UPF0126; pfam03458 357804002740 UPF0126 domain; Region: UPF0126; pfam03458 357804002741 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 357804002742 active site residue [active] 357804002743 N-acetylglutamate synthase; Validated; Region: PRK05279 357804002744 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...; Region: AAK_NAGS-ABP; cd04237 357804002745 putative feedback inhibition sensing region; other site 357804002746 putative nucleotide binding site [chemical binding]; other site 357804002747 putative substrate binding site [chemical binding]; other site 357804002748 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 357804002749 Coenzyme A binding pocket [chemical binding]; other site 357804002750 ferric uptake regulator; Provisional; Region: fur; PRK09462 357804002751 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 357804002752 metal binding site 2 [ion binding]; metal-binding site 357804002753 putative DNA binding helix; other site 357804002754 metal binding site 1 [ion binding]; metal-binding site 357804002755 dimer interface [polypeptide binding]; other site 357804002756 structural Zn2+ binding site [ion binding]; other site 357804002757 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 357804002758 LexA regulated protein; Provisional; Region: PRK11675 357804002759 Protein of unknown function (DUF2788); Region: DUF2788; pfam10981 357804002760 acyl-CoA esterase; Provisional; Region: PRK10673 357804002761 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 357804002762 SeqA protein; Region: SeqA; cl11470 357804002763 phosphoglucomutase; Validated; Region: PRK07564 357804002764 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 357804002765 active site 357804002766 substrate binding site [chemical binding]; other site 357804002767 metal binding site [ion binding]; metal-binding site 357804002768 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 357804002769 homodimer interface [polypeptide binding]; other site 357804002770 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 357804002771 active site pocket [active] 357804002772 Protein of unknown function (DUF406); Region: DUF406; cl11449 357804002773 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 357804002774 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 357804002775 ATP binding site [chemical binding]; other site 357804002776 Mg++ binding site [ion binding]; other site 357804002777 motif III; other site 357804002778 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 357804002779 nucleotide binding region [chemical binding]; other site 357804002780 ATP-binding site [chemical binding]; other site 357804002781 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 357804002782 HipA-like N-terminal domain; Region: HipA_N; pfam07805 357804002783 HipA-like C-terminal domain; Region: HipA_C; pfam07804 357804002784 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 357804002785 non-specific DNA binding site [nucleotide binding]; other site 357804002786 salt bridge; other site 357804002787 sequence-specific DNA binding site [nucleotide binding]; other site 357804002788 Membrane transport protein; Region: Mem_trans; cl09117 357804002789 Predicted permease [General function prediction only]; Region: COG2056 357804002790 Na+-H+ antiporter family; Region: Na_H_antiport_2; cl15264 357804002791 Rhomboid family; Region: Rhomboid; cl11446 357804002792 DTW domain; Region: DTW; cl01221 357804002793 RF-1 domain; Region: RF-1; cl02875 357804002794 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 357804002795 dimer interface [polypeptide binding]; other site 357804002796 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 357804002797 N-terminal Early set domain associated with the catalytic domain of Glycogen debranching enzyme and bacterial isoamylase (also called glycogen 6-glucanohydrolase); Region: E_set_GDE_Isoamylase_N; cd02856 357804002798 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 357804002799 active site 357804002800 catalytic site [active] 357804002801 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 357804002802 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 357804002803 metal binding site [ion binding]; metal-binding site 357804002804 dimer interface [polypeptide binding]; other site 357804002805 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 357804002806 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; cl03056 357804002807 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 357804002808 catalytic site [active] 357804002809 subunit interface [polypeptide binding]; other site 357804002810 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 357804002811 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 357804002812 ATP-grasp domain; Region: ATP-grasp_4; cl03087 357804002813 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 357804002814 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 357804002815 ATP-grasp domain; Region: ATP-grasp_4; cl03087 357804002816 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 357804002817 IMP binding site; other site 357804002818 dimer interface [polypeptide binding]; other site 357804002819 interdomain contacts; other site 357804002820 partial ornithine binding site; other site 357804002821 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; cl01261 357804002822 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 357804002823 DNA internalization-related competence protein ComEC/Rec2; Region: ComEC_Rec2; TIGR00361 357804002824 Competence protein; Region: Competence; cl00471 357804002825 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 357804002826 lipid transporter ATP-binding/permease protein; Provisional; Region: PRK11176 357804002827 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 357804002828 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 357804002829 Walker A/P-loop; other site 357804002830 ATP binding site [chemical binding]; other site 357804002831 Q-loop/lid; other site 357804002832 ABC transporter signature motif; other site 357804002833 Walker B; other site 357804002834 D-loop; other site 357804002835 H-loop/switch region; other site 357804002836 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 357804002837 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 357804002838 Trm112p-like protein; Region: Trm112p; cl01066 357804002839 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 357804002840 Ligand binding site; other site 357804002841 oligomer interface; other site 357804002842 Domain of Unknown Function (DUF350); Region: DUF350; pfam03994 357804002843 spermidine synthase; Provisional; Region: PRK03612 357804002844 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; cl16911 357804002845 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 357804002846 Helix-turn-helix domains; Region: HTH; cl00088 357804002847 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 357804002848 GTP-binding protein YchF; Reviewed; Region: PRK09601 357804002849 YchF GTPase; Region: YchF; cd01900 357804002850 G1 box; other site 357804002851 GTP/Mg2+ binding site [chemical binding]; other site 357804002852 Switch I region; other site 357804002853 G2 box; other site 357804002854 Switch II region; other site 357804002855 G3 box; other site 357804002856 G4 box; other site 357804002857 G5 box; other site 357804002858 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 357804002859 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 357804002860 putative active site [active] 357804002861 catalytic residue [active] 357804002862 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 357804002863 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 357804002864 5S rRNA interface [nucleotide binding]; other site 357804002865 CTC domain interface [polypeptide binding]; other site 357804002866 L16 interface [polypeptide binding]; other site 357804002867 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 357804002868 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 357804002869 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 357804002870 active site 357804002871 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 357804002872 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 357804002873 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 357804002874 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 357804002875 recombination and repair protein; Provisional; Region: PRK10869 357804002876 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, and...; Region: ABC_RecN; cd03241 357804002877 Walker A/P-loop; other site 357804002878 ATP binding site [chemical binding]; other site 357804002879 Q-loop/lid; other site 357804002880 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, and...; Region: ABC_RecN; cd03241 357804002881 ABC transporter signature motif; other site 357804002882 Walker B; other site 357804002883 D-loop; other site 357804002884 H-loop/switch region; other site 357804002885 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 357804002886 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK03708 357804002887 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 357804002888 dimer interface [polypeptide binding]; other site 357804002889 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 357804002890 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 357804002891 FGGY family of carbohydrate kinases; Region: FGGY; cl08364 357804002892 chaperone protein DnaJ; Provisional; Region: PRK10767 357804002893 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 Hsp70s; Region: DnaJ; cd06257 357804002894 HSP70 interaction site [polypeptide binding]; other site 357804002895 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 357804002896 substrate binding site [polypeptide binding]; other site 357804002897 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 357804002898 Zn binding sites [ion binding]; other site 357804002899 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 357804002900 dimer interface [polypeptide binding]; other site 357804002901 peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK11570 357804002902 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 357804002903 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 357804002904 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 357804002905 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 357804002906 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 357804002907 active site 357804002908 HIGH motif; other site 357804002909 dimer interface [polypeptide binding]; other site 357804002910 KMSKS motif; other site 357804002911 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 357804002912 Type I GTP cyclohydrolase folE2; Region: GCHY-1; cl00642 357804002913 aerobic respiration control sensor protein ArcB; Provisional; Region: PRK11091 357804002914 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 357804002915 putative active site [active] 357804002916 heme pocket [chemical binding]; other site 357804002917 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...; Region: HisKA; cd00082 357804002918 dimer interface [polypeptide binding]; other site 357804002919 phosphorylation site [posttranslational modification] 357804002920 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 357804002921 ATP binding site [chemical binding]; other site 357804002922 Mg2+ binding site [ion binding]; other site 357804002923 G-X-G motif; other site 357804002924 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 357804002925 active site 357804002926 phosphorylation site [posttranslational modification] 357804002927 intermolecular recognition site; other site 357804002928 dimerization interface [polypeptide binding]; other site 357804002929 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 357804002930 putative binding surface; other site 357804002931 active site 357804002932 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 357804002933 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 357804002934 tandem repeat interface [polypeptide binding]; other site 357804002935 oligomer interface [polypeptide binding]; other site 357804002936 active site residues [active] 357804002937 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 357804002938 Peptidase family M48; Region: Peptidase_M48; cl12018 357804002939 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...; Region: SirA_YedF_YeeD; cl00436 357804002940 Domain of unknown function DUF20; Region: UPF0118; pfam01594 357804002941 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 357804002942 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 reducing...; Region: PRX_BCP; cd03017 357804002943 catalytic triad [active] 357804002944 universal stress protein UspE; Provisional; Region: PRK11175 357804002945 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 357804002946 Ligand Binding Site [chemical binding]; other site 357804002947 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 357804002948 Ligand Binding Site [chemical binding]; other site 357804002949 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 357804002950 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 357804002951 ligand binding site [chemical binding]; other site 357804002952 flexible hinge region; other site 357804002953 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 357804002954 putative switch regulator; other site 357804002955 non-specific DNA interactions [nucleotide binding]; other site 357804002956 DNA binding site [nucleotide binding] 357804002957 sequence specific DNA binding site [nucleotide binding]; other site 357804002958 putative cAMP binding site [chemical binding]; other site 357804002959 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 357804002960 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; cl01253 357804002961 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 357804002962 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 357804002963 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 357804002964 metal-binding site [ion binding] 357804002965 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 357804002966 FixH; Region: FixH; cl01254 357804002967 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 357804002968 Cytochrome c; Region: Cytochrom_C; cl11414 357804002969 Cytochrome c; Region: Cytochrom_C; cl11414 357804002970 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 O2...; Region: cbb3_Oxidase_CcoQ; cl00282 357804002971 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 357804002972 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 357804002973 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 reduction...; Region: cbb3_Oxidase_I; cd01661 357804002974 Low-spin heme binding site [chemical binding]; other site 357804002975 Putative water exit pathway; other site 357804002976 Binuclear center (active site) [active] 357804002977 Putative proton exit pathway; other site 357804002978 DoxX; Region: DoxX; cl00976 357804002979 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 357804002980 SCP_bacterial: SCP-like extracellular protein domain, as found in bacteria and archaea. The wider family of SCP containing proteins includes plant pathogenesis-related protein 1 (PR-1), CRISPs, mammalian cysteine-rich secretory proteins, and allergen 5...; Region: SCP_bacterial; cd05379 357804002981 Protein of unknown function (DUF692); Region: DUF692; cl01263 357804002982 Predicted integral membrane protein (DUF2282); Region: DUF2282; cl02366 357804002983 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 357804002984 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 357804002985 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 357804002986 Protein of unknown function (DUF3379); Region: DUF3379; pfam11859 357804002987 PAS fold; Region: PAS_3; pfam08447 357804002988 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 357804002989 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 357804002990 PAS domain; Region: PAS_9; pfam13426 357804002991 putative active site [active] 357804002992 heme pocket [chemical binding]; other site 357804002993 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804002994 metal binding site [ion binding]; metal-binding site 357804002995 active site 357804002996 I-site; other site 357804002997 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 357804002998 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 357804002999 short chain dehydrogenase; Provisional; Region: PRK09072 357804003000 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804003001 NAD(P) binding site [chemical binding]; other site 357804003002 active site 357804003003 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 357804003004 AMP-binding enzyme; Region: AMP-binding; cl15778 357804003005 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 357804003006 heme binding pocket [chemical binding]; other site 357804003007 heme ligand [chemical binding]; other site 357804003008 Thermostable hemolysin; Region: T_hemolysin; pfam12261 357804003009 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 357804003010 Ligand Binding Site [chemical binding]; other site 357804003011 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 357804003012 Ligand Binding Site [chemical binding]; other site 357804003013 heat shock protein 90; Provisional; Region: PRK05218 357804003014 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 357804003015 ATP binding site [chemical binding]; other site 357804003016 Mg2+ binding site [ion binding]; other site 357804003017 G-X-G motif; other site 357804003018 adenylate kinase; Reviewed; Region: adk; PRK00279 357804003019 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 357804003020 AMP-binding site [chemical binding]; other site 357804003021 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 357804003022 NlpC/P60 family; Region: NLPC_P60; cl11438 357804003023 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 357804003024 Ligand Binding Site [chemical binding]; other site 357804003025 Uncharacterized conserved protein [Function unknown]; Region: COG2850 357804003026 JmjC domain, hydroxylase; Region: JmjC; cl15814 357804003027 adenylosuccinate lyase; Provisional; Region: PRK09285 357804003028 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 357804003029 tetramer interface [polypeptide binding]; other site 357804003030 active site 357804003031 Protein of unknown function (DUF489); Region: DUF489; cl01097 357804003032 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 357804003033 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 357804003034 putative transporter; Provisional; Region: PRK11660 357804003035 Sulfate transporter family; Region: Sulfate_transp; cl15842 357804003036 Sulfate transporter family; Region: Sulfate_transp; cl15842 357804003037 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 357804003038 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 357804003039 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 357804003040 ligand binding site [chemical binding]; other site 357804003041 flexible hinge region; other site 357804003042 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with either the CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain or the PB1 (Phox and Bem1p) domain; Region: CBS_pair_CAP-ED_DUF294_PBI_assoc2; cd04800 357804003043 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 357804003044 metal binding triad; other site 357804003045 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 357804003046 active site 357804003047 catalytic site [active] 357804003048 substrate binding site [chemical binding]; other site 357804003049 BCCT family transporter; Region: BCCT; cl00569 357804003050 Domain of unknown function (DUF4328); Region: DUF4328; pfam14219 357804003051 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 357804003052 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 357804003053 putative substrate binding site [chemical binding]; other site 357804003054 putative ATP binding site [chemical binding]; other site 357804003055 PTS system, sucrose-specific IIBC component; Region: PTS-II-BC-sucr; TIGR01996 357804003056 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 family...; Region: PTS_IIB_glc; cd00212 357804003057 active site turn [active] 357804003058 phosphorylation site [posttranslational modification] 357804003059 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; cl00557 357804003060 Transcriptional regulators [Transcription]; Region: PurR; COG1609 357804003061 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 357804003062 DNA binding site [nucleotide binding] 357804003063 domain linker motif; other site 357804003064 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 357804003065 dimerization interface [polypeptide binding]; other site 357804003066 ligand binding site [chemical binding]; other site 357804003067 Beta-fructosidases (levanase/invertase) [Carbohydrate transport and metabolism]; Region: SacC; COG1621 357804003068 Glycosyl hydrolase family 32, beta-fructosidases; Region: GH32_B_Fructosidase; cd08996 357804003069 substrate binding [chemical binding]; other site 357804003070 active site 357804003071 Glycosyl hydrolases family 32 C terminal; Region: Glyco_hydro_32C; pfam08244 357804003072 putative molybdenum transport ATP-binding protein ModF; Provisional; Region: PRK10938 357804003073 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804003074 Walker A/P-loop; other site 357804003075 ATP binding site [chemical binding]; other site 357804003076 Q-loop/lid; other site 357804003077 ABC transporter signature motif; other site 357804003078 Walker B; other site 357804003079 D-loop; other site 357804003080 H-loop/switch region; other site 357804003081 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804003082 Walker A/P-loop; other site 357804003083 ATP binding site [chemical binding]; other site 357804003084 Q-loop/lid; other site 357804003085 ABC transporter signature motif; other site 357804003086 Walker B; other site 357804003087 D-loop; other site 357804003088 H-loop/switch region; other site 357804003089 Response regulator receiver domain; Region: Response_reg; pfam00072 357804003090 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 357804003091 active site 357804003092 phosphorylation site [posttranslational modification] 357804003093 intermolecular recognition site; other site 357804003094 dimerization interface [polypeptide binding]; other site 357804003095 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804003096 metal binding site [ion binding]; metal-binding site 357804003097 active site 357804003098 I-site; other site 357804003099 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 inorganic...; Region: PBPb; cd00134 357804003100 substrate binding pocket [chemical binding]; other site 357804003101 membrane-bound complex binding site; other site 357804003102 hinge residues; other site 357804003103 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 357804003104 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 inorganic...; Region: PBPb; cd00134 357804003105 substrate binding pocket [chemical binding]; other site 357804003106 membrane-bound complex binding site; other site 357804003107 hinge residues; other site 357804003108 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 357804003109 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 inorganic...; Region: PBPb; cd00134 357804003110 substrate binding pocket [chemical binding]; other site 357804003111 membrane-bound complex binding site; other site 357804003112 hinge residues; other site 357804003113 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...; Region: HisKA; cd00082 357804003114 dimer interface [polypeptide binding]; other site 357804003115 phosphorylation site [posttranslational modification] 357804003116 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 357804003117 ATP binding site [chemical binding]; other site 357804003118 Mg2+ binding site [ion binding]; other site 357804003119 G-X-G motif; other site 357804003120 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 357804003121 Response regulator receiver domain; Region: Response_reg; pfam00072 357804003122 active site 357804003123 phosphorylation site [posttranslational modification] 357804003124 intermolecular recognition site; other site 357804003125 dimerization interface [polypeptide binding]; other site 357804003126 Response regulator receiver domain; Region: Response_reg; pfam00072 357804003127 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 357804003128 active site 357804003129 phosphorylation site [posttranslational modification] 357804003130 intermolecular recognition site; other site 357804003131 dimerization interface [polypeptide binding]; other site 357804003132 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 357804003133 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 357804003134 pseudouridine synthase; Region: TIGR00093 357804003135 active site 357804003136 Monomeric isocitrate dehydrogenase; Region: IDH; cl15383 357804003137 Mannitol repressor; Region: MtlR; cl11450 357804003138 Transcriptional regulator [Transcription]; Region: MtlR; COG3722 357804003139 Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism]; Region: MtlA; COG2213 357804003140 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; cl00557 357804003141 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 transmembrane...; Region: PTS_IIB_mannitol; cd05567 357804003142 active site 357804003143 P-loop; other site 357804003144 phosphorylation site [posttranslational modification] 357804003145 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 357804003146 putative deacylase active site [active] 357804003147 signal transduction histidine-protein kinase BaeS; Provisional; Region: PRK10549 357804003148 Histidine kinase, Adenylyl cyclase, 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...; Region: HAMP; cd06225 357804003149 dimerization interface [polypeptide binding]; other site 357804003150 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...; Region: HisKA; cd00082 357804003151 dimer interface [polypeptide binding]; other site 357804003152 phosphorylation site [posttranslational modification] 357804003153 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 357804003154 ATP binding site [chemical binding]; other site 357804003155 Mg2+ binding site [ion binding]; other site 357804003156 G-X-G motif; other site 357804003157 DNA-binding transcriptional regulator BaeR; Provisional; Region: PRK10710 357804003158 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 357804003159 active site 357804003160 phosphorylation site [posttranslational modification] 357804003161 intermolecular recognition site; other site 357804003162 dimerization interface [polypeptide binding]; other site 357804003163 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 and...; Region: trans_reg_C; cd00383 357804003164 DNA binding site [nucleotide binding] 357804003165 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 357804003166 classical (c) SDRs; Region: SDR_c; cd05233 357804003167 NAD(P) binding site [chemical binding]; other site 357804003168 active site 357804003169 Secreted protein acidic and rich in cysteine Ca binding region; Region: SPARC_Ca_bdg; pfam10591 357804003170 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl08302 357804003171 Protein of unknown function (DUF1439); Region: DUF1439; cl06345 357804003172 Uncharacterized protein, similar to the N-terminal domain of Lon protease [General function prediction only]; Region: COG2802 357804003173 RNA polymerase sigma factor; Provisional; Region: PRK12526 357804003174 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 357804003175 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 or...; Region: Sigma70_r4; cd06171 357804003176 DNA binding residues [nucleotide binding] 357804003177 anti-sigma factor, putative, ChrR family; Region: anti_sig_ChrR; TIGR02451 357804003178 Cupin domain; Region: Cupin_2; cl09118 357804003179 Protein of unknown function (DUF523); Region: DUF523; cl00733 357804003180 Protein of unknown function (DUF1722); Region: DUF1722; cl01284 357804003181 deoxyribodipyrimidine photolyase; Provisional; Region: PRK10674 357804003182 DNA photolyase; Region: DNA_photolyase; pfam00875 357804003183 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 357804003184 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 357804003185 short chain dehydrogenase; Provisional; Region: PRK06101 357804003186 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804003187 NAD(P) binding site [chemical binding]; other site 357804003188 active site 357804003189 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 357804003190 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804003191 Uncharacterized conserved protein [Function unknown]; Region: COG3496 357804003192 Protein of unknown function (DUF1365); Region: DUF1365; pfam07103 357804003193 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 357804003194 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 357804003195 S-adenosylmethionine binding site [chemical binding]; other site 357804003196 Protein of unknown function (DUF2878); Region: DUF2878; pfam11086 357804003197 Chalcone-flavanone isomerase; Region: Chalcone; cl03589 357804003198 Protein of unknown function (DUF3833); Region: DUF3833; pfam12915 357804003199 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 357804003200 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...; Region: GltS; cd00713 357804003201 active site 357804003202 dimer interface [polypeptide binding]; other site 357804003203 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 357804003204 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, yeast...; Region: GltS_FMN; cd02808 357804003205 active site 357804003206 FMN binding site [chemical binding]; other site 357804003207 substrate binding site [chemical binding]; other site 357804003208 3Fe-4S cluster binding site [ion binding]; other site 357804003209 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 357804003210 domain interface; other site 357804003211 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 357804003212 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804003213 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 357804003214 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; cl16911 357804003215 LysE type translocator; Region: LysE; cl00565 357804003216 chromosome replication initiation inhibitor protein; Validated; Region: PRK03635 357804003217 Helix-turn-helix domains; Region: HTH; cl00088 357804003218 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 357804003219 dimerization interface [polypeptide binding]; other site 357804003220 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 357804003221 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 facilitated...; Region: ABCF_EF-3; cd03221 357804003222 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 facilitated...; Region: ABCF_EF-3; cd03221 357804003223 ABC transporter; Region: ABC_tran_2; pfam12848 357804003224 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 facilitated...; Region: ABCF_EF-3; cd03221 357804003225 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08974 357804003226 AMP-binding enzyme; Region: AMP-binding; cl15778 357804003227 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 357804003228 Dodecin; Region: Dodecin; cl01328 357804003229 hypothetical protein; Provisional; Region: PRK04946 357804003230 Smr domain; Region: Smr; cl02619 357804003231 HemK family putative methylases; Region: hemK_fam; TIGR00536 357804003232 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 357804003233 S-adenosylmethionine binding site [chemical binding]; other site 357804003234 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 357804003235 Tetramer interface [polypeptide binding]; other site 357804003236 active site 357804003237 FMN-binding site [chemical binding]; other site 357804003238 AsmA family; Region: AsmA; pfam05170 357804003239 AsmA-like C-terminal region; Region: AsmA_2; cl15864 357804003240 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 357804003241 putative catalytic site [active] 357804003242 putative metal binding site [ion binding]; other site 357804003243 putative phosphate binding site [ion binding]; other site 357804003244 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; cd00143 357804003245 active site 357804003246 Catalytic domain of Protein Kinases; Region: PKc; cd00180 357804003247 active site 357804003248 ATP binding site [chemical binding]; other site 357804003249 substrate binding site [chemical binding]; other site 357804003250 activation loop (A-loop); other site 357804003251 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 357804003252 putative substrate translocation pore; other site 357804003253 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 357804003254 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 357804003255 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 while...; Region: Rieske_NirD; cd03529 357804003256 nitrite reductase subunit NirD; Provisional; Region: PRK14989 357804003257 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 357804003258 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 357804003259 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 357804003260 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 357804003261 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 357804003262 Nitrate reductases, NapA (Nitrate-R-NapA), 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...; Region: MopB_Nitrate-R-NapA-like; cd02754 357804003263 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 357804003264 [4Fe-4S] binding site [ion binding]; other site 357804003265 molybdopterin cofactor binding site; other site 357804003266 Nitrate reductases, NapA (Nitrate-R-NapA), 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...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 357804003267 molybdopterin cofactor binding site; other site 357804003268 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 357804003269 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 357804003270 formyltetrahydrofolate deformylase; Reviewed; Region: PRK13011 357804003271 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 357804003272 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 357804003273 putative active site [active] 357804003274 putative substrate binding site [chemical binding]; other site 357804003275 putative cosubstrate binding site; other site 357804003276 catalytic site [active] 357804003277 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 357804003278 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 357804003279 active sites [active] 357804003280 tetramer interface [polypeptide binding]; other site 357804003281 urocanate hydratase; Provisional; Region: PRK05414 357804003282 Arginase family; Region: Arginase; cl00306 357804003283 imidazolonepropionase; Validated; Region: PRK09356 357804003284 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 357804003285 active site 357804003286 histidine utilization repressor, proteobacterial; Region: his_ut_repres; TIGR02018 357804003287 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 357804003288 DNA-binding site [nucleotide binding]; DNA binding site 357804003289 UTRA domain; Region: UTRA; cl01230 357804003290 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 357804003291 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 357804003292 active site 357804003293 Zn binding site [ion binding]; other site 357804003294 Yhdh putative quinone oxidoreductases; Region: MDR_yhdh; cd08288 357804003295 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 357804003296 NADP binding site [chemical binding]; other site 357804003297 dimer interface [polypeptide binding]; other site 357804003298 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 357804003299 Helix-turn-helix domains; Region: HTH; cl00088 357804003300 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 357804003301 substrate binding pocket [chemical binding]; other site 357804003302 dimerization interface [polypeptide binding]; other site 357804003303 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 357804003304 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 triad...; Region: Tryp_SPc; cl00149 357804003305 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...; Region: PDZ_serine_protease; cd00987 357804003306 protein binding site [polypeptide binding]; other site 357804003307 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...; Region: PDZ_serine_protease; cd00987 357804003308 chaperone-modulator protein CbpM; Provisional; Region: PRK10265 357804003309 curved DNA-binding protein CbpA; Provisional; Region: PRK10266 357804003310 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 Hsp70s; Region: DnaJ; cd06257 357804003311 HSP70 interaction site [polypeptide binding]; other site 357804003312 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 357804003313 substrate binding site [polypeptide binding]; other site 357804003314 dimer interface [polypeptide binding]; other site 357804003315 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 357804003316 Clp amino terminal domain; Region: Clp_N; pfam02861 357804003317 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 ABC; Region: AAA; cd00009 357804003318 Walker A motif; other site 357804003319 ATP binding site [chemical binding]; other site 357804003320 Walker B motif; other site 357804003321 arginine finger; other site 357804003322 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 ABC; Region: AAA; cd00009 357804003323 Walker A motif; other site 357804003324 ATP binding site [chemical binding]; other site 357804003325 Walker B motif; other site 357804003326 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 357804003327 YceI-like domain; Region: YceI; cl01001 357804003328 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 357804003329 GST_N family, Omega-like subfamily; composed of uncharacterized proteins with similarity to class Omega 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_Omega_like; cd03060 357804003330 putative GSH binding site (G-site) [chemical binding]; other site 357804003331 active site cysteine [active] 357804003332 putative C-terminal domain interface [polypeptide binding]; other site 357804003333 putative dimer interface [polypeptide binding]; other site 357804003334 C-terminal, alpha helical domain of an unknown subfamily 5 of Glutathione S-transferases; Region: GST_C_5; cd03196 357804003335 putative N-terminal domain interface [polypeptide binding]; other site 357804003336 putative dimer interface [polypeptide binding]; other site 357804003337 putative substrate binding pocket (H-site) [chemical binding]; other site 357804003338 Uncharacterized protein conserved in bacteria (DUF2333); Region: DUF2333; cl11978 357804003339 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; Region: DHFR; cd00209 357804003340 folate binding site [chemical binding]; other site 357804003341 NADP+ binding site [chemical binding]; other site 357804003342 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 357804003343 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 357804003344 active site 357804003345 metal binding site [ion binding]; metal-binding site 357804003346 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; cl16911 357804003347 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 357804003348 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 357804003349 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 357804003350 SurA N-terminal domain; Region: SurA_N_3; cl07813 357804003351 PPIC-type PPIASE domain; Region: Rotamase; cl08278 357804003352 PPIC-type PPIASE domain; Region: Rotamase; cl08278 357804003353 LPS assembly outer membrane complex protein LptD; Provisional; Region: PRK03761 357804003354 OstA-like protein; Region: OstA; cl00844 357804003355 Organic solvent tolerance protein; Region: OstA_C; pfam04453 357804003356 Dna-J like membrane chaperone protein; Provisional; Region: djlA; PRK09430 357804003357 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 357804003358 putative metal binding site [ion binding]; other site 357804003359 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 Hsp70s; Region: DnaJ; cd06257 357804003360 HSP70 interaction site [polypeptide binding]; other site 357804003361 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase; Region: DapD_gpp; TIGR03536 357804003362 Putative 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (THP succinyltransferase), C-terminal left-handed parallel alpha-helix (LbH) domain: This group is composed of mostly uncharacterized proteins containing an N-terminal...; Region: LbH_THP_succinylT_putative; cd04649 357804003363 putative trimer interface [polypeptide binding]; other site 357804003364 putative CoA binding site [chemical binding]; other site 357804003365 YCII-related domain; Region: YCII; cl00999 357804003366 Intracellular septation protein A; Region: IspA; cl01098 357804003367 tryptophan synthase subunit alpha; Provisional; Region: trpA; PRK13111 357804003368 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 both...; Region: Tryptophan_synthase_alpha; cd04724 357804003369 substrate binding site [chemical binding]; other site 357804003370 active site 357804003371 catalytic residues [active] 357804003372 heterodimer interface [polypeptide binding]; other site 357804003373 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 357804003374 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804003375 catalytic residue [active] 357804003376 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase; Provisional; Region: PRK09427 357804003377 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 357804003378 active site 357804003379 ribulose/triose binding site [chemical binding]; other site 357804003380 phosphate binding site [ion binding]; other site 357804003381 substrate (anthranilate) binding pocket [chemical binding]; other site 357804003382 product (indole) binding pocket [chemical binding]; other site 357804003383 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 357804003384 active site 357804003385 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 357804003386 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 357804003387 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 357804003388 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 357804003389 Glutamine amidotransferase class-I; Region: GATase; pfam00117 357804003390 glutamine binding [chemical binding]; other site 357804003391 catalytic triad [active] 357804003392 anthranilate synthase component I; Provisional; Region: PRK13564 357804003393 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 357804003394 chorismate binding enzyme; Region: Chorismate_bind; cl10555 357804003395 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 357804003396 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 357804003397 23S rRNA pseudouridylate synthase B; Provisional; Region: PRK10700 357804003398 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 357804003399 Pseudouridine synthase, Escherichia coli RluB like; Region: PseudoU_synth_RluB; cd02556 357804003400 probable active site [active] 357804003401 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 357804003402 active site 357804003403 tetramer interface; other site 357804003404 N-acetylmuramic acid-6-phosphate etherase; Reviewed; Region: murQ; PRK05441 357804003405 N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid...; Region: SIS_Etherase; cd05007 357804003406 putative active site [active] 357804003407 LrgA family; Region: LrgA; cl00608 357804003408 LrgB-like family; Region: LrgB; cl00596 357804003409 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 357804003410 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 357804003411 active site 357804003412 substrate binding site [chemical binding]; other site 357804003413 cosubstrate binding site; other site 357804003414 catalytic site [active] 357804003415 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 357804003416 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 biosynthesis; Region: PurM; cd02196 357804003417 dimerization interface [polypeptide binding]; other site 357804003418 putative ATP binding site [chemical binding]; other site 357804003419 Uncharacterized protein conserved in bacteria (DUF2066); Region: DUF2066; pfam09839 357804003420 DnaA regulatory inactivator Hda; Region: DnaA_homol_Hda; TIGR03420 357804003421 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804003422 Predicted membrane protein (DUF2069); Region: DUF2069; cl01299 357804003423 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 357804003424 ArsC family; Region: ArsC; pfam03960 357804003425 catalytic residues [active] 357804003426 Flagellin N-methylase; Region: FliB; cl00497 357804003427 Transglycosylase SLT domain; Region: SLT_2; pfam13406 357804003428 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 357804003429 N-acetyl-D-glucosamine binding site [chemical binding]; other site 357804003430 catalytic residue [active] 357804003431 YcgL domain; Region: YcgL; cl01189 357804003432 septum formation inhibitor; Reviewed; Region: minC; PRK04804 357804003433 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 357804003434 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 357804003435 cell division inhibitor MinD; Provisional; Region: PRK10818 357804003436 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 pivotal...; Region: MinD; cd02036 357804003437 Switch I; other site 357804003438 Switch II; other site 357804003439 Septum formation topological specificity factor MinE; Region: MinE; cl00538 357804003440 peptidyl-prolyl cis-trans isomerase B (rotamase B); Provisional; Region: PRK10791 357804003441 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 357804003442 active site 357804003443 hypothetical protein; Provisional; Region: PRK11627 357804003444 Uncharacterized lipoprotein; Region: Lipoprotein_16; pfam03923 357804003445 excinuclease ABC subunit B; Provisional; Region: PRK05298 357804003446 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 357804003447 ATP binding site [chemical binding]; other site 357804003448 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 357804003449 nucleotide binding region [chemical binding]; other site 357804003450 ATP-binding site [chemical binding]; other site 357804003451 Ultra-violet resistance protein B; Region: UvrB; pfam12344 357804003452 UvrB/uvrC motif; Region: UVR; pfam02151 357804003453 Maf-like protein; Region: Maf; pfam02545 357804003454 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 357804003455 active site 357804003456 dimer interface [polypeptide binding]; other site 357804003457 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 357804003458 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 357804003459 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 357804003460 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 357804003461 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 357804003462 dimer interface [polypeptide binding]; other site 357804003463 active site 357804003464 CoA binding pocket [chemical binding]; other site 357804003465 Acyl transferase domain; Region: Acyl_transf_1; cl08282 357804003466 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 357804003467 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 357804003468 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 357804003469 NAD(P) binding site [chemical binding]; other site 357804003470 homotetramer interface [polypeptide binding]; other site 357804003471 homodimer interface [polypeptide binding]; other site 357804003472 active site 357804003473 Phosphopantetheine attachment site; Region: PP-binding; cl09936 357804003474 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 357804003475 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 357804003476 dimer interface [polypeptide binding]; other site 357804003477 active site 357804003478 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 357804003479 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804003480 catalytic residue [active] 357804003481 YceG-like family; Region: YceG; pfam02618 357804003482 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 357804003483 dimerization interface [polypeptide binding]; other site 357804003484 thymidylate kinase; Validated; Region: tmk; PRK00698 357804003485 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 step...; Region: TMPK; cd01672 357804003486 TMP-binding site; other site 357804003487 ATP-binding site [chemical binding]; other site 357804003488 DNA polymerase III, delta' subunit; Region: holB; TIGR00678 357804003489 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 357804003490 active site 357804003491 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 357804003492 DNA-binding site [nucleotide binding]; DNA binding site 357804003493 RNA-binding motif; other site 357804003494 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804003495 AAA domain; Region: AAA_28; pfam13521 357804003496 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 357804003497 Ligand Binding Site [chemical binding]; other site 357804003498 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 357804003499 ATP-dependent RNA helicase HrpA; Provisional; Region: PRK11131 357804003500 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 357804003501 ATP binding site [chemical binding]; other site 357804003502 putative Mg++ binding site [ion binding]; other site 357804003503 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 357804003504 nucleotide binding region [chemical binding]; other site 357804003505 ATP-binding site [chemical binding]; other site 357804003506 Helicase associated domain (HA2); Region: HA2; cl04503 357804003507 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 357804003508 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 357804003509 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 357804003510 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 357804003511 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 357804003512 putative active site [active] 357804003513 putative substrate binding site [chemical binding]; other site 357804003514 putative cosubstrate binding site; other site 357804003515 catalytic site [active] 357804003516 hypothetical protein; Provisional; Region: PRK02250 357804003517 SEC-C motif; Region: SEC-C; pfam02810 357804003518 asparagine synthetase B; Provisional; Region: asnB; PRK09431 357804003519 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 357804003520 active site 357804003521 dimer interface [polypeptide binding]; other site 357804003522 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 the...; Region: Asn_Synthase_B_C; cd01991 357804003523 Ligand Binding Site [chemical binding]; other site 357804003524 Molecular Tunnel; other site 357804003525 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 357804003526 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 357804003527 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804003528 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 357804003529 Sel1 repeat; Region: Sel1; cl02723 357804003530 Sel1 repeat; Region: Sel1; cl02723 357804003531 Sel1 repeat; Region: Sel1; cl02723 357804003532 Sel1 repeat; Region: Sel1; cl02723 357804003533 Sel1 repeat; Region: Sel1; cl02723 357804003534 Sel1 repeat; Region: Sel1; cl02723 357804003535 Sel1 repeat; Region: Sel1; cl02723 357804003536 Sel1 repeat; Region: Sel1; cl02723 357804003537 Sel1 repeat; Region: Sel1; cl02723 357804003538 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 357804003539 catalytic loop [active] 357804003540 iron binding site [ion binding]; other site 357804003541 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 357804003542 dimer interface [polypeptide binding]; other site 357804003543 putative radical transfer pathway; other site 357804003544 diiron center [ion binding]; other site 357804003545 tyrosyl radical; other site 357804003546 Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_sugar_binding_like; cd01536 357804003547 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 357804003548 ligand binding site [chemical binding]; other site 357804003549 Histidine kinase, Adenylyl cyclase, 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...; Region: HAMP; cl01054 357804003550 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 357804003551 PAS fold; Region: PAS_3; pfam08447 357804003552 putative active site [active] 357804003553 heme pocket [chemical binding]; other site 357804003554 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804003555 metal binding site [ion binding]; metal-binding site 357804003556 active site 357804003557 I-site; other site 357804003558 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 357804003559 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09103 357804003560 ATP cone domain; Region: ATP-cone; pfam03477 357804003561 Class I ribonucleotide reductase; Region: RNR_I; cd01679 357804003562 active site 357804003563 dimer interface [polypeptide binding]; other site 357804003564 catalytic residues [active] 357804003565 effector binding site; other site 357804003566 R2 peptide binding site; other site 357804003567 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 357804003568 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 357804003569 S-adenosylmethionine binding site [chemical binding]; other site 357804003570 DNA gyrase subunit A; Validated; Region: PRK05560 357804003571 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 DNA...; Region: TOP4c; cd00187 357804003572 CAP-like domain; other site 357804003573 active site 357804003574 primary dimer interface [polypeptide binding]; other site 357804003575 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 357804003576 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 357804003577 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 357804003578 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 357804003579 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 357804003580 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 357804003581 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 as...; Region: PSAT_like; cd00611 357804003582 homodimer interface [polypeptide binding]; other site 357804003583 substrate-cofactor binding pocket; other site 357804003584 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804003585 catalytic residue [active] 357804003586 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 357804003587 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 357804003588 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804003589 homodimer interface [polypeptide binding]; other site 357804003590 catalytic residue [active] 357804003591 3-phosphoshikimate 1-carboxyvinyltransferase; Region: PLN02338 357804003592 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...; Region: EPSP_synthase; cd01556 357804003593 hinge; other site 357804003594 active site 357804003595 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 357804003596 PAS fold; Region: PAS; pfam00989 357804003597 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804003598 metal binding site [ion binding]; metal-binding site 357804003599 active site 357804003600 I-site; other site 357804003601 rod shape-determining protein MreB; Provisional; Region: PRK13927 357804003602 Actin; An ubiquitous protein involved in the formation of filaments that are a major component of the cytoskeleton. Interaction with myosin provides the basis of muscular contraction and many aspects of cell motility. Each actin protomer binds one...; Region: ACTIN; cl11528 357804003603 ATP binding site [chemical binding]; other site 357804003604 profilin binding site; other site 357804003605 rod shape-determining protein MreC; Region: mreC; TIGR00219 357804003606 rod shape-determining protein MreC; Region: MreC; pfam04085 357804003607 rod shape-determining protein MreD; Region: MreD; cl01087 357804003608 Maf-like protein; Region: Maf; pfam02545 357804003609 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 357804003610 active site 357804003611 dimer interface [polypeptide binding]; other site 357804003612 ribonuclease G; Provisional; Region: PRK11712 357804003613 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 357804003614 homodimer interface [polypeptide binding]; other site 357804003615 oligonucleotide binding site [chemical binding]; other site 357804003616 TIGR02099 family protein; Region: TIGR02099 357804003617 AsmA-like C-terminal region; Region: AsmA_2; cl15864 357804003618 Predicted amidohydrolase [General function prediction only]; Region: COG0388 357804003619 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 357804003620 putative active site [active] 357804003621 catalytic triad [active] 357804003622 dimer interface [polypeptide binding]; other site 357804003623 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 357804003624 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 357804003625 Haemolysin-III related; Region: HlyIII; cl03831 357804003626 Protein of unknown function (DUF615); Region: DUF615; cl01147 357804003627 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 357804003628 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 357804003629 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 357804003630 Sporulation related domain; Region: SPOR; cl10051 357804003631 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 357804003632 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 357804003633 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 357804003634 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 357804003635 Uncharacterized conserved protein [Function unknown]; Region: COG1576; cl00679 357804003636 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; pfam02590 357804003637 Oligomerisation domain; Region: Oligomerisation; cl00519 357804003638 cell division protein MraZ; Reviewed; Region: PRK00326 357804003639 MraZ protein; Region: MraZ; pfam02381 357804003640 MraZ protein; Region: MraZ; pfam02381 357804003641 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 357804003642 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; cl16911 357804003643 Septum formation initiator; Region: DivIC; cl11433 357804003644 peptidoglycan synthase FtsI; Provisional; Region: PRK15105 357804003645 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 357804003646 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 357804003647 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 357804003648 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 357804003649 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 357804003650 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 357804003651 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 357804003652 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 357804003653 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 357804003654 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 357804003655 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 357804003656 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...; Region: GT_MraY; cd06852 357804003657 Mg++ binding site [ion binding]; other site 357804003658 putative catalytic motif [active] 357804003659 putative substrate binding site [chemical binding]; other site 357804003660 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03803 357804003661 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 357804003662 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 357804003663 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 357804003664 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 357804003665 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 pentapeptide...; Region: GT1_MurG; cd03785 357804003666 active site 357804003667 homodimer interface [polypeptide binding]; other site 357804003668 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 357804003669 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 357804003670 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 357804003671 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 357804003672 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 357804003673 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 357804003674 ATP-grasp domain; Region: ATP-grasp_4; cl03087 357804003675 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 357804003676 Cell division protein FtsQ; Region: FtsQ; pfam03799 357804003677 cell division protein FtsA; Reviewed; Region: ftsA; PRK09472 357804003678 Cell division protein FtsA; Region: FtsA; cl11496 357804003679 Cell division protein FtsA; Region: FtsA; cl11496 357804003680 cell division protein FtsZ; Validated; Region: PRK09330 357804003681 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 at...; Region: FtsZ_type1; cd02201 357804003682 nucleotide binding site [chemical binding]; other site 357804003683 SulA interaction site; other site 357804003684 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 357804003685 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 357804003686 Protein of unknown function (DUF721); Region: DUF721; cl02324 357804003687 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 357804003688 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804003689 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 357804003690 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804003691 nucleotide binding region [chemical binding]; other site 357804003692 ATP-binding site [chemical binding]; other site 357804003693 SEC-C motif; Region: SEC-C; pfam02810 357804003694 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 357804003695 active site 357804003696 8-oxo-dGMP binding site [chemical binding]; other site 357804003697 nudix motif; other site 357804003698 metal binding site [ion binding]; metal-binding site 357804003699 DNA ligase; Provisional; Region: PRK09125 357804003700 Adenylation domain of kDNA ligases and similar proteins; Region: Adenylation_kDNA_ligase_like; cd07896 357804003701 DNA binding site [nucleotide binding] 357804003702 active site 357804003703 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of kDNA ligase-like ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit; Region: OBF_kDNA_ligase_like; cd08041 357804003704 DNA binding site [nucleotide binding] 357804003705 quinolinate phosphoribosyltransferase; Validated; Region: PRK09016 357804003706 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...; Region: QPRTase; cd01572 357804003707 dimerization interface [polypeptide binding]; other site 357804003708 active site 357804003709 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 357804003710 CoA-binding site [chemical binding]; other site 357804003711 Protein of unknown function (DUF1342); Region: DUF1342; cl01892 357804003712 Domain of unknown function (DUF329); Region: DUF329; cl01144 357804003713 translation initiation factor Sui1; Validated; Region: PRK06824 357804003714 Homologs of eIF1/SUI1 including Escherichia coli YciH; Region: YciH_like; cd11567 357804003715 putative rRNA binding site [nucleotide binding]; other site 357804003716 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 357804003717 Helix-turn-helix domains; Region: HTH; cl00088 357804003718 Helix-turn-helix domains; Region: HTH; cl00088 357804003719 Integrase core domain; Region: rve; cl01316 357804003720 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 357804003721 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 357804003722 FeS/SAM binding site; other site 357804003723 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 357804003724 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 357804003725 binding surface 357804003726 TPR motif; other site 357804003727 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 357804003728 ribonuclease E; Reviewed; Region: rne; PRK10811 357804003729 cytoskeletal protein RodZ; Provisional; Region: PRK10856 357804003730 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 357804003731 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 357804003732 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 357804003733 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 357804003734 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 357804003735 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 357804003736 dimer interface [polypeptide binding]; other site 357804003737 motif 1; other site 357804003738 active site 357804003739 motif 2; other site 357804003740 motif 3; other site 357804003741 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 357804003742 anticodon binding site; other site 357804003743 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 357804003744 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 357804003745 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 357804003746 binding surface 357804003747 TPR motif; other site 357804003748 outer membrane biogenesis protein BamB; Provisional; Region: PRK11138 357804003749 Beta-barrel assembly machinery (Bam) complex component B and related proteins; Region: BamB_YfgL; cd10276 357804003750 Trp docking motif [polypeptide binding]; other site 357804003751 GTP-binding protein Der; Reviewed; Region: PRK00093 357804003752 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 357804003753 G1 box; other site 357804003754 GTP/Mg2+ binding site [chemical binding]; other site 357804003755 Switch I region; other site 357804003756 G2 box; other site 357804003757 Switch II region; other site 357804003758 G3 box; other site 357804003759 G4 box; other site 357804003760 G5 box; other site 357804003761 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 357804003762 G1 box; other site 357804003763 GTP/Mg2+ binding site [chemical binding]; other site 357804003764 Switch I region; other site 357804003765 G2 box; other site 357804003766 G3 box; other site 357804003767 Switch II region; other site 357804003768 G4 box; other site 357804003769 G5 box; other site 357804003770 Protein of unknown function (DUF1407); Region: DUF1407; pfam07191 357804003771 outer membrane lipoprotein; Provisional; Region: PRK11023 357804003772 BON domain; Region: BON; cl02771 357804003773 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 357804003774 dimer interface [polypeptide binding]; other site 357804003775 active site 357804003776 Restriction endonuclease; Region: Mrr_cat; cl00516 357804003777 Putative lipoprotein [General function prediction only]; Region: LppC; COG3107 357804003778 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 357804003779 putative ligand binding site [chemical binding]; other site 357804003780 SAM-dependent 16S ribosomal RNA C1402 ribose 2'-O-methyltransferase; Provisional; Region: PRK14994 357804003781 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 357804003782 OpgC protein; Region: OpgC_C; cl00792 357804003783 multiple promoter invertase; Provisional; Region: mpi; PRK13413 357804003784 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 357804003785 catalytic residues [active] 357804003786 catalytic nucleophile [active] 357804003787 Helix-turn-helix domains; Region: HTH; cl00088 357804003788 HTH-like domain; Region: HTH_21; pfam13276 357804003789 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 357804003790 Integrase core domain; Region: rve; cl01316 357804003791 Integrase core domain; Region: rve_3; cl15866 357804003792 PEP-CTERM motif; Region: VPEP; pfam07589 357804003793 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 357804003794 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 357804003795 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 357804003796 active site 357804003797 (T/H)XGH motif; other site 357804003798 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 357804003799 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 357804003800 Lipopolysaccharide-assembly; Region: LptE; cl01125 357804003801 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 357804003802 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 357804003803 HIGH motif; other site 357804003804 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 357804003805 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 357804003806 active site 357804003807 KMSKS motif; other site 357804003808 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 357804003809 tRNA binding surface [nucleotide binding]; other site 357804003810 response regulator; Provisional; Region: PRK09483 357804003811 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 357804003812 active site 357804003813 phosphorylation site [posttranslational modification] 357804003814 intermolecular recognition site; other site 357804003815 dimerization interface [polypeptide binding]; other site 357804003816 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. Many...; Region: LuxR_C_like; cd06170 357804003817 DNA binding residues [nucleotide binding] 357804003818 dimerization interface [polypeptide binding]; other site 357804003819 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 357804003820 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 357804003821 GIY-YIG motif/motif A; other site 357804003822 active site 357804003823 catalytic site [active] 357804003824 putative DNA binding site [nucleotide binding]; other site 357804003825 metal binding site [ion binding]; metal-binding site 357804003826 UvrB/uvrC motif; Region: UVR; pfam02151 357804003827 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 357804003828 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 357804003829 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 357804003830 two-component response regulator; Provisional; Region: PRK11173 357804003831 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 357804003832 active site 357804003833 phosphorylation site [posttranslational modification] 357804003834 intermolecular recognition site; other site 357804003835 dimerization interface [polypeptide binding]; other site 357804003836 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 and...; Region: trans_reg_C; cd00383 357804003837 DNA binding site [nucleotide binding] 357804003838 Transglycosylase associated protein; Region: Transgly_assoc; cl00978 357804003839 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804003840 I-site; other site 357804003841 active site 357804003842 metal binding site [ion binding]; metal-binding site 357804003843 ECF-type riboflavin transporter, S component; Region: ECF-ribofla_trS; cl01942 357804003844 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 357804003845 cyclic-di-GMP phosphodiesterase; Provisional; Region: PRK11359 357804003846 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 357804003847 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 357804003848 putative active site [active] 357804003849 heme pocket [chemical binding]; other site 357804003850 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804003851 metal binding site [ion binding]; metal-binding site 357804003852 active site 357804003853 I-site; other site 357804003854 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 357804003855 hypothetical protein; Provisional; Region: PRK13560 357804003856 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 357804003857 GAF domain; Region: GAF_2; pfam13185 357804003858 GAF domain; Region: GAF; cl15785 357804003859 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804003860 metal binding site [ion binding]; metal-binding site 357804003861 active site 357804003862 I-site; other site 357804003863 FIST N domain; Region: FIST; cl10701 357804003864 FIST C domain; Region: FIST_C; pfam10442 357804003865 PAS domain; Region: PAS_9; pfam13426 357804003866 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 357804003867 putative active site [active] 357804003868 heme pocket [chemical binding]; other site 357804003869 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804003870 metal binding site [ion binding]; metal-binding site 357804003871 active site 357804003872 I-site; other site 357804003873 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 357804003874 Uncharacterized conserved protein [Function unknown]; Region: COG3287 357804003875 FIST N domain; Region: FIST; cl10701 357804003876 FIST C domain; Region: FIST_C; pfam10442 357804003877 PAS domain; Region: PAS_9; pfam13426 357804003878 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 357804003879 putative active site [active] 357804003880 heme pocket [chemical binding]; other site 357804003881 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804003882 metal binding site [ion binding]; metal-binding site 357804003883 active site 357804003884 I-site; other site 357804003885 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 357804003886 FIST N domain; Region: FIST; cl10701 357804003887 FIST C domain; Region: FIST_C; pfam10442 357804003888 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 357804003889 PAS domain; Region: PAS_9; pfam13426 357804003890 putative active site [active] 357804003891 heme pocket [chemical binding]; other site 357804003892 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804003893 metal binding site [ion binding]; metal-binding site 357804003894 active site 357804003895 I-site; other site 357804003896 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 357804003897 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 357804003898 PAS domain S-box; Region: sensory_box; TIGR00229 357804003899 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804003900 metal binding site [ion binding]; metal-binding site 357804003901 active site 357804003902 I-site; other site 357804003903 Protein of unknown function (DUF523); Region: DUF523; cl00733 357804003904 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypD; COG0409 357804003905 Hydrogenase formation hypA family; Region: HypD; cl12072 357804003906 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 357804003907 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 357804003908 substrate binding site [chemical binding]; other site 357804003909 oxyanion hole (OAH) forming residues; other site 357804003910 trimer interface [polypeptide binding]; other site 357804003911 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 357804003912 active site 357804003913 substrate binding site [chemical binding]; other site 357804003914 cosubstrate binding site; other site 357804003915 catalytic site [active] 357804003916 C-terminal subdomain of the Formyltransferase-like domain found in HypX-like proteins; Region: FMT_C_HypX; cd08701 357804003917 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 357804003918 dimerization interface [polypeptide binding]; other site 357804003919 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 357804003920 ATP binding site [chemical binding]; other site 357804003921 HupF/HypC family; Region: HupF_HypC; cl00394 357804003922 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804003923 hydrogenase nickel incorporation protein; Provisional; Region: hypA; cl00418 357804003924 Endopeptidases that belong to the bidirectional NAD-linked hydrogenase group. This group of endopeptidases are highly specific carboxyl-terminal protease (HoxW protease) which releases a 24-amino-acid peptide from HoxH prior to progression of subunit...; Region: H2MP_NAD-link-bidir; cd06066 357804003925 nickel binding site [ion binding]; other site 357804003926 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 357804003927 NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75 kD subunit (chain G) [Energy production and conversion]; Region: NuoG; COG1034 357804003928 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; cl00159 357804003929 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; cl11210 357804003930 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl15792 357804003931 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 357804003932 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 357804003933 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 357804003934 SLBB domain; Region: SLBB; pfam10531 357804003935 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; cl11211 357804003936 Acylphosphatase; Region: Acylphosphatase; cl00551 357804003937 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 357804003938 HypF finger; Region: zf-HYPF; pfam07503 357804003939 HypF finger; Region: zf-HYPF; pfam07503 357804003940 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 357804003941 Protein of unknown function (DUF1538); Region: DUF1538; pfam07556 357804003942 Protein of unknown function (DUF1538); Region: DUF1538; pfam07556 357804003943 Nitrogen regulatory protein P-II; Region: P-II; smart00938 357804003944 FOG: CBS domain [General function prediction only]; Region: COG0517 357804003945 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-called...; Region: CBS_pair_17; cd04630 357804003946 Protein required for attachment to host cells; Region: Host_attach; cl02398 357804003947 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 357804003948 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 357804003949 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 357804003950 active site 357804003951 phosphorylation site [posttranslational modification] 357804003952 intermolecular recognition site; other site 357804003953 dimerization interface [polypeptide binding]; other site 357804003954 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 and...; Region: trans_reg_C; cd00383 357804003955 DNA binding site [nucleotide binding] 357804003956 sensor protein QseC; Provisional; Region: PRK10337 357804003957 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...; Region: HisKA; cd00082 357804003958 phosphorylation site [posttranslational modification] 357804003959 dimer interface [polypeptide binding]; other site 357804003960 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 357804003961 ATP binding site [chemical binding]; other site 357804003962 Mg2+ binding site [ion binding]; other site 357804003963 G-X-G motif; other site 357804003964 EamA-like transporter family; Region: EamA; cl01037 357804003965 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 357804003966 EamA-like transporter family; Region: EamA; cl01037 357804003967 Domain of unknown function (DUF2760); Region: DUF2760; pfam10816 357804003968 Molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: DnaK; COG0443 357804003969 Molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: DnaK; COG0443 357804003970 DNA-K related protein; Region: DUF3731; pfam12531 357804003971 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 357804003972 Ligand Binding Site [chemical binding]; other site 357804003973 bifunctional glutathionylspermidine amidase/glutathionylspermidine synthetase; Provisional; Region: PRK10507 357804003974 NlpC/P60 family; Region: NLPC_P60; cl11438 357804003975 Circularly permuted ATP-grasp type 2; Region: CP_ATPgrasp_2; cl00503 357804003976 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 357804003977 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 357804003978 Zn2+ binding site [ion binding]; other site 357804003979 Mg2+ binding site [ion binding]; other site 357804003980 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 357804003981 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 357804003982 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804003983 metal binding site [ion binding]; metal-binding site 357804003984 active site 357804003985 I-site; other site 357804003986 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 357804003987 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; cl15357 357804003988 transmembrane helices; other site 357804003989 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; cl15357 357804003990 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; cl15357 357804003991 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 357804003992 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 357804003993 Domain of unknown function (DUF336); Region: DUF336; cl01249 357804003994 putative oxidoreductase; Provisional; Region: PRK11579 357804003995 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804003996 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 357804003997 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 357804003998 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 357804003999 active site 357804004000 phosphorylation site [posttranslational modification] 357804004001 intermolecular recognition site; other site 357804004002 dimerization interface [polypeptide binding]; other site 357804004003 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 ABC; Region: AAA; cd00009 357804004004 Walker A motif; other site 357804004005 ATP binding site [chemical binding]; other site 357804004006 Walker B motif; other site 357804004007 arginine finger; other site 357804004008 Helix-turn-helix domains; Region: HTH; cl00088 357804004009 This domain family includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa; Region: ACD_sHsps_p23-like; cd00298 357804004010 AAA family ATPase, CDC48 subfamily; Region: CDC48; TIGR01243 357804004011 Cell division protein 48 (CDC48), N-terminal domain; Region: CDC48_N; pfam02359 357804004012 Cell division protein 48 (CDC48), domain 2; Region: CDC48_2; cl08380 357804004013 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 ABC; Region: AAA; cd00009 357804004014 Walker A motif; other site 357804004015 ATP binding site [chemical binding]; other site 357804004016 Walker B motif; other site 357804004017 arginine finger; other site 357804004018 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 ABC; Region: AAA; cd00009 357804004019 ATP binding site [chemical binding]; other site 357804004020 Walker B motif; other site 357804004021 arginine finger; other site 357804004022 Gas vesicle synthesis protein GvpL/GvpF; Region: GvpL_GvpF; pfam06386 357804004023 Gas vesicle synthesis protein GvpL/GvpF; Region: GvpL_GvpF; pfam06386 357804004024 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 357804004025 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 357804004026 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 357804004027 putative active site [active] 357804004028 heme pocket [chemical binding]; other site 357804004029 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...; Region: HisKA; cd00082 357804004030 dimer interface [polypeptide binding]; other site 357804004031 phosphorylation site [posttranslational modification] 357804004032 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 357804004033 ATP binding site [chemical binding]; other site 357804004034 Mg2+ binding site [ion binding]; other site 357804004035 G-X-G motif; other site 357804004036 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 357804004037 Response regulator receiver domain; Region: Response_reg; pfam00072 357804004038 active site 357804004039 phosphorylation site [posttranslational modification] 357804004040 intermolecular recognition site; other site 357804004041 dimerization interface [polypeptide binding]; other site 357804004042 Gas vesicle protein; Region: Gas_vesicle; cl02954 357804004043 gas vesicle protein GvpN; Region: gas_vesic_GvpN; TIGR02640 357804004044 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 ABC; Region: AAA; cd00009 357804004045 Walker A motif; other site 357804004046 ATP binding site [chemical binding]; other site 357804004047 Walker B motif; other site 357804004048 arginine finger; other site 357804004049 Gas vesicle synthesis protein GvpL/GvpF; Region: GvpL_GvpF; pfam06386 357804004050 Gas vesicle protein; Region: Gas_vesicle; cl02954 357804004051 Gas vesicle protein K; Region: GvpK; pfam05121 357804004052 Gas vesicle protein; Region: Gas_vesicle; cl02954 357804004053 Uncharacterized proteins involved in stress response, homologs of TerZ and putative cAMP-binding protein CABP1 [Signal transduction mechanisms]; Region: TerZ; COG2310 357804004054 Uncharacterized proteins involved in stress response, similar to tellurium resistance terD; Region: TerD_like; cd06974 357804004055 putative metal binding site [ion binding]; other site 357804004056 Uncharacterized proteins involved in stress response, homologs of TerZ and putative cAMP-binding protein CABP1 [Signal transduction mechanisms]; Region: TerZ; COG2310 357804004057 Uncharacterized proteins involved in stress response, similar to tellurium resistance terD; Region: TerD_like; cd06974 357804004058 putative metal binding site [ion binding]; other site 357804004059 Uncharacterized proteins involved in stress response, homologs of TerZ and putative cAMP-binding protein CABP1 [Signal transduction mechanisms]; Region: TerZ; COG2310 357804004060 Uncharacterized proteins involved in stress response, similar to tellurium resistance terD; Region: TerD_like; cd06974 357804004061 putative metal binding site [ion binding]; other site 357804004062 Ca2+/Na+ antiporter [Inorganic ion transport and metabolism]; Region: ECM27; COG0530 357804004063 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 357804004064 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 357804004065 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 357804004066 active site 357804004067 Protein of unknown function (DUF3706); Region: DUF3706; pfam12500 357804004068 Predicted hydrolases of the HAD superfamily [General function prediction only]; Region: Cof; COG0561 357804004069 Protein of unknown function (DUF2983); Region: DUF2983; pfam11202 357804004070 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 357804004071 tellurite resistance protein terB; Region: terB; cd07176 357804004072 putative metal binding site [ion binding]; other site 357804004073 bifunctional aspartokinase I/homoserine dehydrogenase I; Provisional; Region: thrA; PRK09436 357804004074 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...; Region: AAK_AK-HSDH; cd04257 357804004075 putative catalytic residues [active] 357804004076 putative nucleotide binding site [chemical binding]; other site 357804004077 putative aspartate binding site [chemical binding]; other site 357804004078 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA-like_1; cd04921 357804004079 dimer interface [polypeptide binding]; other site 357804004080 putative threonine allosteric regulatory site; other site 357804004081 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA_2; cd04922 357804004082 putative threonine allosteric regulatory site; other site 357804004083 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804004084 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 357804004085 homoserine kinase; Provisional; Region: PRK01212 357804004086 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 357804004087 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 357804004088 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 357804004089 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), tryptophan...; Region: Trp-synth-beta_II; cl00342 357804004090 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 357804004091 catalytic residue [active] 357804004092 acyl-CoA thioesterase II; Provisional; Region: PRK10526 357804004093 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 357804004094 active site 357804004095 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 357804004096 catalytic triad [active] 357804004097 dimer interface [polypeptide binding]; other site 357804004098 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 357804004099 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 357804004100 Glycine radical; Region: Gly_radical; cl12026 357804004101 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 357804004102 ligand binding site [chemical binding]; other site 357804004103 active site 357804004104 UGI interface [polypeptide binding]; other site 357804004105 catalytic site [active] 357804004106 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; cl15774 357804004107 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 357804004108 Uncharacterized ACR, COG1678; Region: DUF179; cl00731 357804004109 glutathione synthetase; Provisional; Region: PRK05246 357804004110 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 357804004111 ATP-grasp domain; Region: ATP-grasp_4; cl03087 357804004112 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385; cl00611 357804004113 RNA methyltransferase; Region: Methyltrans_RNA; pfam04452 357804004114 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 synthase...; Region: MTHFR; cl00246 357804004115 Uncharacterized conserved protein [Function unknown]; Region: COG2966 357804004116 Protein of unknown function (DUF1212); Region: DUF1212; cl01118 357804004117 Protein of unknown function (DUF1212); Region: DUF1212; cl01118 357804004118 SWIM/SEC-C metal-binding motif protein, PBPRA1643 family; Region: SWIM_PBPRA1643; TIGR04102 357804004119 SEC-C motif; Region: SEC-C; pfam02810 357804004120 Protein of unknown function (DUF1244); Region: DUF1244; cl01385 357804004121 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; cl16911 357804004122 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 357804004123 ATP binding site [chemical binding]; other site 357804004124 putative Mg++ binding site [ion binding]; other site 357804004125 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 357804004126 nucleotide binding region [chemical binding]; other site 357804004127 ATP-binding site [chemical binding]; other site 357804004128 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 357804004129 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 357804004130 ligand binding site; other site 357804004131 oligomer interface; other site 357804004132 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...; Region: LbH_G1P_AT_C; cd04651 357804004133 dimer interface [polypeptide binding]; other site 357804004134 N-terminal domain interface [polypeptide binding]; other site 357804004135 sulfate 1 binding site; other site 357804004136 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 357804004137 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 357804004138 ligand binding site [chemical binding]; other site 357804004139 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 357804004140 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 hexoses...; Region: ABC_Carb_Monos_I; cd03216 357804004141 Walker A/P-loop; other site 357804004142 ATP binding site [chemical binding]; other site 357804004143 Q-loop/lid; other site 357804004144 ABC transporter signature motif; other site 357804004145 Walker B; other site 357804004146 D-loop; other site 357804004147 H-loop/switch region; other site 357804004148 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 357804004149 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 357804004150 TM-ABC transporter signature motif; other site 357804004151 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 357804004152 TM-ABC transporter signature motif; other site 357804004153 Peptidase family U32; Region: Peptidase_U32; cl03113 357804004154 Collagenase; Region: DUF3656; pfam12392 357804004155 Peptidase family U32; Region: Peptidase_U32; cl03113 357804004156 exonuclease subunit SbcD; Provisional; Region: PRK10966 357804004157 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 357804004158 active site 357804004159 metal binding site [ion binding]; metal-binding site 357804004160 DNA binding site [nucleotide binding] 357804004161 Type 5 capsule protein repressor C-terminal domain; Region: SbcD_C; pfam12320 357804004162 exonuclease subunit SbcC; Provisional; Region: PRK10246 357804004163 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804004164 Walker A/P-loop; other site 357804004165 ATP binding site [chemical binding]; other site 357804004166 Q-loop/lid; other site 357804004167 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 357804004168 exonuclease subunit SbcC; Provisional; Region: PRK10246 357804004169 SbcCD and other Mre11/Rad50 (MR) complexes are implicated in the metabolism of DNA ends. They cleave ends sealed by hairpin structures and are thought to play a role in removing protein bound to DNA termini; Region: ABC_sbcCD; cd03279 357804004170 Q-loop/lid; other site 357804004171 ABC transporter signature motif; other site 357804004172 Walker B; other site 357804004173 D-loop; other site 357804004174 H-loop/switch region; other site 357804004175 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 357804004176 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804004177 metal binding site [ion binding]; metal-binding site 357804004178 active site 357804004179 I-site; other site 357804004180 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]; Region: COG4260 357804004181 A subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual...; Region: Band_7_5; cd03408 357804004182 zinc-ribbon domain; Region: zf-ribbon_3; cl11198 357804004183 zinc-ribbon domain; Region: zf-ribbon_3; cl11198 357804004184 tellurium resistance terB-like protein; Region: terB_like; cl11965 357804004185 Cytochrome c [Energy production and conversion]; Region: COG3258 357804004186 Cytochrome c; Region: Cytochrom_C; cl11414 357804004187 Cytochrome c; Region: Cytochrom_C; cl11414 357804004188 Cytochrome c; Region: Cytochrom_C; cl11414 357804004189 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 357804004190 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Region: PBP1_ABC_sugar_binding_like_6; cd06315 357804004191 putative ligand binding site [chemical binding]; other site 357804004192 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804004193 metal binding site [ion binding]; metal-binding site 357804004194 active site 357804004195 I-site; other site 357804004196 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 357804004197 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 357804004198 Coenzyme A binding pocket [chemical binding]; other site 357804004199 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 357804004200 Sulfate transporter family; Region: Sulfate_transp; cl15842 357804004201 Sulfate transporter family; Region: Sulfate_transp; cl15842 357804004202 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 357804004203 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 357804004204 active site 357804004205 ADP/pyrophosphate binding site [chemical binding]; other site 357804004206 dimerization interface [polypeptide binding]; other site 357804004207 allosteric effector site; other site 357804004208 fructose-1,6-bisphosphate binding site; other site 357804004209 Uncharacterized protein family (UPF0149); Region: UPF0149; cl01173 357804004210 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 357804004211 active site 357804004212 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 357804004213 putative catalytic site [active] 357804004214 putative phosphate binding site [ion binding]; other site 357804004215 active site 357804004216 metal binding site A [ion binding]; metal-binding site 357804004217 DNA binding site [nucleotide binding] 357804004218 putative AP binding site [nucleotide binding]; other site 357804004219 putative metal binding site B [ion binding]; other site 357804004220 Phosphate-starvation-inducible E; Region: PsiE; cl01264 357804004221 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 357804004222 active site 357804004223 dimerization interface [polypeptide binding]; other site 357804004224 tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ; Provisional; Region: PRK15114 357804004225 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 357804004226 Helix-turn-helix domains; Region: HTH; cl00088 357804004227 Rrf2 family protein; Region: rrf2_super; TIGR00738 357804004228 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 357804004229 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 357804004230 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 357804004231 catalytic residue [active] 357804004232 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 357804004233 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 357804004234 trimerization site [polypeptide binding]; other site 357804004235 active site 357804004236 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 357804004237 co-chaperone HscB; Provisional; Region: hscB; PRK05014 357804004238 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 Hsp70s; Region: DnaJ; cd06257 357804004239 HSP70 interaction site [polypeptide binding]; other site 357804004240 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 357804004241 chaperone protein HscA; Provisional; Region: hscA; PRK05183 357804004242 FGGY family of carbohydrate kinases; Region: FGGY; cl08364 357804004243 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 357804004244 catalytic loop [active] 357804004245 iron binding site [ion binding]; other site 357804004246 Iron-sulphur cluster assembly; Region: Fe-S_assembly; cl01123 357804004247 aminopeptidase B; Provisional; Region: PRK05015 357804004248 Peptidase; Region: DUF3663; pfam12404 357804004249 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 and...; Region: Peptidase_M17; cd00433 357804004250 interface (dimer of trimers) [polypeptide binding]; other site 357804004251 Substrate-binding/catalytic site; other site 357804004252 Zn-binding sites [ion binding]; other site 357804004253 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 357804004254 fructokinase; Reviewed; Region: PRK09557 357804004255 LysE type translocator; Region: LysE; cl00565 357804004256 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 357804004257 nucleophile elbow; other site 357804004258 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 357804004259 Surface antigen; Region: Bac_surface_Ag; cl03097 357804004260 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 357804004261 dimer interface [polypeptide binding]; other site 357804004262 active site 357804004263 Predicted glutamine amidotransferase [General function prediction only]; Region: COG0121 357804004264 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 357804004265 putative active site [active] 357804004266 putative dimer interface [polypeptide binding]; other site 357804004267 DNA alkylation repair enzyme [DNA replication, recombination, and repair]; Region: COG4335 357804004268 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 357804004269 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 357804004270 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 357804004271 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 357804004272 DNA binding residues [nucleotide binding] 357804004273 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 357804004274 metal-binding site [ion binding] 357804004275 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 357804004276 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 357804004277 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 357804004278 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 357804004279 active site 357804004280 DNA polymerase IV; Validated; Region: PRK02406 357804004281 DNA binding site [nucleotide binding] 357804004282 Integrase core domain; Region: rve; cl01316 357804004283 Helix-turn-helix domains; Region: HTH; cl00088 357804004284 Winged helix-turn helix; Region: HTH_29; pfam13551 357804004285 Helix-turn-helix domains; Region: HTH; cl00088 357804004286 Winged helix-turn helix; Region: HTH_33; pfam13592 357804004287 hypothetical protein; Provisional; Region: PRK09272 357804004288 HupE / UreJ protein; Region: HupE_UreJ; cl01011 357804004289 Peptidase family M48; Region: Peptidase_M48; cl12018 357804004290 Helix-turn-helix domains; Region: HTH; cl00088 357804004291 Na+/H+ antiporter subunit; Region: PhaG_MnhG_YufB; cl00583 357804004292 Multiple resistance and pH regulation protein F (MrpF / PhaF); Region: MrpF_PhaF; cl09154 357804004293 Na+/H+ ion antiporter subunit; Region: MNHE; cl00807 357804004294 Na+/H+ ion antiporter subunit; Region: MNHE; cl00807 357804004295 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12666 357804004296 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 357804004297 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 357804004298 putative monovalent cation/H+ antiporter subunit A; Reviewed; Region: PRK12648 357804004299 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 357804004300 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 357804004301 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 357804004302 Helix-turn-helix domains; Region: HTH; cl00088 357804004303 Winged helix-turn helix; Region: HTH_29; pfam13551 357804004304 Helix-turn-helix domains; Region: HTH; cl00088 357804004305 Winged helix-turn helix; Region: HTH_33; pfam13592 357804004306 Integrase core domain; Region: rve; cl01316 357804004307 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 357804004308 S-adenosylmethionine binding site [chemical binding]; other site 357804004309 Phosphate-starvation-inducible E; Region: PsiE; cl01264 357804004310 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 357804004311 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 357804004312 hypothetical protein; Provisional; Region: PRK04164 357804004313 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; cl10498 357804004314 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 357804004315 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 357804004316 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, acyl; Region: Biotinyl_lipoyl_domains; cl11404 357804004317 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 357804004318 copper-resistance protein, CopA family; Region: copper_res_A; TIGR01480 357804004319 Histidine kinase, Adenylyl cyclase, 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...; Region: HAMP; cl01054 357804004320 dimerization interface [polypeptide binding]; other site 357804004321 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...; Region: HisKA; cd00082 357804004322 dimer interface [polypeptide binding]; other site 357804004323 phosphorylation site [posttranslational modification] 357804004324 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 357804004325 ATP binding site [chemical binding]; other site 357804004326 Mg2+ binding site [ion binding]; other site 357804004327 G-X-G motif; other site 357804004328 osmolarity response regulator; Provisional; Region: ompR; PRK09468 357804004329 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 357804004330 active site 357804004331 phosphorylation site [posttranslational modification] 357804004332 intermolecular recognition site; other site 357804004333 dimerization interface [polypeptide binding]; other site 357804004334 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 and...; Region: trans_reg_C; cd00383 357804004335 DNA binding site [nucleotide binding] 357804004336 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 357804004337 dimer interface [polypeptide binding]; other site 357804004338 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 357804004339 catalytic residues [active] 357804004340 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 357804004341 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 CXXC...; Region: DsbA_Com1_like; cd03023 357804004342 catalytic residues [active] 357804004343 Protein of unknown function (DUF3081); Region: DUF3081; pfam11280 357804004344 copper exporting ATPase; Provisional; Region: copA; PRK10671 357804004345 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 357804004346 metal-binding site [ion binding] 357804004347 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 357804004348 metal-binding site [ion binding] 357804004349 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 357804004350 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 357804004351 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 357804004352 Protein of unknown function (DUF2933); Region: DUF2933; pfam11666 357804004353 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 357804004354 Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; Region: HTH_HMRTR; cd04770 357804004355 DNA binding residues [nucleotide binding] 357804004356 dimer interface [polypeptide binding]; other site 357804004357 metal binding site [ion binding]; metal-binding site 357804004358 Cytochrome c; Region: Cytochrom_C; cl11414 357804004359 Cytochrome c; Region: Cytochrom_C; cl11414 357804004360 Bacterial Ig-like domain; Region: Big_5; cl01012 357804004361 Copper resistance protein D; Region: CopD; cl00563 357804004362 MarC family integral membrane protein; Region: MarC; cl00919 357804004363 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3314 357804004364 Nucleoside recognition; Region: Gate; cl00486 357804004365 integron integrase; Region: integrase_gron; TIGR02249 357804004366 IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains. This CD includes integrases which are components of multiresistant integrons and mediate recombination between a proximal attI site and...; Region: INT_IntI; cd01193 357804004367 Int/Topo IB signature motif; other site 357804004368 Transposase domain (DUF772); Region: DUF772; pfam05598 357804004369 DDE superfamily endonuclease; Region: DDE_4; cl15789 357804004370 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08261 357804004371 CRISPR/Cas system-associated protein Csy1; Region: Csy1_I-F; cd09735 357804004372 CRISPR/Cas system-associated RAMP superfamily protein Csy2; Region: Csy2_I-F; cd09736 357804004373 CRISPR/Cas system-associated RAMP superfamily protein Csy3; Region: Csy3_I-F; cd09737 357804004374 CRISPR/Cas system-associated RAMP superfamily protein Cas6f; Region: Cas6_I-F; cd09739 357804004375 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 357804004376 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 357804004377 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 357804004378 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 357804004379 dimer interface [polypeptide binding]; other site 357804004380 motif 1; other site 357804004381 active site 357804004382 motif 2; other site 357804004383 motif 3; other site 357804004384 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 357804004385 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 357804004386 putative tRNA-binding site [nucleotide binding]; other site 357804004387 B3/4 domain; Region: B3_4; cl11458 357804004388 tRNA synthetase B5 domain; Region: B5; cl08394 357804004389 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 357804004390 dimer interface [polypeptide binding]; other site 357804004391 motif 1; other site 357804004392 motif 3; other site 357804004393 motif 2; other site 357804004394 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 357804004395 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...; Region: HU_IHF; cd00591 357804004396 IHF dimer interface [polypeptide binding]; other site 357804004397 IHF - DNA interface [nucleotide binding]; other site 357804004398 NAD-dependent deacetylase; Provisional; Region: PRK00481 357804004399 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 which...; Region: SIRT5_Af1_CobB; cd01412 357804004400 NAD+ binding site [chemical binding]; other site 357804004401 substrate binding site [chemical binding]; other site 357804004402 Zn binding site [ion binding]; other site 357804004403 Predicted integral membrane protein (DUF2189); Region: DUF2189; cl02291 357804004404 Protein of unknown function (DUF2987); Region: DUF2987; pfam11205 357804004405 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 357804004406 Phosphotransferase enzyme family; Region: APH; pfam01636 357804004407 active site 357804004408 ATP binding site [chemical binding]; other site 357804004409 substrate binding site [chemical binding]; other site 357804004410 dimer interface [polypeptide binding]; other site 357804004411 phosphoglycolate phosphatase; Provisional; Region: PRK13222 357804004412 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 357804004413 motif II; other site 357804004414 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK05318 357804004415 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 357804004416 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 357804004417 Domain of unknown function (DUF4250); Region: DUF4250; pfam14056 357804004418 methylated-DNA--protein-cysteine methyltransferase; Provisional; Region: PRK00901 357804004419 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 357804004420 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 357804004421 DNA binding site [nucleotide binding] 357804004422 active site 357804004423 Protein of unknown function (DUF3389); Region: DUF3389; pfam11869 357804004424 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 357804004425 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase; Region: PLPDE_III_ODC; cd00622 357804004426 dimer interface [polypeptide binding]; other site 357804004427 active site 357804004428 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 357804004429 catalytic residues [active] 357804004430 substrate binding site [chemical binding]; other site 357804004431 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 357804004432 Predicted amidohydrolase [General function prediction only]; Region: COG0388 357804004433 Uncharacterized subgroup of the nitrilase superfamily; some members of this subgroup have an N-terminal RimI domain (class 12 nitrilases); Region: nitrilase_Rim1_like; cd07574 357804004434 putative active site [active] 357804004435 catalytic triad [active] 357804004436 putative dimer interface [polypeptide binding]; other site 357804004437 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 357804004438 FAD binding domain; Region: FAD_binding_4; pfam01565 357804004439 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 357804004440 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; cl00674 357804004441 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]; Region: COG1139 357804004442 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; cl00674 357804004443 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...; Region: HCP_like; cl14655 357804004444 Domain of unknown function (DUF3390); Region: DUF3390; pfam11870 357804004445 Cysteine-rich domain; Region: CCG; pfam02754 357804004446 Cysteine-rich domain; Region: CCG; pfam02754 357804004447 L-lactate permease; Region: Lactate_perm; cl00701 357804004448 glycolate transporter; Provisional; Region: PRK09695 357804004449 transcriptional regulator; Provisional; Region: PRK10632 357804004450 Helix-turn-helix domains; Region: HTH; cl00088 357804004451 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 357804004452 putative effector binding pocket; other site 357804004453 dimerization interface [polypeptide binding]; other site 357804004454 NosL; Region: NosL; cl01769 357804004455 ABC-2 type transporter; Region: ABC2_membrane; cl11417 357804004456 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 357804004457 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 357804004458 Walker A/P-loop; other site 357804004459 ATP binding site [chemical binding]; other site 357804004460 Q-loop/lid; other site 357804004461 ABC transporter signature motif; other site 357804004462 Walker B; other site 357804004463 D-loop; other site 357804004464 H-loop/switch region; other site 357804004465 nitrous oxide reductase family maturation protein NosD; Region: NosD_copper_fam; TIGR04247 357804004466 nitrous-oxide reductase; Validated; Region: PRK02888 357804004467 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 357804004468 Regulator of nitric oxide reductase transcription [Transcription]; Region: NosR; COG3901 357804004469 FMN-binding domain; Region: FMN_bind; cl01081 357804004470 FMN-binding domain; Region: FMN_bind; cl01081 357804004471 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 357804004472 4Fe-4S binding domain; Region: Fer4_5; pfam12801 357804004473 Bacterial Ig-like domain (group 2); Region: Big_2; cl02708 357804004474 Uncharacterized conserved protein (DUF2196); Region: DUF2196; cl02044 357804004475 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 357804004476 Bacterial putative lipoprotein (DUF940); Region: DUF940; pfam06082 357804004477 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 357804004478 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 facilitated...; Region: ABCF_EF-3; cd03221 357804004479 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 facilitated...; Region: ABCF_EF-3; cd03221 357804004480 ABC transporter; Region: ABC_tran_2; pfam12848 357804004481 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 facilitated...; Region: ABCF_EF-3; cd03221 357804004482 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 357804004483 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 hydroxymethyl...; Region: SHMT; cd00378 357804004484 dimer interface [polypeptide binding]; other site 357804004485 active site 357804004486 glycine-pyridoxal phosphate binding site [chemical binding]; other site 357804004487 folate binding site [chemical binding]; other site 357804004488 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 357804004489 ATP cone domain; Region: ATP-cone; pfam03477 357804004490 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 357804004491 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 357804004492 catalytic motif [active] 357804004493 Zn binding site [ion binding]; other site 357804004494 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; Region: DHFR; cl00161 357804004495 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 357804004496 Lumazine binding domain; Region: Lum_binding; pfam00677 357804004497 Lumazine binding domain; Region: Lum_binding; pfam00677 357804004498 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 357804004499 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 357804004500 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 357804004501 dimerization interface [polypeptide binding]; other site 357804004502 active site 357804004503 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 357804004504 homopentamer interface [polypeptide binding]; other site 357804004505 active site 357804004506 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 357804004507 putative RNA binding site [nucleotide binding]; other site 357804004508 Protein of unknown function (DUF445); Region: DUF445; pfam04286 357804004509 EamA-like transporter family; Region: EamA; cl01037 357804004510 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 357804004511 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 357804004512 Histidine kinase, Adenylyl cyclase, 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...; Region: HAMP; cl01054 357804004513 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804004514 metal binding site [ion binding]; metal-binding site 357804004515 active site 357804004516 I-site; other site 357804004517 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 357804004518 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 357804004519 FAD binding domain; Region: FAD_binding_4; pfam01565 357804004520 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 357804004521 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 357804004522 CoenzymeA binding site [chemical binding]; other site 357804004523 subunit interaction site [polypeptide binding]; other site 357804004524 PHB binding site; other site 357804004525 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 357804004526 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 357804004527 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 357804004528 hypothetical protein; Provisional; Region: PRK11281 357804004529 Mechanosensitive ion channel inner membrane domain 1; Region: MscS_TM; pfam12794 357804004530 Mechanosensitive ion channel; Region: MS_channel; pfam00924 357804004531 putative metal dependent hydrolase; Provisional; Region: PRK11598 357804004532 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 357804004533 Sulfatase; Region: Sulfatase; cl10460 357804004534 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 357804004535 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 a...; Region: metallo-dependent_hydrolases; cl00281 357804004536 active site 357804004537 Protein of unknown function (DUF3012); Region: DUF3012; pfam11216 357804004538 exonuclease V subunit gamma; Provisional; Region: recC; PRK11069 357804004539 exodeoxyribonuclease V, gamma subunit; Region: recC; TIGR01450 357804004540 exonuclease V subunit beta; Provisional; Region: recB; PRK10876 357804004541 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804004542 exonuclease V subunit alpha; Provisional; Region: recD; PRK10875 357804004543 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804004544 Family description; Region: UvrD_C_2; cl15862 357804004545 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 357804004546 putative deacylase active site [active] 357804004547 EamA-like transporter family; Region: EamA; cl01037 357804004548 MarC family integral membrane protein; Region: MarC; cl00919 357804004549 trigger factor; Provisional; Region: tig; PRK01490 357804004550 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 357804004551 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 357804004552 Clp protease; Region: CLP_protease; pfam00574 357804004553 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 357804004554 oligomer interface [polypeptide binding]; other site 357804004555 active site residues [active] 357804004556 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 357804004557 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 357804004558 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 ABC; Region: AAA; cd00009 357804004559 Walker A motif; other site 357804004560 ATP binding site [chemical binding]; other site 357804004561 Walker B motif; other site 357804004562 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 357804004563 DNA-binding ATP-dependent protease La; Provisional; Region: PRK10787 357804004564 Found in ATP-dependent protease La (LON); Region: LON; smart00464 357804004565 Found in ATP-dependent protease La (LON); Region: LON; smart00464 357804004566 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 ABC; Region: AAA; cd00009 357804004567 Walker A motif; other site 357804004568 ATP binding site [chemical binding]; other site 357804004569 Walker B motif; other site 357804004570 arginine finger; other site 357804004571 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 357804004572 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...; Region: HU_IHF; cd00591 357804004573 IHF dimer interface [polypeptide binding]; other site 357804004574 IHF - DNA interface [nucleotide binding]; other site 357804004575 periplasmic folding chaperone; Provisional; Region: PRK10788 357804004576 SurA N-terminal domain; Region: SurA_N_3; cl07813 357804004577 PPIC-type PPIASE domain; Region: Rotamase; cl08278 357804004578 elongation factor P; Provisional; Region: PRK04542 357804004579 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 357804004580 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...; Region: S1_EF-P_repeat_1; cd04470 357804004581 RNA binding site [nucleotide binding]; other site 357804004582 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...; Region: S1_EF-P_repeat_2; cd05794 357804004583 RNA binding site [nucleotide binding]; other site 357804004584 DsrC like protein; Region: DsrC; cl01101 357804004585 TIGR01666 family membrane protein; Region: YCCS 357804004586 FUSC-like inner membrane protein yccS; Region: FUSC-like; pfam12805 357804004587 Fusaric acid resistance protein-like; Region: FUSC_2; cl15844 357804004588 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 357804004589 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 357804004590 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 357804004591 homodimer interface [polypeptide binding]; other site 357804004592 NADP binding site [chemical binding]; other site 357804004593 substrate binding site [chemical binding]; other site 357804004594 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. Trimers...; Region: gram_neg_porins; cd00342 357804004595 eyelet of channel; other site 357804004596 trimer interface [polypeptide binding]; other site 357804004597 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 357804004598 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 357804004599 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804004600 homodimer interface [polypeptide binding]; other site 357804004601 catalytic residue [active] 357804004602 DNA-binding transcriptional regulator MetR; Provisional; Region: PRK15421 357804004603 Helix-turn-helix domains; Region: HTH; cl00088 357804004604 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 357804004605 putative dimerization interface [polypeptide binding]; other site 357804004606 molybdopterin biosynthesis protein MoeA; Provisional; Region: PRK10680 357804004607 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 357804004608 dimer interface [polypeptide binding]; other site 357804004609 putative functional site; other site 357804004610 putative MPT binding site; other site 357804004611 NeuB family; Region: NeuB; cl00496 357804004612 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 357804004613 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 357804004614 active site 357804004615 zinc binding site [ion binding]; other site 357804004616 pyridoxamine-phosphate oxidase; Region: pdxH; TIGR00558 357804004617 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 357804004618 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 357804004619 Protein of unknown function, DUF462; Region: DUF462; cl01190 357804004620 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 sites; Region: 4HBT; cd00586 357804004621 active site 357804004622 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 357804004623 Helix-turn-helix domains; Region: HTH; cl00088 357804004624 Helix-turn-helix domains; Region: HTH; cl00088 357804004625 Integrase core domain; Region: rve; cl01316 357804004626 GAF domain; Region: GAF; cl15785 357804004627 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 pathway; Region: UMPK; cd02023 357804004628 Sugar specificity; other site 357804004629 Pyrimidine base specificity; other site 357804004630 ATP-binding site [chemical binding]; other site 357804004631 Protein of unknown function (DUF3581); Region: DUF3581; pfam12119 357804004632 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 357804004633 active site 357804004634 Glycosyl transferase family 1; Region: Glyco_trans_1_3; pfam13528 357804004635 DNA-binding transcriptional repressor FabR; Provisional; Region: PRK11202 357804004636 Helix-turn-helix domains; Region: HTH; cl00088 357804004637 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 357804004638 Fatty acid desaturase; Region: FA_desaturase; pfam00487 357804004639 Di-iron ligands [ion binding]; other site 357804004640 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 357804004641 Sel1 repeat; Region: Sel1; cl02723 357804004642 Sel1 repeat; Region: Sel1; cl02723 357804004643 Sel1 repeat; Region: Sel1; cl02723 357804004644 Sel1 repeat; Region: Sel1; cl02723 357804004645 Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones]; Region: PflA; COG1180 357804004646 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 357804004647 FeS/SAM binding site; other site 357804004648 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 357804004649 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 357804004650 TPR motif; other site 357804004651 binding surface 357804004652 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 357804004653 binding surface 357804004654 TPR motif; other site 357804004655 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 357804004656 TPR motif; other site 357804004657 binding surface 357804004658 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 357804004659 binding surface 357804004660 TPR motif; other site 357804004661 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 357804004662 TPR motif; other site 357804004663 TPR repeat; Region: TPR_11; pfam13414 357804004664 binding surface 357804004665 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 357804004666 Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise a...; Region: Rieske_RO_ferredoxin; cd03528 357804004667 [2Fe-2S] cluster binding site [ion binding]; other site 357804004668 Domain of unknown function DUF59; Region: DUF59; cl00941 357804004669 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 357804004670 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 357804004671 trimerization site [polypeptide binding]; other site 357804004672 active site 357804004673 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 357804004674 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 357804004675 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 357804004676 catalytic residue [active] 357804004677 Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]; Region: SufB; COG0719 357804004678 Uncharacterized protein family (UPF0051); Region: UPF0051; cl03223 357804004679 Uncharacterized protein family (UPF0051); Region: UPF0051; cl03223 357804004680 sulfate ABC transporter protein; Validated; Region: ycf16; CHL00131 357804004681 ABC-type transport system involved in Fe-S cluster assembly, ATPase component. Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under...; Region: ABC_FeS_Assembly; cd03217 357804004682 Walker A/P-loop; other site 357804004683 ATP binding site [chemical binding]; other site 357804004684 Q-loop/lid; other site 357804004685 ABC transporter signature motif; other site 357804004686 Walker B; other site 357804004687 D-loop; other site 357804004688 H-loop/switch region; other site 357804004689 Uncharacterized protein family (UPF0051); Region: UPF0051; cl03223 357804004690 putative ABC transporter; Region: ycf24; CHL00085 357804004691 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 357804004692 metal ion-dependent adhesion site (MIDAS); other site 357804004693 Integrase core domain; Region: rve; cl01316 357804004694 Helix-turn-helix domains; Region: HTH; cl00088 357804004695 Winged helix-turn helix; Region: HTH_29; pfam13551 357804004696 Helix-turn-helix domains; Region: HTH; cl00088 357804004697 Winged helix-turn helix; Region: HTH_33; pfam13592 357804004698 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 357804004699 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804004700 Walker A/P-loop; other site 357804004701 ATP binding site [chemical binding]; other site 357804004702 Q-loop/lid; other site 357804004703 ABC transporter signature motif; other site 357804004704 Walker B; other site 357804004705 D-loop; other site 357804004706 H-loop/switch region; other site 357804004707 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 357804004708 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, and...; Region: TM_PBP2; cd06261 357804004709 dimer interface [polypeptide binding]; other site 357804004710 conserved gate region; other site 357804004711 putative PBP binding loops; other site 357804004712 ABC-ATPase subunit interface; other site 357804004713 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 357804004714 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, and...; Region: TM_PBP2; cd06261 357804004715 dimer interface [polypeptide binding]; other site 357804004716 conserved gate region; other site 357804004717 putative PBP binding loops; other site 357804004718 ABC-ATPase subunit interface; other site 357804004719 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 357804004720 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 inorganic...; Region: PBPb; cd00134 357804004721 substrate binding pocket [chemical binding]; other site 357804004722 membrane-bound complex binding site; other site 357804004723 hinge residues; other site 357804004724 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 357804004725 putative catalytic site [active] 357804004726 putative metal binding site [ion binding]; other site 357804004727 putative phosphate binding site [ion binding]; other site 357804004728 Phospholipid methyltransferase; Region: PEMT; cl00763 357804004729 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 357804004730 Interdomain contacts; other site 357804004731 Cytokine receptor motif; other site 357804004732 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 357804004733 putative substrate translocation pore; other site 357804004734 Protein of unknown function (DUF2970); Region: DUF2970; pfam11174 357804004735 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 357804004736 Uncharacterized protein conserved in bacteria (DUF2237); Region: DUF2237; cl01467 357804004737 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_cladeD; cd03379 357804004738 active site clefts [active] 357804004739 zinc binding site [ion binding]; other site 357804004740 dimer interface [polypeptide binding]; other site 357804004741 Uncharacterized protein conserved in bacteria (DUF2237); Region: DUF2237; cl01467 357804004742 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 357804004743 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 357804004744 active site 357804004745 helicase 45; Provisional; Region: PTZ00424 357804004746 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 357804004747 ATP binding site [chemical binding]; other site 357804004748 Mg++ binding site [ion binding]; other site 357804004749 motif III; other site 357804004750 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 357804004751 nucleotide binding region [chemical binding]; other site 357804004752 ATP-binding site [chemical binding]; other site 357804004753 Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and...; Region: ACD_LpsHSP_like; cd06471 357804004754 putative dimer interface [polypeptide binding]; other site 357804004755 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 357804004756 nucleoside/Zn binding site; other site 357804004757 dimer interface [polypeptide binding]; other site 357804004758 catalytic motif [active] 357804004759 DDE superfamily endonuclease; Region: DDE_4; cl15789 357804004760 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 357804004761 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11905 357804004762 Proline dehydrogenase; Region: Pro_dh; cl03282 357804004763 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 357804004764 Glutamate binding site [chemical binding]; other site 357804004765 NAD binding site [chemical binding]; other site 357804004766 catalytic residues [active] 357804004767 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 357804004768 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 357804004769 NAD(P) binding site [chemical binding]; other site 357804004770 Peptidase family M23; Region: Peptidase_M23; pfam01551 357804004771 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 357804004772 cryptochrome, DASH family; Region: crypto_DASH; TIGR02765 357804004773 DNA photolyase; Region: DNA_photolyase; pfam00875 357804004774 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 357804004775 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 357804004776 DNA photolyase; Region: DNA_photolyase; pfam00875 357804004777 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 357804004778 Uncharacterized protein conserved in bacteria (DUF2256); Region: DUF2256; cl01792 357804004779 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]; Region: COG3046 357804004780 Deoxyribodipyrimidine photo-lyase-related protein; Region: DPRP; pfam04244 357804004781 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 357804004782 DDE superfamily endonuclease; Region: DDE_4; cl15789 357804004783 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 357804004784 DDE superfamily endonuclease; Region: DDE_4; cl15789 357804004785 MarC family integral membrane protein; Region: MarC; cl00919 357804004786 PEP-CTERM motif; Region: VPEP; pfam07589 357804004787 Insertion element 4 transposase N-terminal; Region: Nterm_IS4; pfam13006 357804004788 Coiled-coil receptor-binding R-domain of colicin E2; Region: E2R135; pfam11570 357804004789 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804004790 metal binding site [ion binding]; metal-binding site 357804004791 active site 357804004792 I-site; other site 357804004793 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 357804004794 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 357804004795 active site 357804004796 catalytic triad [active] 357804004797 dimer interface [polypeptide binding]; other site 357804004798 Uncharacterized conserved protein [Function unknown]; Region: COG0397; cl00428 357804004799 Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_1; cd02432 357804004800 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 357804004801 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 357804004802 Cyanate permease [Inorganic ion transport and metabolism]; Region: CynX; COG2807 357804004803 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 357804004804 putative substrate translocation pore; other site 357804004805 Predicted ATPase [General function prediction only]; Region: COG1485 357804004806 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, like sugars, ions, peptides, and more complex organic molecules. The...; Region: ABC_ATPase; cd00267 357804004807 Walker A/P-loop; other site 357804004808 ATP binding site [chemical binding]; other site 357804004809 ABC transporter signature motif; other site 357804004810 Walker B; other site 357804004811 D-loop; other site 357804004812 H-loop/switch region; other site 357804004813 Transposase; Region: DEDD_Tnp_IS110; pfam01548 357804004814 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 357804004815 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 357804004816 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 357804004817 Walker A/P-loop; other site 357804004818 ATP binding site [chemical binding]; other site 357804004819 Q-loop/lid; other site 357804004820 ABC transporter signature motif; other site 357804004821 Walker B; other site 357804004822 D-loop; other site 357804004823 H-loop/switch region; other site 357804004824 FtsX-like permease family; Region: FtsX; cl15850 357804004825 Hydroxyneurosporene synthase (CrtC); Region: CrtC; cl12101 357804004826 Domain of unknown function (DUF4102); Region: DUF4102; pfam13356 357804004827 helicase Cas3; Provisional; Region: PRK09694 357804004828 CRISPR/Cas system-associated protein Cas3''; Region: Cas3''_I; cd09641 357804004829 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804004830 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 357804004831 CRISPR/Cas system-associated RAMP superfamily protein Cas6e; Region: Cas6_I-E; cd09727 357804004832 CRISPR/Cas system-associated protein Cse2; Region: Cse2_I-E; cl09719 357804004833 CRISPR/Cas system-associated RAMP superfamily protein Cas7; Region: Cas7_I-E; cl09608 357804004834 CRISPR-associated protein (Cas_Cas5); Region: Cas_Cas5d; pfam09704 357804004835 CRISPR/Cas system-associated RAMP superfamily protein Cas5; Region: Cas5_I-E; cd09645 357804004836 CRISPR/Cas system-associated protein Cse1; Region: Cse1_I-E; cd09729 357804004837 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-E; cd09719 357804004838 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I-E; cd09648 357804004839 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 357804004840 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 357804004841 catalytic residues [active] 357804004842 catalytic nucleophile [active] 357804004843 Presynaptic Site I dimer interface [polypeptide binding]; other site 357804004844 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 357804004845 Synaptic Flat tetramer interface [polypeptide binding]; other site 357804004846 Synaptic Site I dimer interface [polypeptide binding]; other site 357804004847 DNA binding site [nucleotide binding] 357804004848 Protein of unknown function (DUF3296); Region: DUF3296; pfam11726 357804004849 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 357804004850 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 357804004851 integrase; Provisional; Region: PRK09692 357804004852 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 357804004853 active site 357804004854 Int/Topo IB signature motif; other site 357804004855 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 357804004856 SmpB-tmRNA interface; other site 357804004857 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 357804004858 putative coenzyme Q binding site [chemical binding]; other site 357804004859 The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information...; Region: TGS; cl15768 357804004860 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 357804004861 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 357804004862 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 357804004863 tRNA; other site 357804004864 putative tRNA binding site [nucleotide binding]; other site 357804004865 putative NADP binding site [chemical binding]; other site 357804004866 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 357804004867 peptide chain release factor 1; Validated; Region: prfA; PRK00591 357804004868 RF-1 domain; Region: RF-1; cl02875 357804004869 RF-1 domain; Region: RF-1; cl02875 357804004870 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 357804004871 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 357804004872 S-adenosylmethionine binding site [chemical binding]; other site 357804004873 Invasion gene expression up-regulator, SirB; Region: SirB; cl01184 357804004874 Uncharacterized conserved protein [Function unknown]; Region: COG2912 357804004875 Transglutaminase-like superfamily; Region: Transglut_core2; pfam13369 357804004876 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 357804004877 binding surface 357804004878 TPR motif; other site 357804004879 NeuB family; Region: NeuB; cl00496 357804004880 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 357804004881 Protein of unknown function (DUF423); Region: DUF423; cl01008 357804004882 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional; Region: PRK11760 357804004883 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; cl16911 357804004884 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 357804004885 Peptidase M15; Region: Peptidase_M15_3; cl01194 357804004886 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 357804004887 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 357804004888 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 357804004889 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 357804004890 PspC domain; Region: PspC; cl00864 357804004891 phage shock protein C; Region: phageshock_pspC; TIGR02978 357804004892 Phage shock protein B; Region: PspB; cl05946 357804004893 PPIC-type PPIASE domain; Region: Rotamase; cl08278 357804004894 HAD-superfamily subfamily IIA hydrolase, TIGR01458; Region: HAD-SF-IIA-hyp3 357804004895 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 357804004896 active site 357804004897 motif I; other site 357804004898 motif II; other site 357804004899 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 357804004900 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 357804004901 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 357804004902 Protein of unknown function (DUF502); Region: DUF502; cl01107 357804004903 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 357804004904 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 357804004905 active site 357804004906 HIGH motif; other site 357804004907 KMSKS motif; other site 357804004908 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 357804004909 tRNA binding surface [nucleotide binding]; other site 357804004910 anticodon binding site; other site 357804004911 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 357804004912 dimer interface [polypeptide binding]; other site 357804004913 putative tRNA-binding site [nucleotide binding]; other site 357804004914 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 357804004915 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 357804004916 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 357804004917 active site 357804004918 HIGH motif; other site 357804004919 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 357804004920 active site 357804004921 KMSKS motif; other site 357804004922 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 357804004923 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 357804004924 active site 357804004925 uracil-xanthine permease; Region: ncs2; TIGR00801 357804004926 DDE superfamily endonuclease; Region: DDE_5; cl02413 357804004927 Predicted enzyme involved in methoxymalonyl-ACP biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FkbH; COG3882 357804004928 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 357804004929 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; cl16911 357804004930 Phosphopantetheine attachment site; Region: PP-binding; cl09936 357804004931 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 357804004932 dimer interface [polypeptide binding]; other site 357804004933 substrate binding site [chemical binding]; other site 357804004934 metal binding site [ion binding]; metal-binding site 357804004935 MBOAT, membrane-bound O-acyltransferase family; Region: MBOAT; cl00738 357804004936 putative transposase OrfB; Reviewed; Region: PHA02517 357804004937 HTH-like domain; Region: HTH_21; pfam13276 357804004938 Integrase core domain; Region: rve; cl01316 357804004939 Integrase core domain; Region: rve_3; cl15866 357804004940 Helix-turn-helix domains; Region: HTH; cl00088 357804004941 Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]; Region: NfeD; COG1030 357804004942 Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Region: Clp_protease_NfeD_1; cd07020 357804004943 dimer interface [polypeptide binding]; other site 357804004944 active site residues [active] 357804004945 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 357804004946 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 357804004947 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 357804004948 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]; Region: COG1979 357804004949 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 357804004950 dimer interface [polypeptide binding]; other site 357804004951 active site 357804004952 metal binding site [ion binding]; metal-binding site 357804004953 Phosphoribosyl-AMP cyclohydrolase; Region: PRA-CH; cl00344 357804004954 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed; Region: PRK02759 357804004955 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase (HisIE or PRATP-PH) and its homologs; Region: NTP-PPase_HisIE_like; cd11534 357804004956 metal binding site [ion binding]; metal-binding site 357804004957 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)...; Region: HisF; cd04731 357804004958 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 357804004959 substrate binding site [chemical binding]; other site 357804004960 glutamase interaction surface [polypeptide binding]; other site 357804004961 Protein of unknown function, DUF; Region: DUF411; cl01142 357804004962 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 357804004963 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; Region: TIGR00007 357804004964 catalytic residues [active] 357804004965 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13170 357804004966 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 357804004967 putative active site [active] 357804004968 oxyanion strand; other site 357804004969 catalytic triad [active] 357804004970 imidazole glycerol-phosphate dehydratase/histidinol phosphatase; Provisional; Region: PRK05446 357804004971 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 357804004972 active site 357804004973 motif I; other site 357804004974 motif II; other site 357804004975 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 357804004976 putative active site pocket [active] 357804004977 4-fold oligomerization interface [polypeptide binding]; other site 357804004978 metal binding residues [ion binding]; metal-binding site 357804004979 3-fold/trimer interface [polypeptide binding]; other site 357804004980 histidinol-phosphate aminotransferase; Region: hisC; TIGR01141 357804004981 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 357804004982 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804004983 homodimer interface [polypeptide binding]; other site 357804004984 catalytic residue [active] 357804004985 Histidinol dehydrogenase, HisD, 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...; Region: Histidinol_dh; cd06572 357804004986 histidinol dehydrogenase; Region: hisD; TIGR00069 357804004987 NAD binding site [chemical binding]; other site 357804004988 dimerization interface [polypeptide binding]; other site 357804004989 product binding site; other site 357804004990 substrate binding site [chemical binding]; other site 357804004991 zinc binding site [ion binding]; other site 357804004992 catalytic residues [active] 357804004993 ATP phosphoribosyltransferase; Reviewed; Region: hisG; PRK00489 357804004994 ATP phosphoribosyltransferase; Region: HisG; cl15266 357804004995 HisG, C-terminal domain; Region: HisG_C; cl06867 357804004996 Protein of unknown function (DUF2986); Region: DUF2986; pfam11661 357804004997 Cysteine-rich CWC; Region: Cys_rich_CWC; pfam14375 357804004998 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 357804004999 fatty acid metabolism regulator; Provisional; Region: PRK04984 357804005000 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 357804005001 DNA-binding site [nucleotide binding]; DNA binding site 357804005002 FCD domain; Region: FCD; cl11656 357804005003 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 357804005004 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 357804005005 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804005006 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 357804005007 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 357804005008 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 357804005009 recombination factor protein RarA; Reviewed; Region: PRK13342 357804005010 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 ABC; Region: AAA; cd00009 357804005011 Walker A motif; other site 357804005012 ATP binding site [chemical binding]; other site 357804005013 Walker B motif; other site 357804005014 arginine finger; other site 357804005015 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 357804005016 CrcB-like protein; Region: CRCB; cl09114 357804005017 seryl-tRNA synthetase; Provisional; Region: PRK05431 357804005018 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 357804005019 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 bound...; Region: SerRS_core; cd00770 357804005020 dimer interface [polypeptide binding]; other site 357804005021 active site 357804005022 motif 1; other site 357804005023 motif 2; other site 357804005024 motif 3; other site 357804005025 muropeptide transporter; Reviewed; Region: ampG; PRK11902 357804005026 muropeptide transporter; Validated; Region: ampG; PRK11010 357804005027 ribonuclease D; Provisional; Region: PRK10829 357804005028 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 357804005029 catalytic site [active] 357804005030 putative active site [active] 357804005031 putative substrate binding site [chemical binding]; other site 357804005032 HRDC domain; Region: HRDC; cl02578 357804005033 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 357804005034 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 357804005035 substrate binding site [chemical binding]; other site 357804005036 ligand binding site [chemical binding]; other site 357804005037 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...; Region: IPMI_Swivel; cd01577 357804005038 substrate binding site [chemical binding]; other site 357804005039 Peptidase C1A subfamily (MEROPS database nomenclature); composed of cysteine peptidases (CPs) similar to papain, including the mammalian CPs (cathepsins B, C, F, H, L, K, O, S, V, X and W). Papain is an endopeptidase with specific substrate preferences; Region: Peptidase_C1A; cd02248 357804005040 active site 357804005041 S2 subsite; other site 357804005042 Protein of unknown function (DUF3010); Region: DUF3010; pfam11215 357804005043 ferredoxin-NADP reductase; Provisional; Region: PRK10926 357804005044 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 357804005045 FAD binding pocket [chemical binding]; other site 357804005046 FAD binding motif [chemical binding]; other site 357804005047 phosphate binding motif [ion binding]; other site 357804005048 beta-alpha-beta structure motif; other site 357804005049 NAD binding pocket [chemical binding]; other site 357804005050 Protein of unknown function (DUF330); Region: DUF330; cl01135 357804005051 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 357804005052 mce related protein; Region: MCE; pfam02470 357804005053 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 357804005054 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 357804005055 Walker A/P-loop; other site 357804005056 ATP binding site [chemical binding]; other site 357804005057 Q-loop/lid; other site 357804005058 ABC transporter signature motif; other site 357804005059 Walker B; other site 357804005060 D-loop; other site 357804005061 H-loop/switch region; other site 357804005062 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 357804005063 Permease; Region: Permease; cl00510 357804005064 Conserved hypothetical protein 698; Region: Cons_hypoth698; cl01075 357804005065 Helix-turn-helix domains; Region: HTH; cl00088 357804005066 polyketide-type polyunsaturated fatty acid synthase PfaA; Region: omega_3_PfaA; TIGR02813 357804005067 polyketide synthases (PKSs) polymerize simple fatty acids into a large variety of different products, called polyketides, by successive decarboxylating Claisen condensations. PKSs can be divided into 2 groups, modular type I PKSs consisting of one or...; Region: PKS; cd00833 357804005068 active site 357804005069 Acyl transferase domain; Region: Acyl_transf_1; cl08282 357804005070 Phosphopantetheine attachment site; Region: PP-binding; cl09936 357804005071 Phosphopantetheine attachment site; Region: PP-binding; cl09936 357804005072 ketoreductase (KR), subgroup 2, complex (x) SDRs; Region: KR_2_SDR_x; cd08953 357804005073 putative NADP binding site [chemical binding]; other site 357804005074 active site 357804005075 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 357804005076 active site 357804005077 Acyl transferase domain; Region: Acyl_transf_1; cl08282 357804005078 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 357804005079 polyketide synthases (PKSs) polymerize simple fatty acids into a large variety of different products, called polyketides, by successive decarboxylating Claisen condensations. PKSs can be divided into 2 groups, modular type I PKSs consisting of one or...; Region: PKS; cd00833 357804005080 active site 357804005081 polyketide synthases (PKSs) polymerize simple fatty acids into a large variety of different products, called polyketides, by successive decarboxylating Claisen condensations. PKSs can be divided into 2 groups, modular type I PKSs consisting of one or...; Region: PKS; cd00833 357804005082 active site 357804005083 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 357804005084 active site 1 [active] 357804005085 dimer interface [polypeptide binding]; other site 357804005086 active site 2 [active] 357804005087 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 357804005088 active site 1 [active] 357804005089 dimer interface [polypeptide binding]; other site 357804005090 active site 2 [active] 357804005091 2-Nitropropane dioxygenase (NPD)-like domain, associated with the (acyl-carrier-protein) S-malonyltransferase FabD. NPD is part of the nitroalkaneoxidizing enzyme family, that catalyzes oxidative denitrification of nitroalkanes to their corresponding...; Region: NPD_FabD; cd04742 357804005092 FMN binding site [chemical binding]; other site 357804005093 substrate binding site [chemical binding]; other site 357804005094 putative catalytic residue [active] 357804005095 Transcriptional regulator [Transcription]; Region: LysR; COG0583 357804005096 Helix-turn-helix domains; Region: HTH; cl00088 357804005097 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 357804005098 putative effector binding pocket; other site 357804005099 dimerization interface [polypeptide binding]; other site 357804005100 CoB--CoM heterodisulfide reductase, subunit B; Region: CoB_CoM_SS_B; TIGR03288 357804005101 Cysteine-rich domain; Region: CCG; pfam02754 357804005102 Cysteine-rich domain; Region: CCG; pfam02754 357804005103 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]; Region: COG1139 357804005104 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; cl00674 357804005105 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...; Region: HCP_like; cl14655 357804005106 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; cl00674 357804005107 Lipoate-protein ligase A [Coenzyme metabolism]; Region: LplA; COG0095 357804005108 Protein of unknown function (DUF3010); Region: DUF3010; pfam11215 357804005109 GAF domain; Region: GAF; cl15785 357804005110 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804005111 metal binding site [ion binding]; metal-binding site 357804005112 active site 357804005113 I-site; other site 357804005114 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 357804005115 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 357804005116 fructokinase; Reviewed; Region: PRK09557 357804005117 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 357804005118 active site 357804005119 catalytic triad [active] 357804005120 oxyanion hole [active] 357804005121 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_18; cd08357 357804005122 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 357804005123 putative metal binding site [ion binding]; other site 357804005124 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 357804005125 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 357804005126 Protein of unknown function (DUF2798); Region: DUF2798; pfam11391 357804005127 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 357804005128 S-adenosylmethionine binding site [chemical binding]; other site 357804005129 Cupin domain; Region: Cupin_2; cl09118 357804005130 protein structure with unknown function; Region: DUF4144; pfam13642 357804005131 PAP2_like_5 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_5; cd03394 357804005132 active site 357804005133 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; cl00526 357804005134 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 357804005135 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804005136 NmrA-like family; Region: NmrA; pfam05368 357804005137 NAD(P) binding site [chemical binding]; other site 357804005138 active site 357804005139 LGFP repeat; Region: LGFP; pfam08310 357804005140 LGFP repeat; Region: LGFP; pfam08310 357804005141 LGFP repeat; Region: LGFP; pfam08310 357804005142 Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism]; Region: MntH; COG1914 357804005143 Iron-binding zinc finger CDGSH type; Region: zf-CDGSH; cl02748 357804005144 Iron-binding zinc finger CDGSH type; Region: zf-CDGSH; cl02748 357804005145 Protein of unknown function (DUF3565); Region: DUF3565; pfam12088 357804005146 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 357804005147 EamA-like transporter family; Region: EamA; cl01037 357804005148 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 357804005149 PAS domain; Region: PAS_9; pfam13426 357804005150 putative active site [active] 357804005151 heme pocket [chemical binding]; other site 357804005152 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804005153 metal binding site [ion binding]; metal-binding site 357804005154 active site 357804005155 I-site; other site 357804005156 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 357804005157 Class-II DAHP synthetase family; Region: DAHP_synth_2; cl03230 357804005158 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 357804005159 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 357804005160 catalytic triad [active] 357804005161 metal binding site [ion binding]; metal-binding site 357804005162 conserved cis-peptide bond; other site 357804005163 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 357804005164 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 357804005165 active site 357804005166 galactoside O-acetyltransferase; Reviewed; Region: lacA; PRK09527 357804005167 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 357804005168 active site 357804005169 substrate binding site [chemical binding]; other site 357804005170 trimer interface [polypeptide binding]; other site 357804005171 CoA binding site [chemical binding]; other site 357804005172 magnesium Mg(2+) and cobalt Co(2+) transport protein (corA); Region: corA; TIGR00383 357804005173 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 357804005174 K-Cl cotransporter; Region: 2a30; TIGR00930 357804005175 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 357804005176 Protein of unknown function (DUF3584); Region: DUF3584; pfam12128 357804005177 Mechanosensitive ion channel; Region: MS_channel; pfam00924 357804005178 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 357804005179 Protein of unknown function, DUF399; Region: DUF399; cl01139 357804005180 Predicted integral membrane protein (DUF2189); Region: DUF2189; cl02291 357804005181 fumarate hydratase; Reviewed; Region: fumC; PRK00485 357804005182 Class II fumarases; Region: Fumarase_classII; cd01362 357804005183 active site 357804005184 tetramer interface [polypeptide binding]; other site 357804005185 Glutamate-cysteine ligase family 2(GCS2); Region: GCS2; cl00954 357804005186 Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup; Region: M14_ASTE_ASPA_like_6; cd06256 357804005187 putative active site [active] 357804005188 Zn binding site [ion binding]; other site 357804005189 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 357804005190 C-terminal, alpha helical domain of an unknown subfamily 5 of Glutathione S-transferases; Region: GST_C_5; cd03196 357804005191 putative N-terminal domain interface [polypeptide binding]; other site 357804005192 putative dimer interface [polypeptide binding]; other site 357804005193 putative substrate binding pocket (H-site) [chemical binding]; other site 357804005194 Uncharacterized conserved protein (DUF2132); Region: DUF2132; cl01894 357804005195 malate dehydrogenase; Provisional; Region: PRK13529 357804005196 Malic enzyme, N-terminal domain; Region: malic; pfam00390 357804005197 NAD(P) binding domain of malic enzyme (ME), subgroup 1; Region: NAD_bind_1_malic_enz; cd05312 357804005198 NAD(P) binding site [chemical binding]; other site 357804005199 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 357804005200 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 357804005201 active site 357804005202 phosphorylation site [posttranslational modification] 357804005203 intermolecular recognition site; other site 357804005204 dimerization interface [polypeptide binding]; other site 357804005205 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 ABC; Region: AAA; cd00009 357804005206 Walker A motif; other site 357804005207 ATP binding site [chemical binding]; other site 357804005208 Walker B motif; other site 357804005209 arginine finger; other site 357804005210 Helix-turn-helix domains; Region: HTH; cl00088 357804005211 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 357804005212 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 357804005213 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 357804005214 putative active site [active] 357804005215 heme pocket [chemical binding]; other site 357804005216 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...; Region: HisKA; cd00082 357804005217 dimer interface [polypeptide binding]; other site 357804005218 phosphorylation site [posttranslational modification] 357804005219 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 357804005220 ATP binding site [chemical binding]; other site 357804005221 Mg2+ binding site [ion binding]; other site 357804005222 G-X-G motif; other site 357804005223 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 357804005224 Response regulator receiver domain; Region: Response_reg; pfam00072 357804005225 active site 357804005226 phosphorylation site [posttranslational modification] 357804005227 intermolecular recognition site; other site 357804005228 dimerization interface [polypeptide binding]; other site 357804005229 Gas vesicle protein; Region: Gas_vesicle; cl02954 357804005230 gas vesicle protein GvpN; Region: gas_vesic_GvpN; TIGR02640 357804005231 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 ABC; Region: AAA; cd00009 357804005232 Walker A motif; other site 357804005233 ATP binding site [chemical binding]; other site 357804005234 Walker B motif; other site 357804005235 threonine synthase; Validated; Region: PRK06260 357804005236 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 357804005237 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 357804005238 catalytic residues [active] 357804005239 Protein of unknown function (DUF465); Region: DUF465; cl01070 357804005240 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 357804005241 Protein export membrane protein; Region: SecD_SecF; cl14618 357804005242 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 357804005243 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, acyl; Region: Biotinyl_lipoyl_domains; cl11404 357804005244 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 357804005245 Helix-turn-helix domains; Region: HTH; cl00088 357804005246 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 357804005247 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 357804005248 YrhK-like protein; Region: YrhK; pfam14145 357804005249 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 357804005250 30S subunit binding site; other site 357804005251 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; cl01747 357804005252 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 357804005253 ABC-type phosphate/phosphonate transport system, permease component [Inorganic ion transport and metabolism]; Region: COG3639 357804005254 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: COG3638 357804005255 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804005256 Walker A/P-loop; other site 357804005257 ATP binding site [chemical binding]; other site 357804005258 Q-loop/lid; other site 357804005259 ABC transporter signature motif; other site 357804005260 Walker B; other site 357804005261 D-loop; other site 357804005262 H-loop/switch region; other site 357804005263 NMT1-like family; Region: NMT1_2; cl15260 357804005264 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 357804005265 erythrose 4-phosphate dehydrogenase; Provisional; Region: PRK13535 357804005266 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804005267 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 357804005268 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 357804005269 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804005270 NAD(P) binding site [chemical binding]; other site 357804005271 active site 357804005272 Protein of unknown function (DUF2867); Region: DUF2867; pfam11066 357804005273 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 357804005274 Late embryogenesis abundant protein; Region: LEA_2; cl12118 357804005275 M18 Peptidase Aspartyl aminopeptidase; Region: M18_DAP; cd05658 357804005276 Aminopeptidase I zinc metalloprotease (M18); Region: Peptidase_M18; pfam02127 357804005277 active site 357804005278 metal binding site [ion binding]; metal-binding site 357804005279 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 357804005280 PAS domain; Region: PAS_9; pfam13426 357804005281 putative active site [active] 357804005282 heme pocket [chemical binding]; other site 357804005283 Esterase/lipase [Lipid metabolism]; Region: Aes; COG0657 357804005284 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 357804005285 Protein of unknown function (DUF3494); Region: DUF3494; pfam11999 357804005286 SOUL heme-binding protein; Region: SOUL; pfam04832 357804005287 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 357804005288 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 357804005289 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 357804005290 Protein of unknown function (DUF2805); Region: DUF2805; cl11923 357804005291 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 357804005292 Helix-turn-helix domains; Region: HTH; cl00088 357804005293 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804005294 Monoamine oxidase [Amino acid transport and metabolism]; Region: COG1231 357804005295 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 357804005296 GST_N family, Saccharomyces cerevisiae GTT2-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT2. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing...; Region: GST_N_GTT2_like; cd03051 357804005297 putative C-terminal domain interface [polypeptide binding]; other site 357804005298 putative GSH binding site (G-site) [chemical binding]; other site 357804005299 putative dimer interface [polypeptide binding]; other site 357804005300 C-terminal, alpha helical domain of GTT2-like Glutathione S-transferases; Region: GST_C_GTT2_like; cd03182 357804005301 putative N-terminal domain interface [polypeptide binding]; other site 357804005302 putative dimer interface [polypeptide binding]; other site 357804005303 putative substrate binding pocket (H-site) [chemical binding]; other site 357804005304 Transcriptional activator [Transcription]; Region: ChrR; COG3806 357804005305 Cupin domain; Region: Cupin_2; cl09118 357804005306 Cupin domain; Region: Cupin_2; cl09118 357804005307 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 357804005308 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; cd01635 357804005309 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 357804005310 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 357804005311 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 357804005312 Protein of unknown function (DUF1499); Region: DUF1499; cl01841 357804005313 Peptidase family M48; Region: Peptidase_M48; cl12018 357804005314 Uncharacterized protein conserved in bacteria (DUF2057); Region: DUF2057; cl11437 357804005315 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 357804005316 putative substrate translocation pore; other site 357804005317 putative MFS family transporter protein; Provisional; Region: PRK03633 357804005318 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 357804005319 EamA-like transporter family; Region: EamA; cl01037 357804005320 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 357804005321 EamA-like transporter family; Region: EamA; cl01037 357804005322 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 357804005323 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 357804005324 Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and...; Region: ACD_LpsHSP_like; cd06471 357804005325 putative dimer interface [polypeptide binding]; other site 357804005326 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 357804005327 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 357804005328 ATP binding site [chemical binding]; other site 357804005329 Mg++ binding site [ion binding]; other site 357804005330 motif III; other site 357804005331 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 357804005332 nucleotide binding region [chemical binding]; other site 357804005333 ATP-binding site [chemical binding]; other site 357804005334 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 357804005335 nucleoside/Zn binding site; other site 357804005336 dimer interface [polypeptide binding]; other site 357804005337 catalytic motif [active] 357804005338 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 357804005339 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804005340 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 357804005341 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 357804005342 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 357804005343 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 expression; Region: S1_Tex; cd05685 357804005344 RNA binding site [nucleotide binding]; other site 357804005345 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; cl16911 357804005346 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_27; cd04686 357804005347 nudix motif; other site 357804005348 Protein of unknown function (DUF2913); Region: DUF2913; pfam11140 357804005349 Ion channel; Region: Ion_trans_2; cl11596 357804005350 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 357804005351 Helix-turn-helix domains; Region: HTH; cl00088 357804005352 Helix-turn-helix domains; Region: HTH; cl00088 357804005353 Integrase core domain; Region: rve; cl01316 357804005354 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 357804005355 putative active site [active] 357804005356 putative metal binding site [ion binding]; other site 357804005357 YEATS family; Region: YEATS; pfam03366 357804005358 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 357804005359 Predicted transcriptional regulator [Transcription]; Region: COG1959 357804005360 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 357804005361 putative active site [active] 357804005362 heme pocket [chemical binding]; other site 357804005363 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804005364 metal binding site [ion binding]; metal-binding site 357804005365 active site 357804005366 I-site; other site 357804005367 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 357804005368 Sulfotransferase family; Region: Sulfotransfer_3; cl14559 357804005369 Sulfotransferase domain; Region: Sulfotransfer_1; pfam00685 357804005370 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 357804005371 putative manganese-dependent inorganic pyrophosphatase; Provisional; Region: PRK05427 357804005372 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-called...; Region: CBS_pair; cl15354 357804005373 DHHA2 domain; Region: DHHA2; pfam02833 357804005374 Predicted permease; Region: DUF318; pfam03773 357804005375 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 357804005376 Cytochrome c; Region: Cytochrom_C; cl11414 357804005377 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 357804005378 Cytochrome c; Region: Cytochrom_C; cl11414 357804005379 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 357804005380 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; cl00159 357804005381 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 357804005382 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 357804005383 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 357804005384 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 357804005385 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 357804005386 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 357804005387 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 357804005388 Ligand binding site; other site 357804005389 metal-binding site 357804005390 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 357804005391 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 357804005392 XdhC Rossmann domain; Region: XdhC_C; pfam13478 357804005393 CHASE domain; Region: CHASE; cl01369 357804005394 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 357804005395 PAS fold; Region: PAS_3; pfam08447 357804005396 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804005397 metal binding site [ion binding]; metal-binding site 357804005398 active site 357804005399 I-site; other site 357804005400 pyridine nucleotide-disulfide oxidoreductase family protein; Region: Nterm_to_SelD; TIGR03169 357804005401 PAS domain S-box; Region: sensory_box; TIGR00229 357804005402 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 357804005403 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 357804005404 PAS domain; Region: PAS_9; pfam13426 357804005405 putative active site [active] 357804005406 heme pocket [chemical binding]; other site 357804005407 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804005408 metal binding site [ion binding]; metal-binding site 357804005409 active site 357804005410 I-site; other site 357804005411 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 357804005412 CheB methylesterase; Region: CheB_methylest; pfam01339 357804005413 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 357804005414 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 357804005415 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; cl16911 357804005416 IncA protein; Region: IncA; pfam04156 357804005417 PAS domain; Region: PAS_10; pfam13596 357804005418 MAEBL; Provisional; Region: PTZ00121 357804005419 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804005420 metal binding site [ion binding]; metal-binding site 357804005421 active site 357804005422 I-site; other site 357804005423 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 357804005424 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 357804005425 Membrane transport protein; Region: Mem_trans; cl09117 357804005426 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 357804005427 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 357804005428 active site 357804005429 nucleophile elbow; other site 357804005430 Protein of unknown function (DUF1415); Region: DUF1415; cl01301 357804005431 Protein of unknown function (DUF3584); Region: DUF3584; pfam12128 357804005432 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 357804005433 Protein of unknown function (DUF3087); Region: DUF3087; pfam11286 357804005434 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 357804005435 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); Region: KBL_like; cd06454 357804005436 substrate-cofactor binding pocket; other site 357804005437 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804005438 catalytic residue [active] 357804005439 L-threonine 3-dehydrogenase; Validated; Region: tdh; PRK05396 357804005440 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 357804005441 NAD(P) binding site [chemical binding]; other site 357804005442 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 357804005443 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 357804005444 DNA polymerase II; Reviewed; Region: PRK05762 357804005445 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases; Region: DNA_polB_II_exo; cd05784 357804005446 active site 357804005447 catalytic site [active] 357804005448 substrate binding site [chemical binding]; other site 357804005449 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 357804005450 active site 357804005451 metal-binding site 357804005452 Cysteine-rich CPXCG; Region: Cys_rich_CPXG; pfam14255 357804005453 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 357804005454 ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria; Region: ybbN; cd02956 357804005455 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 357804005456 binding surface 357804005457 TPR motif; other site 357804005458 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 357804005459 dihydrodipicolinate synthase; Region: dapA; TIGR00674 357804005460 dimer interface [polypeptide binding]; other site 357804005461 active site 357804005462 catalytic residue [active] 357804005463 lipoprotein; Provisional; Region: PRK11679 357804005464 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 357804005465 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 357804005466 ATP binding site [chemical binding]; other site 357804005467 active site 357804005468 substrate binding site [chemical binding]; other site 357804005469 Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]; Region: CitB; COG4565 357804005470 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 357804005471 active site 357804005472 phosphorylation site [posttranslational modification] 357804005473 intermolecular recognition site; other site 357804005474 dimerization interface [polypeptide binding]; other site 357804005475 Transcriptional regulator; Region: CitT; pfam12431 357804005476 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 357804005477 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 357804005478 AMP-binding enzyme; Region: AMP-binding; cl15778 357804005479 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 357804005480 probable AcnD-accessory protein PrpF; Region: prpF; TIGR02334 357804005481 PrpF protein; Region: PrpF; pfam04303 357804005482 2-methylisocitrate dehydratase, Fe/S-dependent; Region: 2met_isocit_dHY; TIGR02333 357804005483 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 357804005484 substrate binding site [chemical binding]; other site 357804005485 ligand binding site [chemical binding]; other site 357804005486 Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme...; Region: Aconitase_swivel; cl00215 357804005487 substrate binding site [chemical binding]; other site 357804005488 Escherichia coli (Ec) 2-methylcitrate synthase (2MCS)_like. 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxalacetate (OAA) to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. Citrate synthase (CS) catalyzes...; Region: Ec2MCS_like; cd06108 357804005489 dimer interface [polypeptide binding]; other site 357804005490 Citrate synthase; Region: Citrate_synt; pfam00285 357804005491 active site 357804005492 citrylCoA binding site [chemical binding]; other site 357804005493 oxalacetate/citrate binding site [chemical binding]; other site 357804005494 coenzyme A binding site [chemical binding]; other site 357804005495 catalytic triad [active] 357804005496 PEP phosphonomutase and related enzymes [Carbohydrate transport and metabolism]; Region: PrpB; COG2513 357804005497 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 357804005498 tetramer interface [polypeptide binding]; other site 357804005499 active site 357804005500 Mg2+/Mn2+ binding site [ion binding]; other site 357804005501 Transcriptional regulators [Transcription]; Region: GntR; COG1802 357804005502 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 357804005503 DNA-binding site [nucleotide binding]; DNA binding site 357804005504 FCD domain; Region: FCD; cl11656 357804005505 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 357804005506 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 357804005507 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 357804005508 NMT1-like family; Region: NMT1_2; cl15260 357804005509 sugar phosphate phosphatase; Provisional; Region: PRK10513 357804005510 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 357804005511 active site 357804005512 motif I; other site 357804005513 motif II; other site 357804005514 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 357804005515 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 357804005516 DNA replication terminus site-binding protein (Ter protein); Region: Ter; cl11502 357804005517 Protein of unknown function (DUF3047); Region: DUF3047; pfam11249 357804005518 Uncharacterized conserved protein (DUF2132); Region: DUF2132; cl01894 357804005519 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 357804005520 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 357804005521 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804005522 metal binding site [ion binding]; metal-binding site 357804005523 active site 357804005524 I-site; other site 357804005525 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 357804005526 DNA-binding site [nucleotide binding]; DNA binding site 357804005527 RNA-binding motif; other site 357804005528 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 357804005529 PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_2; cd03392 357804005530 active site 357804005531 LssY C-terminus; Region: LssY_C; pfam14067 357804005532 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 357804005533 nudix motif; other site 357804005534 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 357804005535 active site 357804005536 catalytic site [active] 357804005537 substrate binding site [chemical binding]; other site 357804005538 Tryptophan-rich protein (DUF2389); Region: DUF2389; cl09726 357804005539 Transcriptional regulator [Transcription]; Region: LysR; COG0583 357804005540 Helix-turn-helix domains; Region: HTH; cl00088 357804005541 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 357804005542 dimerization interface [polypeptide binding]; other site 357804005543 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 357804005544 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 357804005545 tetramerization interface [polypeptide binding]; other site 357804005546 NAD(P) binding site [chemical binding]; other site 357804005547 catalytic residues [active] 357804005548 4-aminobutyrate aminotransferase; Provisional; Region: PRK07495 357804005549 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 357804005550 inhibitor-cofactor binding pocket; inhibition site 357804005551 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804005552 catalytic residue [active] 357804005553 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 357804005554 Mechanosensitive ion channel; Region: MS_channel; pfam00924 357804005555 Uncharacterized protein family UPF0052; Region: UPF0052; pfam01933 357804005556 family of mostly uncharacterized proteins similar to B.subtilis YvcK; Region: YvcK_like; cd07187 357804005557 phosphate binding site [ion binding]; other site 357804005558 putative substrate binding pocket [chemical binding]; other site 357804005559 dimer interface [polypeptide binding]; other site 357804005560 Lipase (class 3). 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...; Region: Lipase_3; cd00519 357804005561 active site flap/lid [active] 357804005562 nucleophilic elbow; other site 357804005563 catalytic triad [active] 357804005564 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: HsdR; COG4096 357804005565 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 357804005566 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 357804005567 ATP binding site [chemical binding]; other site 357804005568 putative Mg++ binding site [ion binding]; other site 357804005569 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 357804005570 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 357804005571 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804005572 Walker A/P-loop; other site 357804005573 ATP binding site [chemical binding]; other site 357804005574 Q-loop/lid; other site 357804005575 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 357804005576 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804005577 Family description; Region: UvrD_C_2; cl15862 357804005578 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 357804005579 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 357804005580 active site 357804005581 DNA binding site [nucleotide binding] 357804005582 Int/Topo IB signature motif; other site 357804005583 Cache domain; Region: Cache_1; pfam02743 357804005584 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 357804005585 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 357804005586 nuc_hydro: Nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These enzymes vary in their substrate specificity. This group contains eukaryotic, bacterial and archeal...; Region: nuc_hydro; cl00226 357804005587 active site 357804005588 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_2; cd03139 357804005589 conserved cys residue [active] 357804005590 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 357804005591 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 357804005592 active site 357804005593 metal binding site [ion binding]; metal-binding site 357804005594 CYTH-like Clostridium thermocellum TTM-like subgroup 1; Region: CYTH-like_CthTTM-like_1; cd07891 357804005595 putative active site [active] 357804005596 putative metal binding residues [ion binding]; other site 357804005597 signature motif; other site 357804005598 putative dimer interface [polypeptide binding]; other site 357804005599 putative phosphate binding site [ion binding]; other site 357804005600 hypothetical protein; Provisional; Region: PRK11239 357804005601 Protein of unknown function, DUF480; Region: DUF480; cl01209 357804005602 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; cl00614 357804005603 putative beta-lysine N-acetyltransferase; Region: GNAT_ablB; TIGR03827 357804005604 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 357804005605 Coenzyme A binding pocket [chemical binding]; other site 357804005606 Domain of unknown function (DUF4145); Region: DUF4145; pfam13643 357804005607 Sucrose-6-phosphate phosphohydrolase C-terminal; Region: S6PP_C; pfam08472 357804005608 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 357804005609 active site 357804005610 metal binding site [ion binding]; metal-binding site 357804005611 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 357804005612 Family of unknown function (DUF490); Region: DUF490; pfam04357 357804005613 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 357804005614 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 357804005615 Surface antigen; Region: Bac_surface_Ag; cl03097 357804005616 Peptidase family M48; Region: Peptidase_M48; cl12018 357804005617 PPIC-type PPIASE domain; Region: Rotamase; cl08278 357804005618 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 357804005619 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. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 357804005620 Walker A/P-loop; other site 357804005621 ATP binding site [chemical binding]; other site 357804005622 Q-loop/lid; other site 357804005623 ABC transporter signature motif; other site 357804005624 Walker B; other site 357804005625 D-loop; other site 357804005626 H-loop/switch region; other site 357804005627 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 357804005628 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, and...; Region: TM_PBP2; cd06261 357804005629 dimer interface [polypeptide binding]; other site 357804005630 conserved gate region; other site 357804005631 putative PBP binding loops; other site 357804005632 ABC-ATPase subunit interface; other site 357804005633 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 357804005634 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 inorganic...; Region: PBPb; cd00134 357804005635 substrate binding pocket [chemical binding]; other site 357804005636 membrane-bound complex binding site; other site 357804005637 hinge residues; other site 357804005638 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804005639 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 357804005640 S-adenosylmethionine binding site [chemical binding]; other site 357804005641 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; cl16911 357804005642 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 357804005643 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); Region: KBL_like; cd06454 357804005644 substrate-cofactor binding pocket; other site 357804005645 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804005646 catalytic residue [active] 357804005647 biotin synthase; Provisional; Region: PRK15108 357804005648 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 357804005649 FeS/SAM binding site; other site 357804005650 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 357804005651 adenosylmethionine--8-amino-7-oxononanoate transaminase; Validated; Region: PRK07986 357804005652 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 357804005653 inhibitor-cofactor binding pocket; inhibition site 357804005654 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804005655 catalytic residue [active] 357804005656 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 357804005657 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 (OB...; Region: EcAsnRS_like_N; cd04318 357804005658 putative dimer interface [polypeptide binding]; other site 357804005659 putative anticodon binding site; other site 357804005660 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 as...; Region: AsxRS_core; cd00776 357804005661 homodimer interface [polypeptide binding]; other site 357804005662 motif 1; other site 357804005663 motif 2; other site 357804005664 active site 357804005665 motif 3; other site 357804005666 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 357804005667 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 357804005668 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 357804005669 Coenzyme A binding pocket [chemical binding]; other site 357804005670 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 357804005671 Nitronate monooxygenase; Region: NMO; pfam03060 357804005672 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 oxidoreductase...; Region: NPD_like; cd04730 357804005673 FMN binding site [chemical binding]; other site 357804005674 substrate binding site [chemical binding]; other site 357804005675 putative catalytic residue [active] 357804005676 Ion transport protein; Region: Ion_trans; pfam00520 357804005677 Ion channel; Region: Ion_trans_2; cl11596 357804005678 Stress responsive A/B Barrel Domain; Region: Dabb; cl15807 357804005679 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Region: HTH_MerR1; cd04783 357804005680 Hg(II)-responsive transcriptional regulator; Region: MerR; TIGR02051 357804005681 DNA binding residues [nucleotide binding] 357804005682 dimer interface [polypeptide binding]; other site 357804005683 mercury binding site [ion binding]; other site 357804005684 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 357804005685 metal-binding site [ion binding] 357804005686 Flavin Reductases; Region: FlaRed; cl00801 357804005687 Protein of unknown function (DUF3429); Region: DUF3429; pfam11911 357804005688 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3314 357804005689 Nucleoside recognition; Region: Gate; cl00486 357804005690 aromatic amino acid exporter; Provisional; Region: PRK11689 357804005691 Cation efflux family; Region: Cation_efflux; cl00316 357804005692 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 357804005693 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 357804005694 DNA-binding site [nucleotide binding]; DNA binding site 357804005695 RNA-binding motif; other site 357804005696 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 357804005697 active site 357804005698 catalytic site [active] 357804005699 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR9; cd08274 357804005700 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 357804005701 putative NAD(P) binding site [chemical binding]; other site 357804005702 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 357804005703 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 357804005704 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, and...; Region: TM_PBP2; cd06261 357804005705 ABC-ATPase subunit interface; other site 357804005706 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 357804005707 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, and...; Region: TM_PBP2; cd06261 357804005708 dimer interface [polypeptide binding]; other site 357804005709 conserved gate region; other site 357804005710 putative PBP binding loops; other site 357804005711 ABC-ATPase subunit interface; other site 357804005712 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 357804005713 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 357804005714 Walker A/P-loop; other site 357804005715 ATP binding site [chemical binding]; other site 357804005716 Q-loop/lid; other site 357804005717 ABC transporter signature motif; other site 357804005718 Walker B; other site 357804005719 D-loop; other site 357804005720 H-loop/switch region; other site 357804005721 amidophosphoribosyltransferase; Provisional; Region: PRK09246 357804005722 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 357804005723 active site 357804005724 tetramer interface [polypeptide binding]; other site 357804005725 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 357804005726 active site 357804005727 Colicin V production protein; Region: Colicin_V; cl00567 357804005728 cell division protein DedD; Provisional; Region: PRK11633 357804005729 Sporulation related domain; Region: SPOR; cl10051 357804005730 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional; Region: PRK10846 357804005731 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 357804005732 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 357804005733 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 357804005734 dimerization interface 3.5A [polypeptide binding]; other site 357804005735 active site 357804005736 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 357804005737 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 the...; Region: TOPRIM_TopoIA_TopoI; cd03363 357804005738 active site 357804005739 interdomain interaction site; other site 357804005740 putative metal-binding site [ion binding]; other site 357804005741 nucleotide binding site [chemical binding]; other site 357804005742 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 DNA...; Region: TOP1Ac; cd00186 357804005743 domain I; other site 357804005744 DNA binding groove [nucleotide binding] 357804005745 phosphate binding site [ion binding]; other site 357804005746 domain II; other site 357804005747 domain III; other site 357804005748 nucleotide binding site [chemical binding]; other site 357804005749 catalytic site [active] 357804005750 domain IV; other site 357804005751 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 357804005752 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 357804005753 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 357804005754 Peptidase family S49 N-terminal; Region: Peptidase_S49_N; pfam08496 357804005755 putative inner membrane peptidase; Provisional; Region: PRK11778 357804005756 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 357804005757 tandem repeat interface [polypeptide binding]; other site 357804005758 oligomer interface [polypeptide binding]; other site 357804005759 active site residues [active] 357804005760 Enoyl-(Acyl carrier protein) reductase; Region: adh_short_C2; pfam13561 357804005761 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804005762 NAD(P) binding site [chemical binding]; other site 357804005763 active site 357804005764 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 357804005765 putative acyl-acceptor binding pocket; other site 357804005766 phosphatidylserine synthase; Provisional; Region: pssA; PRK09428 357804005767 Catalytic domain, repeat 1, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_1; cd09134 357804005768 domain interface [polypeptide binding]; other site 357804005769 putative active site [active] 357804005770 catalytic site [active] 357804005771 Catalytic domain, repeat 2, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_2; cd09136 357804005772 domain interface [polypeptide binding]; other site 357804005773 putative active site [active] 357804005774 catalytic site [active] 357804005775 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 357804005776 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 357804005777 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804005778 homodimer interface [polypeptide binding]; other site 357804005779 catalytic residue [active] 357804005780 Fumarate hydratase (Fumerase); Region: Fumerase; cl00851 357804005781 Fumarase C-terminus; Region: Fumerase_C; cl00795 357804005782 aminodeoxychorismate synthase subunit I; Provisional; Region: pabB; PRK15465 357804005783 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 357804005784 chorismate binding enzyme; Region: Chorismate_bind; cl10555 357804005785 transcriptional regulator CysB; Reviewed; Region: cysB; PRK12681 357804005786 Helix-turn-helix domains; Region: HTH; cl00088 357804005787 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 357804005788 substrate binding site [chemical binding]; other site 357804005789 dimerization interface [polypeptide binding]; other site 357804005790 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 357804005791 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 357804005792 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 357804005793 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 357804005794 dimer interface [polypeptide binding]; other site 357804005795 active site 1 [active] 357804005796 active site 2 [active] 357804005797 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 357804005798 tandem repeat interface [polypeptide binding]; other site 357804005799 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 357804005800 oligomer interface [polypeptide binding]; other site 357804005801 active site residues [active] 357804005802 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 357804005803 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 357804005804 tandem repeat interface [polypeptide binding]; other site 357804005805 oligomer interface [polypeptide binding]; other site 357804005806 active site residues [active] 357804005807 Protein of unknown function (DUF2919); Region: DUF2919; pfam11143 357804005808 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 357804005809 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 357804005810 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 357804005811 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 357804005812 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cl00107 357804005813 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cl00107 357804005814 putative semialdehyde dehydrogenase; Provisional; Region: PRK08040 357804005815 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804005816 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 357804005817 erythronate-4-phosphate dehydrogenase; Validated; Region: PRK00257 357804005818 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804005819 Domain of unknown function (DUF3410); Region: DUF3410; pfam11890 357804005820 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 357804005821 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 357804005822 dimer interface [polypeptide binding]; other site 357804005823 active site 357804005824 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 357804005825 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; cl16911 357804005826 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804005827 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09258 357804005828 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 357804005829 dimer interface [polypeptide binding]; other site 357804005830 active site 357804005831 CoA binding pocket [chemical binding]; other site 357804005832 haloalkane dehalogenase; Provisional; Region: PRK00870 357804005833 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 357804005834 peptide synthase; Provisional; Region: PRK09274 357804005835 AMP-binding enzyme; Region: AMP-binding; cl15778 357804005836 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804005837 3-beta hydroxysteroid dehydrogenase/isomerase family; Region: 3Beta_HSD; pfam01073 357804005838 NAD(P) binding site [chemical binding]; other site 357804005839 active site 357804005840 glyceraldehyde-3-phosphate dehydrogenase; Reviewed; Region: PRK08289 357804005841 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804005842 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 357804005843 Uncharacterized proteins involved in stress response, similar to tellurium resistance terD; Region: TerD_like; cd06974 357804005844 putative metal binding site [ion binding]; other site 357804005845 Uncharacterized protein involved in stress response [General function prediction only]; Region: COG4110 357804005846 Uncharacterized proteins involved in stress response, similar to tellurium resistance terD; Region: TerD_like; cd06974 357804005847 putative metal binding site [ion binding]; other site 357804005848 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 357804005849 putative diguanylate cyclase; Provisional; Region: PRK09776 357804005850 putative active site [active] 357804005851 heme pocket [chemical binding]; other site 357804005852 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804005853 metal binding site [ion binding]; metal-binding site 357804005854 active site 357804005855 I-site; other site 357804005856 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 357804005857 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 357804005858 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 357804005859 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 357804005860 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, and...; Region: TM_PBP2; cd06261 357804005861 dimer interface [polypeptide binding]; other site 357804005862 conserved gate region; other site 357804005863 putative PBP binding loops; other site 357804005864 ABC-ATPase subunit interface; other site 357804005865 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 357804005866 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, and...; Region: TM_PBP2; cd06261 357804005867 dimer interface [polypeptide binding]; other site 357804005868 conserved gate region; other site 357804005869 putative PBP binding loops; other site 357804005870 ABC-ATPase subunit interface; other site 357804005871 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 357804005872 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 357804005873 Walker A/P-loop; other site 357804005874 ATP binding site [chemical binding]; other site 357804005875 Q-loop/lid; other site 357804005876 ABC transporter signature motif; other site 357804005877 Walker B; other site 357804005878 D-loop; other site 357804005879 H-loop/switch region; other site 357804005880 TOBE domain; Region: TOBE_2; cl01440 357804005881 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 family...; Region: PTS_IIB_glc; cd00212 357804005882 active site turn [active] 357804005883 phosphorylation site [posttranslational modification] 357804005884 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 family...; Region: PTS_IIB_glc; cd00212 357804005885 active site turn [active] 357804005886 phosphorylation site [posttranslational modification] 357804005887 lac repressor; Reviewed; Region: lacI; PRK09526 357804005888 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 357804005889 DNA binding site [nucleotide binding] 357804005890 domain linker motif; other site 357804005891 Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_LacI; cd01574 357804005892 ligand binding site [chemical binding]; other site 357804005893 dimerization interface (open form) [polypeptide binding]; other site 357804005894 dimerization interface (closed form) [polypeptide binding]; other site 357804005895 Alpha-galactosidase [Carbohydrate transport and metabolism]; Region: GalA; COG3345 357804005896 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-glucosyltransferase; Region: GH31; cl11402 357804005897 UDP-galactose-4-epimerase; Provisional; Region: PRK10675 357804005898 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 357804005899 NAD binding site [chemical binding]; other site 357804005900 homodimer interface [polypeptide binding]; other site 357804005901 active site 357804005902 substrate binding site [chemical binding]; other site 357804005903 galactose-1-phosphate uridylyltransferase; Provisional; Region: PRK11720 357804005904 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 357804005905 dimer interface [polypeptide binding]; other site 357804005906 active site 357804005907 galactokinase; Provisional; Region: PRK05101 357804005908 Galactokinase galactose-binding signature; Region: GalKase_gal_bdg; pfam10509 357804005909 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 357804005910 Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism]; Region: GalM; COG2017 357804005911 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 357804005912 active site 357804005913 catalytic residues [active] 357804005914 beta-D-galactosidase; Reviewed; Region: lacZ; PRK09525 357804005915 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; cl08371 357804005916 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 357804005917 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; cl15381 357804005918 Beta galactosidase small chain; Region: Bgal_small_N; cl03787 357804005919 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 357804005920 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 357804005921 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 357804005922 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 357804005923 nitrogen fixation negative regulator NifL; Region: nifL_nitrog; TIGR02938 357804005924 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 357804005925 putative active site [active] 357804005926 heme pocket [chemical binding]; other site 357804005927 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 357804005928 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...; Region: HisKA; cl00080 357804005929 dimer interface [polypeptide binding]; other site 357804005930 phosphorylation site [posttranslational modification] 357804005931 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 357804005932 ATP binding site [chemical binding]; other site 357804005933 Mg2+ binding site [ion binding]; other site 357804005934 G-X-G motif; other site 357804005935 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 357804005936 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 357804005937 active site 357804005938 phosphorylation site [posttranslational modification] 357804005939 intermolecular recognition site; other site 357804005940 dimerization interface [polypeptide binding]; other site 357804005941 Response regulator receiver domain; Region: Response_reg; pfam00072 357804005942 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 357804005943 active site 357804005944 phosphorylation site [posttranslational modification] 357804005945 intermolecular recognition site; other site 357804005946 dimerization interface [polypeptide binding]; other site 357804005947 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 357804005948 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 357804005949 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 357804005950 A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity...; Region: APP_MetAP; cl00279 357804005951 active site 357804005952 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 357804005953 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 357804005954 metal binding site [ion binding]; metal-binding site 357804005955 putative dimer interface [polypeptide binding]; other site 357804005956 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2964 357804005957 YheO-like PAS domain; Region: PAS_6; pfam08348 357804005958 Helix-turn-helix domains; Region: HTH; cl00088 357804005959 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 357804005960 homotrimer interaction site [polypeptide binding]; other site 357804005961 putative active site [active] 357804005962 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 357804005963 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), tryptophan...; Region: Trp-synth-beta_II; cd00640 357804005964 catalytic residue [active] 357804005965 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 357804005966 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 357804005967 EamA-like transporter family; Region: EamA; cl01037 357804005968 DctM-like transporters; Region: DctM; pfam06808 357804005969 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 357804005970 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 357804005971 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 357804005972 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 357804005973 UDP-galactopyranose mutase [Cell envelope biogenesis, outer membrane]; Region: Glf; COG0562 357804005974 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804005975 UDP-galactopyranose mutase; Region: GLF; pfam03275 357804005976 MatE; Region: MatE; cl10513 357804005977 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 357804005978 Transposase [DNA replication, recombination, and repair]; Region: COG5433 357804005979 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 357804005980 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 357804005981 dimerization interface [polypeptide binding]; other site 357804005982 DPS ferroxidase diiron center [ion binding]; other site 357804005983 ion pore; other site 357804005984 Transcriptional regulator [Transcription]; Region: LysR; COG0583 357804005985 Helix-turn-helix domains; Region: HTH; cl00088 357804005986 The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; Region: PBP2_CbbR_RubisCO_like; cd08419 357804005987 putative dimerization interface [polypeptide binding]; other site 357804005988 AIR carboxylase; Region: AIRC; cl00310 357804005989 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 357804005990 ATP-grasp domain; Region: ATP-grasp_4; cl03087 357804005991 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 357804005992 Sulfate transporter family; Region: Sulfate_transp; cl15842 357804005993 Sulfate transporter family; Region: Sulfate_transp; cl15842 357804005994 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 357804005995 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 357804005996 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 357804005997 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 357804005998 putative active site [active] 357804005999 heme pocket [chemical binding]; other site 357804006000 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804006001 metal binding site [ion binding]; metal-binding site 357804006002 active site 357804006003 I-site; other site 357804006004 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 357804006005 transaldolase-like protein; Provisional; Region: PTZ00411 357804006006 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 357804006007 active site 357804006008 dimer interface [polypeptide binding]; other site 357804006009 catalytic residue [active] 357804006010 PTS system sugar-specific permease component; Region: EIIC-GAT; cl04451 357804006011 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 357804006012 active site 357804006013 P-loop; other site 357804006014 phosphorylation site [posttranslational modification] 357804006015 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 357804006016 active site 357804006017 phosphorylation site [posttranslational modification] 357804006018 Transcriptional regulators [Transcription]; Region: PurR; COG1609 357804006019 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 357804006020 DNA binding site [nucleotide binding] 357804006021 domain linker motif; other site 357804006022 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 357804006023 putative ligand binding site [chemical binding]; other site 357804006024 putative dimerization interface [polypeptide binding]; other site 357804006025 haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED; Region: HAD-SF-IA-v3; TIGR01509 357804006026 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 357804006027 motif II; other site 357804006028 Protein of unknown function DUF45; Region: DUF45; cl00636 357804006029 Uncharacterized conserved protein [Function unknown]; Region: COG0397; cl00428 357804006030 Uncharacterized ACR, YdiU/UPF0061 family; Region: UPF0061; pfam02696 357804006031 Transcriptional regulator; Region: Transcrip_reg; cl00361 357804006032 NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide reductase...; Region: NrdH; cd02976 357804006033 catalytic residues [active] 357804006034 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_7; cd04664 357804006035 nudix motif; other site 357804006036 SCP-2 sterol transfer family; Region: SCP2; cl01225 357804006037 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 357804006038 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 357804006039 MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1. In fact, the...; Region: ABC_MTABC3_MDL1_MDL2; cd03249 357804006040 Walker A/P-loop; other site 357804006041 ATP binding site [chemical binding]; other site 357804006042 Q-loop/lid; other site 357804006043 ABC transporter signature motif; other site 357804006044 Walker B; other site 357804006045 D-loop; other site 357804006046 H-loop/switch region; other site 357804006047 transcriptional regulator BetI; Validated; Region: PRK00767 357804006048 Helix-turn-helix domains; Region: HTH; cl00088 357804006049 Bacterial transcriptional repressor; Region: TetR_C_6; cl07106 357804006050 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 357804006051 NAD+-dependent 4-trimethylaminobutyraldehyde dehydrogenase, ALDH family 9A1; Region: ALDH_F9_TMBADH; cd07090 357804006052 tetrameric interface [polypeptide binding]; other site 357804006053 NAD binding site [chemical binding]; other site 357804006054 catalytic residues [active] 357804006055 choline dehydrogenase; Validated; Region: PRK02106 357804006056 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 357804006057 choline ABC transporter, periplasmic binding protein; Region: ABC_choline_bnd; TIGR03414 357804006058 NMT1-like family; Region: NMT1_2; cl15260 357804006059 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, and...; Region: TM_PBP2; cd06261 357804006060 dimer interface [polypeptide binding]; other site 357804006061 conserved gate region; other site 357804006062 putative PBP binding loops; other site 357804006063 ABC-ATPase subunit interface; other site 357804006064 choline ABC transporter, ATP-binding protein; Region: ABC_choXWV_ATP; TIGR03415 357804006065 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804006066 Walker A/P-loop; other site 357804006067 ATP binding site [chemical binding]; other site 357804006068 Q-loop/lid; other site 357804006069 ABC transporter signature motif; other site 357804006070 Walker B; other site 357804006071 D-loop; other site 357804006072 H-loop/switch region; other site 357804006073 BCCT family transporter; Region: BCCT; cl00569 357804006074 Helix-turn-helix domains; Region: HTH; cl00088 357804006075 Helix-turn-helix domains; Region: HTH; cl00088 357804006076 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 357804006077 BON domain; Region: BON; cl02771 357804006078 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 357804006079 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 357804006080 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804006081 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 357804006082 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 357804006083 alanine racemase; Reviewed; Region: alr; PRK00053 357804006084 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 357804006085 active site 357804006086 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 357804006087 dimer interface [polypeptide binding]; other site 357804006088 substrate binding site [chemical binding]; other site 357804006089 catalytic residues [active] 357804006090 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 357804006091 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804006092 ABC transporter signature motif; other site 357804006093 Walker B; other site 357804006094 D-loop; other site 357804006095 H-loop/switch region; other site 357804006096 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 357804006097 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 357804006098 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 357804006099 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 357804006100 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 357804006101 putative active site [active] 357804006102 heme pocket [chemical binding]; other site 357804006103 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 357804006104 PAS domain; Region: PAS_9; pfam13426 357804006105 putative active site [active] 357804006106 heme pocket [chemical binding]; other site 357804006107 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804006108 metal binding site [ion binding]; metal-binding site 357804006109 active site 357804006110 I-site; other site 357804006111 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 357804006112 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 357804006113 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 357804006114 Coenzyme A binding pocket [chemical binding]; other site 357804006115 DNA-binding transcriptional repressor GlpR; Provisional; Region: PRK10906 357804006116 Helix-turn-helix domains; Region: HTH; cl00088 357804006117 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 357804006118 Glycerophosphodiester phosphodiesterase domain in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase UgpQ and similar proteins; Region: GDPD_EcUgpQ_like; cd08562 357804006119 cytoplasmic glycerophosphodiester phosphodiesterase; Provisional; Region: ugpQ; PRK09454 357804006120 putative active site [active] 357804006121 catalytic site [active] 357804006122 putative metal binding site [ion binding]; other site 357804006123 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 357804006124 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 357804006125 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 357804006126 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, and...; Region: TM_PBP2; cd06261 357804006127 dimer interface [polypeptide binding]; other site 357804006128 conserved gate region; other site 357804006129 putative PBP binding loops; other site 357804006130 ABC-ATPase subunit interface; other site 357804006131 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 357804006132 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, and...; Region: TM_PBP2; cd06261 357804006133 dimer interface [polypeptide binding]; other site 357804006134 conserved gate region; other site 357804006135 putative PBP binding loops; other site 357804006136 ABC-ATPase subunit interface; other site 357804006137 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 357804006138 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 357804006139 Walker A/P-loop; other site 357804006140 ATP binding site [chemical binding]; other site 357804006141 Q-loop/lid; other site 357804006142 ABC transporter signature motif; other site 357804006143 Walker B; other site 357804006144 D-loop; other site 357804006145 H-loop/switch region; other site 357804006146 HAD-superfamily hydrolase, subfamily IIB; Region: HAD-SF-IIB; TIGR01484 357804006147 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 357804006148 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 357804006149 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 357804006150 Protein of unknown function (DUF3185); Region: DUF3185; pfam11381 357804006151 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 357804006152 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the GGDEF (DiGuanylate-Cyclase (DGC)) domain. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain and...; Region: CBS_pair_GGDEF_assoc; cd04598 357804006153 DNA helicase IV; Provisional; Region: helD; PRK11054 357804006154 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804006155 DNA helicase IV; Provisional; Region: helD; PRK11054 357804006156 Family description; Region: UvrD_C_2; cl15862 357804006157 DNA topoisomerase I; Validated; Region: PRK06599 357804006158 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 357804006159 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 357804006160 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804006161 NAD(P) binding site [chemical binding]; other site 357804006162 active site 357804006163 Glycosyl hydrolase family 3 C-terminal domain; Region: Glyco_hydro_3_C; pfam01915 357804006164 Fibronectin type III-like domain; Region: Fn3-like; cl15273 357804006165 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 357804006166 Protein of unknown function, DUF393; Region: DUF393; cl01136 357804006167 short chain dehydrogenase; Provisional; Region: PRK06924 357804006168 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804006169 NAD(P) binding site [chemical binding]; other site 357804006170 active site 357804006171 Complex I intermediate-associated protein 30 (CIA30); Region: CIA30; cl15292 357804006172 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 357804006173 Beta/Gamma crystallin; Region: Crystall; cl02528 357804006174 Beta/Gamma crystallin; Region: Crystall; cl02528 357804006175 Malate/L-lactate dehydrogenase; Region: Ldh_2; cl00900 357804006176 Proline racemase [Amino acid transport and metabolism]; Region: COG3938 357804006177 hydroxyproline-2-epimerase; Provisional; Region: PRK13971 357804006178 Transcriptional regulators [Transcription]; Region: GntR; COG1802 357804006179 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 357804006180 DNA-binding site [nucleotide binding]; DNA binding site 357804006181 FCD domain; Region: FCD; cl11656 357804006182 Isochorismatase family; Region: Isochorismatase; pfam00857 357804006183 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 357804006184 catalytic triad [active] 357804006185 dimer interface [polypeptide binding]; other site 357804006186 conserved cis-peptide bond; other site 357804006187 aconitate hydratase; Validated; Region: PRK09277 357804006188 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 357804006189 substrate binding site [chemical binding]; other site 357804006190 ligand binding site [chemical binding]; other site 357804006191 Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group...; Region: AcnA_IRP_Swivel; cd01580 357804006192 substrate binding site [chemical binding]; other site 357804006193 oxidoreductase alpha (molybdopterin) subunit; Region: Fdhalpha-like; TIGR01701 357804006194 The MopB_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins; Region: MopB_ydeP; cd02767 357804006195 putative molybdopterin cofactor binding site [chemical binding]; other site 357804006196 The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region...; Region: MopB_CT_ydeP; cd02787 357804006197 putative molybdopterin cofactor binding site; other site 357804006198 FdhD/NarQ family; Region: FdhD-NarQ; cl00659 357804006199 Protein of unknown function (DUF3726); Region: DUF3726; pfam12525 357804006200 BCCT family transporter; Region: BCCT; cl00569 357804006201 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 a...; Region: metallo-dependent_hydrolases; cl00281 357804006202 active site 357804006203 Bacillus subtilis NADP+-dependent alpha-ketoglutaric semialdehyde dehydrogenase ycbD-like; Region: ALDH_KGSADH-YcbD; cd07097 357804006204 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 357804006205 NAD(P) binding site [chemical binding]; other site 357804006206 catalytic residues [active] 357804006207 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 357804006208 homotrimer interaction site [polypeptide binding]; other site 357804006209 putative active site [active] 357804006210 Transcriptional regulator [Transcription]; Region: LysR; COG0583 357804006211 Helix-turn-helix domains; Region: HTH; cl00088 357804006212 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 357804006213 putative dimerization interface [polypeptide binding]; other site 357804006214 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 357804006215 Major Facilitator Superfamily; Region: MFS_1; pfam07690 357804006216 putative substrate translocation pore; other site 357804006217 muropeptide transporter; Validated; Region: ampG; PRK11010 357804006218 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 357804006219 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 357804006220 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804006221 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; cl16911 357804006222 DEXH box helicase, DNA ligase-associated; Region: DEXH_lig_assoc; TIGR04121 357804006223 Protein of unknown function (DUF2589); Region: DUF2589; pfam11655 357804006224 Protein of unknown function (DUF2589); Region: DUF2589; pfam11655 357804006225 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 357804006226 Response regulator receiver domain; Region: Response_reg; pfam00072 357804006227 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 357804006228 active site 357804006229 phosphorylation site [posttranslational modification] 357804006230 intermolecular recognition site; other site 357804006231 dimerization interface [polypeptide binding]; other site 357804006232 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 357804006233 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 357804006234 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 357804006235 putative active site [active] 357804006236 heme pocket [chemical binding]; other site 357804006237 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...; Region: HisKA; cd00082 357804006238 dimer interface [polypeptide binding]; other site 357804006239 phosphorylation site [posttranslational modification] 357804006240 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 357804006241 ATP binding site [chemical binding]; other site 357804006242 Mg2+ binding site [ion binding]; other site 357804006243 G-X-G motif; other site 357804006244 Response regulator receiver domain; Region: Response_reg; pfam00072 357804006245 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 357804006246 active site 357804006247 phosphorylation site [posttranslational modification] 357804006248 intermolecular recognition site; other site 357804006249 dimerization interface [polypeptide binding]; other site 357804006250 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 357804006251 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 357804006252 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 357804006253 dimer interface [polypeptide binding]; other site 357804006254 active site 357804006255 heme binding site [chemical binding]; other site 357804006256 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 357804006257 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 357804006258 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 357804006259 Immune inhibitor A peptidase M6; Region: Peptidase_M6; cl11525 357804006260 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 357804006261 EamA-like transporter family; Region: EamA; cl01037 357804006262 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804006263 metal binding site [ion binding]; metal-binding site 357804006264 active site 357804006265 I-site; other site 357804006266 Dehydratase family; Region: ILVD_EDD; cl00340 357804006267 Predicted GTPases [General function prediction only]; Region: COG1161 357804006268 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804006269 G1 box; other site 357804006270 GTP/Mg2+ binding site [chemical binding]; other site 357804006271 G2 box; other site 357804006272 G3 box; other site 357804006273 Switch II region; other site 357804006274 G4 box; other site 357804006275 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 357804006276 G1 box; other site 357804006277 GTP/Mg2+ binding site [chemical binding]; other site 357804006278 G2 box; other site 357804006279 Switch I region; other site 357804006280 G3 box; other site 357804006281 Switch II region; other site 357804006282 G4 box; other site 357804006283 PAS fold; Region: PAS_3; pfam08447 357804006284 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 357804006285 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804006286 metal binding site [ion binding]; metal-binding site 357804006287 active site 357804006288 I-site; other site 357804006289 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 357804006290 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 357804006291 EamA-like transporter family; Region: EamA; cl01037 357804006292 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 357804006293 DNA-binding site [nucleotide binding]; DNA binding site 357804006294 RNA-binding motif; other site 357804006295 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 357804006296 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 357804006297 glutathionine S-transferase; Provisional; Region: PRK10542 357804006298 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 357804006299 C-terminal domain interface [polypeptide binding]; other site 357804006300 dimer interface [polypeptide binding]; other site 357804006301 GSH binding site (G-site) [chemical binding]; other site 357804006302 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 357804006303 N-terminal domain interface [polypeptide binding]; other site 357804006304 dimer interface [polypeptide binding]; other site 357804006305 substrate binding pocket (H-site) [chemical binding]; other site 357804006306 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 357804006307 Tetratricopeptide repeat; Region: TPR_16; pfam13432 357804006308 binding surface 357804006309 TPR motif; other site 357804006310 penicillin-binding protein 1B; Region: PBP_1b; TIGR02071 357804006311 Transglycosylase; Region: Transgly; cl07896 357804006312 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 357804006313 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804006314 molybdenum ABC transporter, ATP-binding protein; Region: modC_ABC; TIGR02142 357804006315 Walker A/P-loop; other site 357804006316 ATP binding site [chemical binding]; other site 357804006317 Q-loop/lid; other site 357804006318 ABC transporter signature motif; other site 357804006319 Walker B; other site 357804006320 D-loop; other site 357804006321 H-loop/switch region; other site 357804006322 TOBE domain; Region: TOBE_2; cl01440 357804006323 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, and...; Region: TM_PBP2; cd06261 357804006324 dimer interface [polypeptide binding]; other site 357804006325 putative PBP binding loops; other site 357804006326 ABC-ATPase subunit interface; other site 357804006327 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 357804006328 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 357804006329 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 357804006330 MoaE homodimer interface [polypeptide binding]; other site 357804006331 MoaD interaction [polypeptide binding]; other site 357804006332 active site residues [active] 357804006333 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 357804006334 MoaE interaction surface [polypeptide binding]; other site 357804006335 MoeB interaction surface [polypeptide binding]; other site 357804006336 thiocarboxylated glycine; other site 357804006337 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 guanosine...; Region: MoaC_PE; cd01420 357804006338 trimer interface [polypeptide binding]; other site 357804006339 dimer interface [polypeptide binding]; other site 357804006340 putative active site [active] 357804006341 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 357804006342 MPT binding site; other site 357804006343 trimer interface [polypeptide binding]; other site 357804006344 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 357804006345 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 357804006346 GTP binding site; other site 357804006347 periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family; Region: napC_nirT; TIGR02161 357804006348 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; cl01153 357804006349 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 357804006350 Nitrate reductases, NapA (Nitrate-R-NapA), 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...; Region: MopB_Nitrate-R-NapA-like; cd02754 357804006351 [4Fe-4S] binding site [ion binding]; other site 357804006352 molybdopterin cofactor binding site; other site 357804006353 Nitrate reductases, NapA (Nitrate-R-NapA), 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...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 357804006354 molybdopterin cofactor binding site; other site 357804006355 NapD protein; Region: NapD; cl01163 357804006356 ferredoxin-type protein; Provisional; Region: PRK10194 357804006357 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...; Region: HCP_like; cl14655 357804006358 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 357804006359 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 357804006360 FeS/SAM binding site; other site 357804006361 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 357804006362 ATP-dependent DNA helicase DinG; Provisional; Region: dinG; PRK11747 357804006363 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804006364 DEAD_2; Region: DEAD_2; pfam06733 357804006365 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804006366 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 357804006367 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 357804006368 Primosomal replication protein priB and priC; Region: priB_priC; cl11483 357804006369 Protein of unknown function (DUF2496); Region: DUF2496; cl11670 357804006370 Acylphosphatase; Region: Acylphosphatase; cl00551 357804006371 LysE type translocator; Region: LysE; cl00565 357804006372 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 357804006373 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 357804006374 active site 357804006375 HIGH motif; other site 357804006376 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 357804006377 KMSKS motif; other site 357804006378 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 357804006379 tRNA binding surface [nucleotide binding]; other site 357804006380 anticodon binding site; other site 357804006381 peptidyl-prolyl cis-trans isomerase B (rotamase B); Provisional; Region: PRK10791 357804006382 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 357804006383 substrate binding site [chemical binding]; other site 357804006384 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 357804006385 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 357804006386 putative active site [active] 357804006387 putative metal binding site [ion binding]; other site 357804006388 carboxy-terminal protease; Provisional; Region: PRK11186 357804006389 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 357804006390 protein binding site [polypeptide binding]; other site 357804006391 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 357804006392 Catalytic dyad [active] 357804006393 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 357804006394 ProP expression regulator; Provisional; Region: PRK04950 357804006395 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 357804006396 putative protease; Provisional; Region: PRK15452 357804006397 Peptidase family U32; Region: Peptidase_U32; cl03113 357804006398 ferredoxin; Validated; Region: PRK07118 357804006399 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 357804006400 MatE; Region: MatE; cl10513 357804006401 MatE; Region: MatE; cl10513 357804006402 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 357804006403 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 357804006404 peptide binding site [polypeptide binding]; other site 357804006405 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, and...; Region: TM_PBP2; cd06261 357804006406 dimer interface [polypeptide binding]; other site 357804006407 conserved gate region; other site 357804006408 putative PBP binding loops; other site 357804006409 ABC-ATPase subunit interface; other site 357804006410 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SapC; COG4171 357804006411 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 357804006412 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, and...; Region: TM_PBP2; cl00427 357804006413 antimicrobial peptide ABC transporter ATP-binding protein; Provisional; Region: PRK15093 357804006414 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 357804006415 Walker A/P-loop; other site 357804006416 ATP binding site [chemical binding]; other site 357804006417 Q-loop/lid; other site 357804006418 ABC transporter signature motif; other site 357804006419 Walker B; other site 357804006420 D-loop; other site 357804006421 H-loop/switch region; other site 357804006422 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 357804006423 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SapF; COG4167 357804006424 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 357804006425 Walker A/P-loop; other site 357804006426 ATP binding site [chemical binding]; other site 357804006427 Q-loop/lid; other site 357804006428 ABC transporter signature motif; other site 357804006429 Walker B; other site 357804006430 D-loop; other site 357804006431 H-loop/switch region; other site 357804006432 putative inner membrane diguanylate cyclase; Provisional; Region: PRK09966 357804006433 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804006434 active site 357804006435 I-site; other site 357804006436 metal binding site [ion binding]; metal-binding site 357804006437 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 357804006438 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 357804006439 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 subfamily; Region: Alpha_ANH_like_II; cd01993 357804006440 Ligand Binding Site [chemical binding]; other site 357804006441 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 357804006442 substrate binding site [chemical binding]; other site 357804006443 dimer interface [polypeptide binding]; other site 357804006444 catalytic triad [active] 357804006445 YccA-like proteins; Region: YccA_like; cd10433 357804006446 outer membrane-specific lipoprotein transporter subunit LolE; Provisional; Region: PRK11146 357804006447 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 357804006448 FtsX-like permease family; Region: FtsX; cl15850 357804006449 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 357804006450 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 357804006451 Walker A/P-loop; other site 357804006452 ATP binding site [chemical binding]; other site 357804006453 Q-loop/lid; other site 357804006454 ABC transporter signature motif; other site 357804006455 Walker B; other site 357804006456 D-loop; other site 357804006457 H-loop/switch region; other site 357804006458 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 357804006459 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 357804006460 FtsX-like permease family; Region: FtsX; cl15850 357804006461 transcription-repair coupling factor; Provisional; Region: PRK10689 357804006462 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 357804006463 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 357804006464 ATP binding site [chemical binding]; other site 357804006465 putative Mg++ binding site [ion binding]; other site 357804006466 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 357804006467 nucleotide binding region [chemical binding]; other site 357804006468 ATP-binding site [chemical binding]; other site 357804006469 TRCF domain; Region: TRCF; cl04088 357804006470 Protein of unknown function (DUF2803); Region: DUF2803; pfam10972 357804006471 Histidine Utilizing Protein, the hut operon positive regulatory protein; Region: HutP; cl07944 357804006472 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 357804006473 RNA binding site [nucleotide binding]; other site 357804006474 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 357804006475 motif II; other site 357804006476 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 357804006477 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 357804006478 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 357804006479 active site 357804006480 ribonuclease E; Reviewed; Region: rne; PRK10811 357804006481 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 357804006482 homodimer interface [polypeptide binding]; other site 357804006483 oligonucleotide binding site [chemical binding]; other site 357804006484 thioredoxin reductase; Provisional; Region: PRK10262 357804006485 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 357804006486 lipoprotein NlpI; Provisional; Region: PRK11189 357804006487 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 357804006488 binding surface 357804006489 TPR motif; other site 357804006490 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 357804006491 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 357804006492 Protein export membrane protein; Region: SecD_SecF; cl14618 357804006493 SecD export protein N-terminal TM region; Region: SecD-TM1; cl08136 357804006494 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 357804006495 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 357804006496 Protein export membrane protein; Region: SecD_SecF; cl14618 357804006497 Preprotein translocase subunit; Region: YajC; cl00806 357804006498 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; cl00409 357804006499 tRNA-guanine transglycosylases, various specificities; Region: tgt_general; TIGR00449 357804006500 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 357804006501 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 357804006502 ribosomal protein L20; Region: rpl20; CHL00068 357804006503 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 357804006504 23S rRNA binding site [nucleotide binding]; other site 357804006505 L21 binding site [polypeptide binding]; other site 357804006506 L13 binding site [polypeptide binding]; other site 357804006507 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 357804006508 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 357804006509 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 357804006510 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 357804006511 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 357804006512 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, and...; Region: TGS_ThrRS_N; cd01667 357804006513 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 357804006514 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 357804006515 active site 357804006516 dimer interface [polypeptide binding]; other site 357804006517 motif 1; other site 357804006518 motif 2; other site 357804006519 motif 3; other site 357804006520 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 357804006521 anticodon binding site; other site 357804006522 YebG protein; Region: YebG; cl01217 357804006523 Paraquat-inducible protein A; Region: PqiA; pfam04403 357804006524 Paraquat-inducible protein A; Region: PqiA; pfam04403 357804006525 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 357804006526 mce related protein; Region: MCE; pfam02470 357804006527 mce related protein; Region: MCE; pfam02470 357804006528 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 357804006529 mce related protein; Region: MCE; pfam02470 357804006530 mce related protein; Region: MCE; pfam02470 357804006531 mce related protein; Region: MCE; pfam02470 357804006532 rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed; Region: yebU; PRK11933 357804006533 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; cl16911 357804006534 pre-rRNA processing and ribosome biogenesis; Region: Nol1_Nop2_Fmu_2; cl01283 357804006535 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 357804006536 putative active site [active] 357804006537 Domain of unknown function (DUF1737); Region: DUF1737; cl10503 357804006538 tRNA s(4)U8 sulfurtransferase; Provisional; Region: PRK01269 357804006539 THUMP domain; Region: THUMP; cl12076 357804006540 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 357804006541 Ligand Binding Site [chemical binding]; other site 357804006542 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 357804006543 active site residue [active] 357804006544 YaeQ protein; Region: YaeQ; cl01913 357804006545 tartrate dehydrogenase; Provisional; Region: PRK08194 357804006546 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 357804006547 Uncharacterized conserved protein [Function unknown]; Region: COG0327 357804006548 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 357804006549 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 357804006550 phosphate regulon sensor protein; Provisional; Region: phoR; PRK11006 357804006551 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...; Region: HisKA; cd00082 357804006552 dimer interface [polypeptide binding]; other site 357804006553 phosphorylation site [posttranslational modification] 357804006554 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 357804006555 ATP binding site [chemical binding]; other site 357804006556 Mg2+ binding site [ion binding]; other site 357804006557 G-X-G motif; other site 357804006558 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 357804006559 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 357804006560 active site 357804006561 phosphorylation site [posttranslational modification] 357804006562 intermolecular recognition site; other site 357804006563 dimerization interface [polypeptide binding]; other site 357804006564 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 and...; Region: trans_reg_C; cd00383 357804006565 DNA binding site [nucleotide binding] 357804006566 Putative exonuclease, RdgC; Region: RdgC; cl01122 357804006567 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 357804006568 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804006569 ATP-grasp domain; Region: ATP-grasp_4; cl03087 357804006570 Cell division inhibitor SulA; Region: SulA; cl01880 357804006571 Uncharacterized protein family (UPF0253); Region: UPF0253; cl11640 357804006572 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 357804006573 ATP binding site [chemical binding]; other site 357804006574 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 357804006575 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 357804006576 substrate binding pocket [chemical binding]; other site 357804006577 chain length determination region; other site 357804006578 substrate-Mg2+ binding site; other site 357804006579 catalytic residues [active] 357804006580 aspartate-rich region 1; other site 357804006581 active site lid residues [active] 357804006582 aspartate-rich region 2; other site 357804006583 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 357804006584 Thiamine pyrophosphate (TPP) family, DXS subfamily, 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...; Region: TPP_DXS; cd02007 357804006585 TPP-binding site; other site 357804006586 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 357804006587 PYR/PP interface [polypeptide binding]; other site 357804006588 dimer interface [polypeptide binding]; other site 357804006589 TPP binding site [chemical binding]; other site 357804006590 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 357804006591 thiamine monophosphate kinase; Provisional; Region: PRK05731 357804006592 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 357804006593 ATP binding site [chemical binding]; other site 357804006594 dimerization interface [polypeptide binding]; other site 357804006595 23S rRNA pseudouridine synthase F; Provisional; Region: PRK10475 357804006596 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 357804006597 RNA binding surface [nucleotide binding]; other site 357804006598 Pseudouridine synthase, Escherichia coli RluF like; Region: PseudoU_synth_RluF; cd02554 357804006599 probable active site [active] 357804006600 Uncharacterized conserved protein (DUF2132); Region: DUF2132; cl01894 357804006601 Protein of unknown function (DUF3622); Region: DUF3622; pfam12286 357804006602 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl00433 357804006603 Protein of unknown function (DUF2789); Region: DUF2789; pfam10982 357804006604 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 357804006605 dimer interface [polypeptide binding]; other site 357804006606 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 357804006607 metal binding site [ion binding]; metal-binding site 357804006608 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 357804006609 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804006610 CoA-ligase; Region: Ligase_CoA; cl02894 357804006611 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 357804006612 ATP-grasp domain; Region: ATP-grasp_4; cl03087 357804006613 CoA-ligase; Region: Ligase_CoA; cl02894 357804006614 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 357804006615 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 357804006616 E3 interaction surface; other site 357804006617 lipoyl attachment site [posttranslational modification]; other site 357804006618 e3 binding domain; Region: E3_binding; pfam02817 357804006619 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 357804006620 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 357804006621 Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, 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...; Region: TPP_E1_OGDC_like; cd02016 357804006622 TPP-binding site [chemical binding]; other site 357804006623 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 357804006624 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 357804006625 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; cl00159 357804006626 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK08958 357804006627 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804006628 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 357804006629 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 357804006630 SdhC subunit interface [polypeptide binding]; other site 357804006631 proximal heme binding site [chemical binding]; other site 357804006632 cardiolipin binding site; other site 357804006633 Iron-sulfur protein interface; other site 357804006634 proximal quinone binding site [chemical binding]; other site 357804006635 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 357804006636 Iron-sulfur protein interface; other site 357804006637 proximal quinone binding site [chemical binding]; other site 357804006638 SdhD (CybS) interface [polypeptide binding]; other site 357804006639 proximal heme binding site [chemical binding]; other site 357804006640 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 357804006641 dimer interface [polypeptide binding]; other site 357804006642 Citrate synthase; Region: Citrate_synt; pfam00285 357804006643 active site 357804006644 citrylCoA binding site [chemical binding]; other site 357804006645 NADH binding [chemical binding]; other site 357804006646 cationic pore residues; other site 357804006647 oxalacetate/citrate binding site [chemical binding]; other site 357804006648 coenzyme A binding site [chemical binding]; other site 357804006649 catalytic triad [active] 357804006650 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 357804006651 FOG: CBS domain [General function prediction only]; Region: COG0517 357804006652 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-called...; Region: CBS_pair_16; cd04629 357804006653 Uncharacterized protein conserved in bacteria (DUF2058); Region: DUF2058; cl01201 357804006654 Protein of unknown function (DUF520); Region: DUF520; cl00723 357804006655 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 357804006656 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804006657 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 357804006658 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3014 357804006659 TolB amino-terminal domain; Region: TolB_N; cl00639 357804006660 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 357804006661 nucleotide binding site/active site [active] 357804006662 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 357804006663 Nucleoid-associated protein [General function prediction only]; Region: COG3081 357804006664 37-kD nucleoid-associated bacterial protein; Region: NA37; cl15473 357804006665 Protein of unknown function (DUF1414); Region: DUF1414; cl01175 357804006666 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]; Region: COG3083 357804006667 Domain of unknown function (DUF3413); Region: DUF3413; pfam11893 357804006668 Sulfatase; Region: Sulfatase; cl10460 357804006669 exoribonuclease II; Provisional; Region: PRK05054 357804006670 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 357804006671 RNB domain; Region: RNB; pfam00773 357804006672 hypothetical protein; Provisional; Region: PRK01254 357804006673 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase; Region: B12-binding_like; cl00293 357804006674 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase; Region: B12-binding_like; cl00293 357804006675 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 357804006676 recombination protein RecR; Reviewed; Region: recR; PRK00076 357804006677 RecR protein; Region: RecR; pfam02132 357804006678 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 357804006679 putative active site [active] 357804006680 putative metal-binding site [ion binding]; other site 357804006681 tetramer interface [polypeptide binding]; other site 357804006682 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804006683 metal binding site [ion binding]; metal-binding site 357804006684 active site 357804006685 I-site; other site 357804006686 YbaB/EbfC DNA-binding family; Region: YbaB_DNA_bd; cl00494 357804006687 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 357804006688 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 ABC; Region: AAA; cd00009 357804006689 Walker A motif; other site 357804006690 ATP binding site [chemical binding]; other site 357804006691 Walker B motif; other site 357804006692 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804006693 arginine finger; other site 357804006694 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 357804006695 DNA polymerase III tau subunit V interacting with alpha; Region: DNA_pol3_tau_5; pfam12170 357804006696 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 357804006697 active site 357804006698 tRNA-dihydrouridine synthase C; Provisional; Region: PRK10550 357804006699 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 also...; Region: DUS_like_FMN; cd02801 357804006700 FMN binding site [chemical binding]; other site 357804006701 active site 357804006702 catalytic residues [active] 357804006703 substrate binding site [chemical binding]; other site 357804006704 Protein of unknown function (DUF3466); Region: DUF3466; pfam11949 357804006705 ABC transporter ATPase component; Reviewed; Region: PRK11147 357804006706 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 facilitated...; Region: ABCF_EF-3; cd03221 357804006707 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 facilitated...; Region: ABCF_EF-3; cd03221 357804006708 ABC transporter; Region: ABC_tran_2; pfam12848 357804006709 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 facilitated...; Region: ABCF_EF-3; cd03221 357804006710 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 357804006711 23S rRNA m(2)G2445 methyltransferase; Provisional; Region: rlmL; PRK11783 357804006712 THUMP domain; Region: THUMP; cl12076 357804006713 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; cl16911 357804006714 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 357804006715 S-adenosylmethionine binding site [chemical binding]; other site 357804006716 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 357804006717 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 357804006718 Histidine kinase, Adenylyl cyclase, 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...; Region: HAMP; cl01054 357804006719 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 357804006720 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 357804006721 ATP binding site [chemical binding]; other site 357804006722 Mg2+ binding site [ion binding]; other site 357804006723 G-X-G motif; other site 357804006724 osmolarity response regulator; Provisional; Region: ompR; PRK09468 357804006725 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 357804006726 active site 357804006727 phosphorylation site [posttranslational modification] 357804006728 intermolecular recognition site; other site 357804006729 dimerization interface [polypeptide binding]; other site 357804006730 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 and...; Region: trans_reg_C; cd00383 357804006731 DNA binding site [nucleotide binding] 357804006732 diaminobutyrate--2-oxoglutarate aminotransferase; Provisional; Region: PRK06938 357804006733 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 357804006734 inhibitor-cofactor binding pocket; inhibition site 357804006735 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804006736 catalytic residue [active] 357804006737 Glutamate decarboxylase and related PLP-dependent proteins [Amino acid transport and metabolism]; Region: GadB; COG0076 357804006738 DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to DOPA/tyrosine decarboxylase (DDC), histidine decarboxylase (HDC), and...; Region: DOPA_deC_like; cd06450 357804006739 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804006740 catalytic residue [active] 357804006741 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 357804006742 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804006743 NAD(P) binding pocket [chemical binding]; other site 357804006744 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 357804006745 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 357804006746 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 357804006747 dimer interface [polypeptide binding]; other site 357804006748 active site 357804006749 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 357804006750 catalytic residues [active] 357804006751 substrate binding site [chemical binding]; other site 357804006752 hypothetical protein; Provisional; Region: PRK13560 357804006753 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 357804006754 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804006755 metal binding site [ion binding]; metal-binding site 357804006756 active site 357804006757 I-site; other site 357804006758 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 357804006759 Beta-eliminating lyase; Region: Beta_elim_lyase; pfam01212 357804006760 tetramer interface [polypeptide binding]; other site 357804006761 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804006762 catalytic residue [active] 357804006763 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 a...; Region: TlpA_like_family; cd02966 357804006764 catalytic residues [active] 357804006765 Dihydroorotase (DHOase) catalyzes the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in the pyrimidine biosynthesis. In contrast to the large polyfunctional CAD proteins of higher organisms, this group of DHOases is...; Region: DHOase; cd01294 357804006766 active site 357804006767 substrate binding pocket [chemical binding]; other site 357804006768 dimer interface [polypeptide binding]; other site 357804006769 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; smart00782 357804006770 PhnA protein; Region: PhnA; pfam03831 357804006771 SAM-dependent 23S ribosomal RNA mG1835 methyltransferase; Provisional; Region: PRK15001 357804006772 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 357804006773 S-adenosylmethionine binding site [chemical binding]; other site 357804006774 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 357804006775 Na2 binding site [ion binding]; other site 357804006776 putative substrate binding site 1 [chemical binding]; other site 357804006777 Na binding site 1 [ion binding]; other site 357804006778 putative substrate binding site 2 [chemical binding]; other site 357804006779 Protein of unknown function (DUF1379); Region: DUF1379; pfam07126 357804006780 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 requires...; Region: DHOD_2_like; cd04738 357804006781 quinone interaction residues [chemical binding]; other site 357804006782 Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Region: PyrD; COG0167 357804006783 active site 357804006784 catalytic residues [active] 357804006785 FMN binding site [chemical binding]; other site 357804006786 substrate binding site [chemical binding]; other site 357804006787 mannosyl-3-phosphoglycerate phosphatase; Reviewed; Region: PRK00192 357804006788 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 357804006789 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 357804006790 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804006791 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804006792 Nitrous oxide-stimulated promoter; Region: YgbA_NO; cl08119 357804006793 TIR domain; Region: TIR_2; cl15770 357804006794 hypothetical protein; Provisional; Region: PRK13560 357804006795 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 357804006796 PAS domain; Region: PAS_9; pfam13426 357804006797 putative active site [active] 357804006798 heme pocket [chemical binding]; other site 357804006799 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804006800 metal binding site [ion binding]; metal-binding site 357804006801 active site 357804006802 I-site; other site 357804006803 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 357804006804 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 357804006805 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 357804006806 acetolactate synthase; Reviewed; Region: PRK08322 357804006807 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 357804006808 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, yeast...; Region: GltS_FMN; cd02808 357804006809 active site 357804006810 FMN binding site [chemical binding]; other site 357804006811 substrate binding site [chemical binding]; other site 357804006812 3Fe-4S cluster binding site [ion binding]; other site 357804006813 Transcriptional regulators [Transcription]; Region: MarR; COG1846 357804006814 Helix-turn-helix domains; Region: HTH; cl00088 357804006815 OsmC-like protein; Region: OsmC; cl00767 357804006816 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 357804006817 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 357804006818 Helix-turn-helix domains; Region: HTH; cl00088 357804006819 The C-terminal substrate domain of LysR-type GcdR, TrPI, 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 357804006820 dimerization interface [polypeptide binding]; other site 357804006821 substrate binding pocket [chemical binding]; other site 357804006822 Protein of unknown function (DUF3494); Region: DUF3494; pfam11999 357804006823 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 357804006824 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 357804006825 HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent...; Region: HprK_C; cd01918 357804006826 active site 357804006827 alpha-L-glutamate ligases, RimK family; Region: rimK_fam; TIGR00768 357804006828 ATP-grasp domain; Region: ATP-grasp_4; cl03087 357804006829 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 357804006830 Fasciclin domain; Region: Fasciclin; cl02663 357804006831 Chromate transporter; Region: Chromate_transp; pfam02417 357804006832 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 357804006833 Chromate transporter; Region: Chromate_transp; pfam02417 357804006834 Sulfotransferase family; Region: Sulfotransfer_3; cl14559 357804006835 Uncharacterized small protein (DUF2158); Region: DUF2158; cl02293 357804006836 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 357804006837 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 357804006838 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804006839 Walker A/P-loop; other site 357804006840 ATP binding site [chemical binding]; other site 357804006841 Q-loop/lid; other site 357804006842 ABC transporter signature motif; other site 357804006843 Walker B; other site 357804006844 D-loop; other site 357804006845 H-loop/switch region; other site 357804006846 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 357804006847 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 357804006848 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804006849 Walker A/P-loop; other site 357804006850 ATP binding site [chemical binding]; other site 357804006851 Q-loop/lid; other site 357804006852 ABC transporter signature motif; other site 357804006853 Walker B; other site 357804006854 D-loop; other site 357804006855 H-loop/switch region; other site 357804006856 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 357804006857 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; cl15357 357804006858 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; cl15357 357804006859 NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]; Region: Lig; COG0272 357804006860 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; cl03295 357804006861 nucleotide binding pocket [chemical binding]; other site 357804006862 K-X-D-G motif; other site 357804006863 catalytic site [active] 357804006864 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 357804006865 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 357804006866 Dimer interface [polypeptide binding]; other site 357804006867 Cell division protein [Cell division and chromosome partitioning]; Region: ZipA; COG3115 357804006868 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 357804006869 FtsZ protein binding site [polypeptide binding]; other site 357804006870 Etoposide-induced protein 2.4 (EI24); Region: EI24; cl01126 357804006871 Response regulator receiver domain; Region: Response_reg; pfam00072 357804006872 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 357804006873 active site 357804006874 phosphorylation site [posttranslational modification] 357804006875 intermolecular recognition site; other site 357804006876 dimerization interface [polypeptide binding]; other site 357804006877 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 357804006878 transmembrane helices; other site 357804006879 Response regulator receiver domain; Region: Response_reg; pfam00072 357804006880 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 357804006881 active site 357804006882 phosphorylation site [posttranslational modification] 357804006883 intermolecular recognition site; other site 357804006884 dimerization interface [polypeptide binding]; other site 357804006885 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 357804006886 transmembrane helices; other site 357804006887 aminopeptidase N; Provisional; Region: pepN; PRK14015 357804006888 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 357804006889 active site 357804006890 Zn binding site [ion binding]; other site 357804006891 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 357804006892 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804006893 CoA-ligase; Region: Ligase_CoA; cl02894 357804006894 ATP-grasp domain; Region: ATP-grasp_4; cl03087 357804006895 multidrug efflux protein; Reviewed; Region: PRK01766 357804006896 MatE; Region: MatE; cl10513 357804006897 MatE; Region: MatE; cl10513 357804006898 glycogen synthase; Provisional; Region: glgA; PRK00654 357804006899 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 357804006900 ADP-binding pocket [chemical binding]; other site 357804006901 homodimer interface [polypeptide binding]; other site 357804006902 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin...; Region: mcbC-like_oxidoreductase; cd02142 357804006903 NADPH bind site [chemical binding]; other site 357804006904 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin...; Region: mcbC-like_oxidoreductase; cd02142 357804006905 putative FMN binding site [chemical binding]; other site 357804006906 NADPH bind site [chemical binding]; other site 357804006907 Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond...; Region: LRR_RI; cl15309 357804006908 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 357804006909 Substrate binding site [chemical binding]; other site 357804006910 Leucine rich repeat; Region: LRR_8; pfam13855 357804006911 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 357804006912 active site 357804006913 ATP binding site [chemical binding]; other site 357804006914 substrate binding site [chemical binding]; other site 357804006915 activation loop (A-loop); other site 357804006916 Protein of unknown function (DUF2805); Region: DUF2805; cl11923 357804006917 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; cl02930 357804006918 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 357804006919 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 357804006920 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 357804006921 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 357804006922 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 357804006923 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 357804006924 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 357804006925 glucokinase, proteobacterial type; Region: glk; TIGR00749 357804006926 DNA-binding transcriptional regulator HexR; Provisional; Region: PRK11302 357804006927 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 357804006928 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 phosphate...; Region: SIS_RpiR; cd05013 357804006929 putative active site [active] 357804006930 pyruvate kinase; Provisional; Region: PRK05826 357804006931 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 357804006932 domain interfaces; other site 357804006933 active site 357804006934 Protein of unknown function (DUF1315); Region: DUF1315; cl01215 357804006935 N-terminal Early set domain associated with the catalytic domain of Glycogen debranching enzyme and bacterial isoamylase (also called glycogen 6-glucanohydrolase); Region: E_set_GDE_Isoamylase_N; cd02856 357804006936 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 357804006937 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 357804006938 active site 357804006939 catalytic site [active] 357804006940 glycogen branching enzyme; Provisional; Region: PRK05402 357804006941 Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; Region: E_set; cl09101 357804006942 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 357804006943 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 357804006944 active site 357804006945 catalytic site [active] 357804006946 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; cl02706 357804006947 4-alpha-glucanotransferase; Provisional; Region: malQ; PRK11052 357804006948 4-alpha-glucanotransferase; Region: Glyco_hydro_77; cl00711 357804006949 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 357804006950 active site 357804006951 phosphate binding residues; other site 357804006952 catalytic residues [active] 357804006953 glyceraldehyde-3-phosphate dehydrogenase A; Provisional; Region: gapA; PRK15425 357804006954 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804006955 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 357804006956 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 357804006957 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 357804006958 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 357804006959 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 357804006960 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 ABC; Region: AAA; cd00009 357804006961 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 357804006962 Walker A motif; other site 357804006963 ATP binding site [chemical binding]; other site 357804006964 Walker B motif; other site 357804006965 arginine finger; other site 357804006966 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_19; cd07262 357804006967 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 357804006968 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-; Region: TMP_TenI; cd00564 357804006969 thiamine phosphate binding site [chemical binding]; other site 357804006970 active site 357804006971 pyrophosphate binding site [ion binding]; other site 357804006972 4-methyl-5-beta-hydroxyethylthiazole (Thz) kinase catalyzes the phosphorylation of the hydroxylgroup of Thz. A reaction that allows cells to recycle Thz into the thiamine biosynthesis pathway, as an alternative to its synthesis from cysteine, tyrosine...; Region: THZ_kinase; cd01170 357804006973 substrate binding site [chemical binding]; other site 357804006974 multimerization interface [polypeptide binding]; other site 357804006975 ATP binding site [chemical binding]; other site 357804006976 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; cl15243 357804006977 NMT1/THI5 like; Region: NMT1; pfam09084 357804006978 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 357804006979 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, and...; Region: TM_PBP2; cd06261 357804006980 dimer interface [polypeptide binding]; other site 357804006981 conserved gate region; other site 357804006982 ABC-ATPase subunit interface; other site 357804006983 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 357804006984 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804006985 Walker A/P-loop; other site 357804006986 ATP binding site [chemical binding]; other site 357804006987 Q-loop/lid; other site 357804006988 ABC transporter signature motif; other site 357804006989 Walker B; other site 357804006990 D-loop; other site 357804006991 H-loop/switch region; other site 357804006992 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 357804006993 dimer interface [polypeptide binding]; other site 357804006994 substrate binding site [chemical binding]; other site 357804006995 ATP binding site [chemical binding]; other site 357804006996 Transcriptional regulator [Transcription]; Region: LysR; COG0583 357804006997 Helix-turn-helix domains; Region: HTH; cl00088 357804006998 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 357804006999 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 357804007000 Alpha amylase catalytic domain found in Sucrose isomerases, oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase), dextran glucosidase (also called glucan 1,6-alpha-glucosidase), and related proteins; Region: AmyAc_SI_OligoGlu_DGase; cd11333 357804007001 Ca binding site [ion binding]; other site 357804007002 active site 357804007003 catalytic site [active] 357804007004 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 357804007005 glucokinase, proteobacterial type; Region: glk; TIGR00749 357804007006 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 357804007007 Alpha amylase catalytic domain found in Sucrose isomerases, oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase), dextran glucosidase (also called glucan 1,6-alpha-glucosidase), and related proteins; Region: AmyAc_SI_OligoGlu_DGase; cd11333 357804007008 Ca binding site [ion binding]; other site 357804007009 active site 357804007010 catalytic site [active] 357804007011 Protein of unknown function (DUF3024); Region: DUF3024; pfam11225 357804007012 Predicted NTPase (NACHT family) [Signal transduction mechanisms]; Region: COG5635 357804007013 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804007014 Helix-turn-helix domains; Region: HTH; cl00088 357804007015 Protein of unknown function (DUF2999); Region: DUF2999; pfam11212 357804007016 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 357804007017 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 357804007018 HflX GTPase family; Region: HflX; cd01878 357804007019 G1 box; other site 357804007020 GTP/Mg2+ binding site [chemical binding]; other site 357804007021 Switch I region; other site 357804007022 G2 box; other site 357804007023 G3 box; other site 357804007024 Switch II region; other site 357804007025 G4 box; other site 357804007026 G5 box; other site 357804007027 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 357804007028 haemagglutination activity domain; Region: Haemagg_act; cl05436 357804007029 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 357804007030 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 357804007031 Surface antigen; Region: Bac_surface_Ag; cl03097 357804007032 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 357804007033 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 357804007034 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 357804007035 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 357804007036 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 357804007037 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 357804007038 tetrameric interface [polypeptide binding]; other site 357804007039 NAD binding site [chemical binding]; other site 357804007040 catalytic residues [active] 357804007041 putative acyltransferase; Provisional; Region: PRK05790 357804007042 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 357804007043 dimer interface [polypeptide binding]; other site 357804007044 active site 357804007045 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 357804007046 Prostaglandin dehydrogenases; Region: PGDH; cd05288 357804007047 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 357804007048 NAD(P) binding site [chemical binding]; other site 357804007049 substrate binding site [chemical binding]; other site 357804007050 dimer interface [polypeptide binding]; other site 357804007051 Uncharacterized protein family (UPF0160); Region: UPF0160; cl01749 357804007052 transcriptional regulator PhoU; Provisional; Region: PRK11115 357804007053 PhoU domain; Region: PhoU; pfam01895 357804007054 PhoU domain; Region: PhoU; pfam01895 357804007055 phosphate transporter ATP-binding protein; Provisional; Region: PRK14235 357804007056 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 357804007057 Walker A/P-loop; other site 357804007058 ATP binding site [chemical binding]; other site 357804007059 Q-loop/lid; other site 357804007060 ABC transporter signature motif; other site 357804007061 Walker B; other site 357804007062 D-loop; other site 357804007063 H-loop/switch region; other site 357804007064 Domain of unknown function (DUF3333); Region: DUF3333; pfam11812 357804007065 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, and...; Region: TM_PBP2; cd06261 357804007066 dimer interface [polypeptide binding]; other site 357804007067 conserved gate region; other site 357804007068 putative PBP binding loops; other site 357804007069 ABC-ATPase subunit interface; other site 357804007070 Phosphate ATP-binding cassette transporter; Region: DUF3708; pfam12501 357804007071 phosphate ABC transporter, permease protein PstC; Region: phosphate_pstC; TIGR02138 357804007072 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, and...; Region: TM_PBP2; cd06261 357804007073 dimer interface [polypeptide binding]; other site 357804007074 conserved gate region; other site 357804007075 putative PBP binding loops; other site 357804007076 ABC-ATPase subunit interface; other site 357804007077 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 357804007078 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 357804007079 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-called...; Region: CBS_pair; cl15354 357804007080 FOG: CBS domain [General function prediction only]; Region: COG0517 357804007081 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804007082 metal binding site [ion binding]; metal-binding site 357804007083 active site 357804007084 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 357804007085 exopolyphosphatase; Provisional; Region: PRK10854 357804007086 polyphosphate kinase 1; Region: poly_P_kin; TIGR03705 357804007087 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 357804007088 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 357804007089 Catalytic C-terminal domain, first repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Region: PLDc_EcPPK1_C1_like; cd09164 357804007090 domain interface [polypeptide binding]; other site 357804007091 active site 357804007092 catalytic site [active] 357804007093 Catalytic C-terminal domain, second repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Region: PLDc_EcPPK1_C2_like; cd09167 357804007094 domain interface [polypeptide binding]; other site 357804007095 active site 357804007096 catalytic site [active] 357804007097 Transcriptional regulator [Transcription]; Region: LysR; COG0583 357804007098 Helix-turn-helix domains; Region: HTH; cl00088 357804007099 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 357804007100 dimerization interface [polypeptide binding]; other site 357804007101 allophanate hydrolase; Provisional; Region: PRK08186 357804007102 Amidase; Region: Amidase; cl11426 357804007103 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_7; cd08512 357804007104 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 357804007105 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 357804007106 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, and...; Region: TM_PBP2; cd06261 357804007107 dimer interface [polypeptide binding]; other site 357804007108 conserved gate region; other site 357804007109 ABC-ATPase subunit interface; other site 357804007110 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 357804007111 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, and...; Region: TM_PBP2; cd06261 357804007112 dimer interface [polypeptide binding]; other site 357804007113 conserved gate region; other site 357804007114 putative PBP binding loops; other site 357804007115 ABC-ATPase subunit interface; other site 357804007116 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 357804007117 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 357804007118 Walker A/P-loop; other site 357804007119 ATP binding site [chemical binding]; other site 357804007120 Q-loop/lid; other site 357804007121 ABC transporter signature motif; other site 357804007122 Walker B; other site 357804007123 D-loop; other site 357804007124 H-loop/switch region; other site 357804007125 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 357804007126 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 357804007127 Walker A/P-loop; other site 357804007128 ATP binding site [chemical binding]; other site 357804007129 Q-loop/lid; other site 357804007130 ABC transporter signature motif; other site 357804007131 Walker B; other site 357804007132 D-loop; other site 357804007133 H-loop/switch region; other site 357804007134 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 357804007135 allantoate amidohydrolase; Reviewed; Region: PRK09290 357804007136 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 357804007137 active site 357804007138 metal binding site [ion binding]; metal-binding site 357804007139 dimer interface [polypeptide binding]; other site 357804007140 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 357804007141 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 357804007142 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 357804007143 catalytic residue [active] 357804007144 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 357804007145 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 357804007146 Amidase; Region: Amidase; cl11426 357804007147 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 357804007148 Membrane transport protein; Region: Mem_trans; cl09117 357804007149 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 357804007150 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 357804007151 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 357804007152 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 357804007153 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. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 357804007154 Walker A/P-loop; other site 357804007155 ATP binding site [chemical binding]; other site 357804007156 Q-loop/lid; other site 357804007157 ABC transporter signature motif; other site 357804007158 Walker B; other site 357804007159 D-loop; other site 357804007160 H-loop/switch region; other site 357804007161 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 357804007162 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, and...; Region: TM_PBP2; cd06261 357804007163 dimer interface [polypeptide binding]; other site 357804007164 conserved gate region; other site 357804007165 putative PBP binding loops; other site 357804007166 ABC-ATPase subunit interface; other site 357804007167 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 357804007168 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, and...; Region: TM_PBP2; cd06261 357804007169 dimer interface [polypeptide binding]; other site 357804007170 conserved gate region; other site 357804007171 putative PBP binding loops; other site 357804007172 ABC-ATPase subunit interface; other site 357804007173 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 357804007174 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 inorganic...; Region: PBPb; cd00134 357804007175 substrate binding pocket [chemical binding]; other site 357804007176 membrane-bound complex binding site; other site 357804007177 hinge residues; other site 357804007178 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 357804007179 EamA-like transporter family; Region: EamA; cl01037 357804007180 HAD-superfamily class IIA hydrolase, TIGR01459; Region: HAD-SF-IIA-hyp4 357804007181 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 357804007182 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 357804007183 exonuclease I; Provisional; Region: sbcB; PRK11779 357804007184 N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; Region: ExoI_N; cd06138 357804007185 active site 357804007186 catalytic site [active] 357804007187 substrate binding site [chemical binding]; other site 357804007188 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 357804007189 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 357804007190 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 357804007191 dimer interface [polypeptide binding]; other site 357804007192 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804007193 catalytic residue [active] 357804007194 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 357804007195 dimerization domain swap beta strand [polypeptide binding]; other site 357804007196 regulatory protein interface [polypeptide binding]; other site 357804007197 active site 357804007198 regulatory phosphorylation site [posttranslational modification]; other site 357804007199 phosphoenolpyruvate-protein phosphotransferase; Provisional; Region: PRK11177 357804007200 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 357804007201 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 357804007202 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 357804007203 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 family...; Region: PTS_IIA_glc; cd00210 357804007204 HPr interaction site; other site 357804007205 glycerol kinase (GK) interaction site [polypeptide binding]; other site 357804007206 active site 357804007207 phosphorylation site [posttranslational modification] 357804007208 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 357804007209 ArsC family; Region: ArsC; pfam03960 357804007210 putative catalytic residues [active] 357804007211 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 357804007212 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 357804007213 metal binding site [ion binding]; metal-binding site 357804007214 dimer interface [polypeptide binding]; other site 357804007215 D-alanyl-D-alanine carboxypeptidase; Region: VanY; cl00813 357804007216 PilZ domain; Region: PilZ; cl01260 357804007217 phosphoserine phosphatase; Provisional; Region: serB; PRK11133 357804007218 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 357804007219 motif II; other site 357804007220 Bacterial virulence factor haemolysin; Region: SMP_2; cl11479 357804007221 superoxide dismutase; Provisional; Region: PRK10543 357804007222 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 357804007223 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 357804007224 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 357804007225 putative GSH binding site [chemical binding]; other site 357804007226 catalytic residues [active] 357804007227 DEDDh 3'-5' exonuclease domain of RNase T; Region: RNaseT; cd06134 357804007228 dimer interface [polypeptide binding]; other site 357804007229 catalytic site [active] 357804007230 putative active site [active] 357804007231 putative substrate binding site [chemical binding]; other site 357804007232 hypothetical protein; Provisional; Region: PRK11295 357804007233 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cl00083 357804007234 MAEBL; Provisional; Region: PTZ00121 357804007235 Protein of unknown function (DUF1043); Region: DUF1043; cl11473 357804007236 GTPase YlqF; Reviewed; Region: rbgA; PRK09563 357804007237 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 357804007238 GTP/Mg2+ binding site [chemical binding]; other site 357804007239 G4 box; other site 357804007240 G5 box; other site 357804007241 G1 box; other site 357804007242 Switch I region; other site 357804007243 G2 box; other site 357804007244 G3 box; other site 357804007245 Switch II region; other site 357804007246 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 357804007247 Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial cardiolipin synthase; Region: PLDc_CLS_unchar1_1; cd09156 357804007248 putative active site [active] 357804007249 catalytic site [active] 357804007250 Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin synthase; Region: PLDc_CLS_unchar1_2; cd09162 357804007251 putative active site [active] 357804007252 catalytic site [active] 357804007253 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 357804007254 putative catalytic site [active] 357804007255 putative metal binding site [ion binding]; other site 357804007256 putative phosphate binding site [ion binding]; other site 357804007257 Peptidase M14 Carboxypeptidase T subfamily; Region: M14_CPT; cd03859 357804007258 putative active site [active] 357804007259 Zn binding site [ion binding]; other site 357804007260 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cl00065 357804007261 ATP-grasp domain; Region: ATP-grasp_4; cl03087 357804007262 ATP-grasp domain; Region: ATP-grasp_4; cl03087 357804007263 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 357804007264 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 357804007265 metal binding site [ion binding]; metal-binding site 357804007266 dimer interface [polypeptide binding]; other site 357804007267 DNA topoisomerase III; Provisional; Region: PRK07726 357804007268 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: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 357804007269 active site 357804007270 putative interdomain interaction site [polypeptide binding]; other site 357804007271 putative metal-binding site [ion binding]; other site 357804007272 putative nucleotide binding site [chemical binding]; other site 357804007273 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 DNA...; Region: TOP1Ac; cd00186 357804007274 domain I; other site 357804007275 DNA binding groove [nucleotide binding] 357804007276 phosphate binding site [ion binding]; other site 357804007277 domain II; other site 357804007278 domain III; other site 357804007279 nucleotide binding site [chemical binding]; other site 357804007280 catalytic site [active] 357804007281 domain IV; other site 357804007282 integrase; Provisional; Region: PRK09692 357804007283 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 357804007284 active site 357804007285 Int/Topo IB signature motif; other site 357804007286 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 357804007287 Predicted transcriptional regulator [Transcription]; Region: COG2378 357804007288 WYL domain; Region: WYL; cl14852 357804007289 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 357804007290 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; cl01481 357804007291 SGNH_hydrolase, or GDSL_hydrolase, is 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 active site closely...; Region: SGNH_hydrolase; cd00229 357804007292 active site 357804007293 catalytic triad [active] 357804007294 oxyanion hole [active] 357804007295 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 357804007296 Pseudomonas aeruginosa PA3087 and related proteins, metallophosphatase domain; Region: MPP_PA3087; cd07413 357804007297 active site 357804007298 metal binding site [ion binding]; metal-binding site 357804007299 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; cl00614 357804007300 Predicted transcriptional regulator [Transcription]; Region: COG2378 357804007301 WYL domain; Region: WYL; cl14852 357804007302 AAA domain; Region: AAA_25; pfam13481 357804007303 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804007304 Walker A motif; other site 357804007305 ATP binding site [chemical binding]; other site 357804007306 Walker B motif; other site 357804007307 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4643 357804007308 TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_primases; cd01029 357804007309 active site 357804007310 metal binding site [ion binding]; metal-binding site 357804007311 interdomain interaction site; other site 357804007312 Phage regulatory protein Rha (Phage_pRha); Region: Phage_pRha; cl10713 357804007313 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 357804007314 Restriction endonuclease [Defense mechanisms]; Region: COG3587 357804007315 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804007316 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 357804007317 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; cl16911 357804007318 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; cl16911 357804007319 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; cl16911 357804007320 Domain of unknown function (DUF4391); Region: DUF4391; pfam14335 357804007321 N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; Region: PLDc_N_DEXD_c; cd10311 357804007322 putative active site [active] 357804007323 catalytic site [active] 357804007324 Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]; Region: HepA; COG0553 357804007325 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 357804007326 ATP binding site [chemical binding]; other site 357804007327 putative Mg++ binding site [ion binding]; other site 357804007328 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 357804007329 nucleotide binding region [chemical binding]; other site 357804007330 ATP-binding site [chemical binding]; other site 357804007331 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 357804007332 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 357804007333 ring oligomerisation interface [polypeptide binding]; other site 357804007334 ATP/Mg binding site [chemical binding]; other site 357804007335 stacking interactions; other site 357804007336 hinge regions; other site 357804007337 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. It...; Region: cpn10; cd00320 357804007338 oligomerisation interface [polypeptide binding]; other site 357804007339 mobile loop; other site 357804007340 roof hairpin; other site 357804007341 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 357804007342 integrase; Provisional; Region: PRK09692 357804007343 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 357804007344 active site 357804007345 Int/Topo IB signature motif; other site 357804007346 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 Hsp70s; Region: DnaJ; cd06257 357804007347 HSP70 interaction site [polypeptide binding]; other site 357804007348 CheB methylesterase; Region: CheB_methylest; pfam01339 357804007349 Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism]; Region: GalM; COG2017 357804007350 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 357804007351 active site 357804007352 catalytic residues [active] 357804007353 Transcriptional regulators [Transcription]; Region: PurR; COG1609 357804007354 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 357804007355 DNA binding site [nucleotide binding] 357804007356 domain linker motif; other site 357804007357 Ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors; Region: PBP1_sucrose_transcription_regulator; cd06288 357804007358 putative dimerization interface [polypeptide binding]; other site 357804007359 putative ligand binding site [chemical binding]; other site 357804007360 Endo-beta-mannanase [Carbohydrate transport and metabolism]; Region: COG3934 357804007361 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; cl15381 357804007362 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, and...; Region: TM_PBP2; cl00427 357804007363 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, and...; Region: TM_PBP2; cd06261 357804007364 putative PBP binding loops; other site 357804007365 dimer interface [polypeptide binding]; other site 357804007366 ABC-ATPase subunit interface; other site 357804007367 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 357804007368 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, and...; Region: TM_PBP2; cd06261 357804007369 dimer interface [polypeptide binding]; other site 357804007370 conserved gate region; other site 357804007371 putative PBP binding loops; other site 357804007372 ABC-ATPase subunit interface; other site 357804007373 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 357804007374 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 357804007375 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 357804007376 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 357804007377 Walker A/P-loop; other site 357804007378 ATP binding site [chemical binding]; other site 357804007379 Q-loop/lid; other site 357804007380 ABC transporter signature motif; other site 357804007381 Walker B; other site 357804007382 D-loop; other site 357804007383 H-loop/switch region; other site 357804007384 TOBE domain; Region: TOBE_2; cl01440 357804007385 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]; Region: COG1979 357804007386 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 357804007387 dimer interface [polypeptide binding]; other site 357804007388 active site 357804007389 metal binding site [ion binding]; metal-binding site 357804007390 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]; Region: COG2425 357804007391 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...; Region: VWA_YIEM_type; cd01462 357804007392 metal ion-dependent adhesion site (MIDAS); other site 357804007393 MoxR-like ATPases [General function prediction only]; Region: COG0714 357804007394 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 ABC; Region: AAA; cd00009 357804007395 Walker A motif; other site 357804007396 ATP binding site [chemical binding]; other site 357804007397 Walker B motif; other site 357804007398 arginine finger; other site 357804007399 TIR domain; Region: TIR_2; cl15770 357804007400 Restriction endonuclease; Region: Mrr_cat; cl00516 357804007401 DNA topoisomerase I; Validated; Region: PRK07219 357804007402 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 357804007403 N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; Region: PLDc_N_DEXD_b3; cd09205 357804007404 putative homodimer interface [polypeptide binding]; other site 357804007405 putative active site [active] 357804007406 catalytic site [active] 357804007407 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: HsdR; COG4096 357804007408 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 357804007409 ATP binding site [chemical binding]; other site 357804007410 putative Mg++ binding site [ion binding]; other site 357804007411 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 357804007412 nucleotide binding region [chemical binding]; other site 357804007413 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 (EC...; Region: S24_LexA-like; cd06529 357804007414 Catalytic site [active] 357804007415 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; cl16911 357804007416 Fic family protein [Function unknown]; Region: COG3177 357804007417 Fic/DOC family N-terminal; Region: Fic_N; pfam13784 357804007418 Fic/DOC family; Region: Fic; cl00960 357804007419 CtsZ (cyclic tetrasaccharide-synthesizing enzyme Z) is a bacterial 6-alpha-glucosyltransferase, first identified in Arthrobacter globiformis, that produces cyclic tetrasaccharides together with a closely related enzyme CtsY. CtsZ and CtsY both have a...; Region: GH31_transferase_CtsZ; cd06598 357804007420 putative active site [active] 357804007421 putative catalytic site [active] 357804007422 The family 20 carbohydrate-binding module (CBM20), also known as the starch-binding domain, is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is...; Region: CBM20; cl15347 357804007423 starch-binding site 2 [chemical binding]; other site 357804007424 starch-binding site 1 [chemical binding]; other site 357804007425 Transposase IS200 like; Region: Y1_Tnp; cl00848 357804007426 Protein of unknown function (DUF3081); Region: DUF3081; pfam11280 357804007427 Protein of unknown function (DUF3081); Region: DUF3081; pfam11280 357804007428 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 357804007429 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 357804007430 S-adenosylmethionine binding site [chemical binding]; other site 357804007431 Ferrochelatase; Region: Ferrochelatase; pfam00762 357804007432 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 357804007433 C-terminal domain interface [polypeptide binding]; other site 357804007434 active site 357804007435 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 357804007436 active site 357804007437 N-terminal domain interface [polypeptide binding]; other site 357804007438 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 357804007439 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 357804007440 active site 357804007441 phosphorylation site [posttranslational modification] 357804007442 intermolecular recognition site; other site 357804007443 dimerization interface [polypeptide binding]; other site 357804007444 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. Many...; Region: LuxR_C_like; cd06170 357804007445 DNA binding residues [nucleotide binding] 357804007446 dimerization interface [polypeptide binding]; other site 357804007447 PAS fold; Region: PAS_7; pfam12860 357804007448 PAS fold; Region: PAS_7; pfam12860 357804007449 PAS fold; Region: PAS_4; pfam08448 357804007450 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...; Region: HisKA; cl00080 357804007451 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 357804007452 ATP binding site [chemical binding]; other site 357804007453 Mg2+ binding site [ion binding]; other site 357804007454 G-X-G motif; other site 357804007455 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 357804007456 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 357804007457 active site 357804007458 phosphorylation site [posttranslational modification] 357804007459 intermolecular recognition site; other site 357804007460 dimerization interface [polypeptide binding]; other site 357804007461 Uncharacterized conserved protein [Function unknown]; Region: COG3287 357804007462 FIST N domain; Region: FIST; cl10701 357804007463 FIST C domain; Region: FIST_C; pfam10442 357804007464 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 357804007465 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 357804007466 NAD(P) binding site [chemical binding]; other site 357804007467 catalytic residues [active] 357804007468 ornithine cyclodeaminase; Validated; Region: PRK06141 357804007469 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804007470 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804007471 acetoin reductases; Region: 23BDH; TIGR02415 357804007472 NAD(P) binding site [chemical binding]; other site 357804007473 active site 357804007474 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 357804007475 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 357804007476 DNA-binding site [nucleotide binding]; DNA binding site 357804007477 RNA-binding motif; other site 357804007478 Methyltransferase domain; Region: Methyltransf_31; pfam13847 357804007479 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 357804007480 S-adenosylmethionine binding site [chemical binding]; other site 357804007481 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 357804007482 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 357804007483 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 357804007484 active site 357804007485 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 357804007486 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 357804007487 sugar efflux transporter B; Provisional; Region: PRK15011 357804007488 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 357804007489 putative substrate translocation pore; other site 357804007490 CheB methylesterase; Region: CheB_methylest; pfam01339 357804007491 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 357804007492 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 357804007493 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; cl16911 357804007494 PAS domain; Region: PAS_10; pfam13596 357804007495 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 357804007496 PAS domain; Region: PAS_9; pfam13426 357804007497 putative active site [active] 357804007498 heme pocket [chemical binding]; other site 357804007499 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 357804007500 PAS domain; Region: PAS_9; pfam13426 357804007501 putative active site [active] 357804007502 heme pocket [chemical binding]; other site 357804007503 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804007504 metal binding site [ion binding]; metal-binding site 357804007505 active site 357804007506 I-site; other site 357804007507 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 357804007508 sequence-specific DNA binding site [nucleotide binding]; other site 357804007509 salt bridge; other site 357804007510 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 357804007511 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 357804007512 ATP binding site [chemical binding]; other site 357804007513 putative Mg++ binding site [ion binding]; other site 357804007514 Protein of unknown function (DUF3494); Region: DUF3494; pfam11999 357804007515 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]; Region: COG3593 357804007516 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804007517 Walker A/P-loop; other site 357804007518 ATP binding site [chemical binding]; other site 357804007519 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 357804007520 putative active site [active] 357804007521 putative metal-binding site [ion binding]; other site 357804007522 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 357804007523 HNH endonuclease; Region: HNH_5; pfam14279 357804007524 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 357804007525 Catalytic site; other site 357804007526 Protein of unknown function DUF262; Region: DUF262; cl14890 357804007527 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 357804007528 active site 357804007529 DNA binding site [nucleotide binding] 357804007530 Int/Topo IB signature motif; other site 357804007531 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 357804007532 Uncharacterized proteins involved in stress response, homologs of TerZ and putative cAMP-binding protein CABP1 [Signal transduction mechanisms]; Region: TerZ; COG2310 357804007533 Uncharacterized proteins involved in stress response, similar to tellurium resistance terD; Region: TerD_like; cd06974 357804007534 putative metal binding site [ion binding]; other site 357804007535 Uncharacterized proteins involved in stress response, similar to tellurium resistance terD; Region: TerD_like; cd06974 357804007536 putative metal binding site [ion binding]; other site 357804007537 Protein of unknown function (DUF4236); Region: DUF4236; pfam14020 357804007538 Uncharacterized proteins involved in stress response, similar to tellurium resistance terD; Region: TerD_like; cd06974 357804007539 putative metal binding site [ion binding]; other site 357804007540 Uncharacterized proteins involved in stress response, homologs of TerZ and putative cAMP-binding protein CABP1 [Signal transduction mechanisms]; Region: TerZ; COG2310 357804007541 Uncharacterized proteins involved in stress response, similar to tellurium resistance terD; Region: TerD_like; cd06974 357804007542 putative metal binding site [ion binding]; other site 357804007543 Bacterial PH domain; Region: DUF304; cl01348 357804007544 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 357804007545 FeS/SAM binding site; other site 357804007546 DNA-specific endonuclease I; Provisional; Region: PRK15137 357804007547 Endonuclease I; Region: Endonuclease_1; cl01003 357804007548 Phage integrase, N-terminal SAM-like domain; Region: Phage_integr_N; cl12235 357804007549 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 357804007550 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 357804007551 active site 357804007552 catalytic residues [active] 357804007553 DNA binding site [nucleotide binding] 357804007554 Int/Topo IB signature motif; other site 357804007555 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 357804007556 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 357804007557 Beta-Casp domain; Region: Beta-Casp; cl12567 357804007558 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 357804007559 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 357804007560 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 357804007561 ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: ModA; COG0725 357804007562 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 357804007563 phosphate ABC transporter, permease protein PstC; Region: phosphate_pstC; TIGR02138 357804007564 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, and...; Region: TM_PBP2; cd06261 357804007565 dimer interface [polypeptide binding]; other site 357804007566 conserved gate region; other site 357804007567 putative PBP binding loops; other site 357804007568 ABC-ATPase subunit interface; other site 357804007569 phosphate ABC transporter, permease protein PstA; Region: 3a0107s02c; TIGR00974 357804007570 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, and...; Region: TM_PBP2; cd06261 357804007571 dimer interface [polypeptide binding]; other site 357804007572 conserved gate region; other site 357804007573 putative PBP binding loops; other site 357804007574 ABC-ATPase subunit interface; other site 357804007575 phosphate ABC transporter ATP-binding protein; Provisional; Region: PRK14253 357804007576 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 357804007577 Walker A/P-loop; other site 357804007578 ATP binding site [chemical binding]; other site 357804007579 Q-loop/lid; other site 357804007580 ABC transporter signature motif; other site 357804007581 Walker B; other site 357804007582 D-loop; other site 357804007583 H-loop/switch region; other site 357804007584 DinB superfamily; Region: DinB_2; pfam12867 357804007585 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; cl15394 357804007586 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 357804007587 S-adenosylmethionine binding site [chemical binding]; other site 357804007588 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 357804007589 NMT1-like family; Region: NMT1_2; cl15260 357804007590 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 357804007591 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 357804007592 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...; Region: BCAT_beta_family; cd01557 357804007593 homodimer interface [polypeptide binding]; other site 357804007594 substrate-cofactor binding pocket; other site 357804007595 catalytic residue [active] 357804007596 MarC family integral membrane protein; Region: MarC; cl00919 357804007597 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 357804007598 Helix-turn-helix domains; Region: HTH; cl00088 357804007599 Helix-turn-helix domains; Region: HTH; cl00088 357804007600 Integrase core domain; Region: rve; cl01316 357804007601 Alpha amylase catalytic domain found in sucrose phosphorylase-like proteins (also called sucrose glucosyltransferase, disaccharide glucosyltransferase, and sucrose-phosphate alpha-D glucosyltransferase); Region: AmyAc_Sucrose_phosphorylase-like_1; cd11356 357804007602 trehalose synthase; Region: treS_nterm; TIGR02456 357804007603 active site 357804007604 homodimer interface [polypeptide binding]; other site 357804007605 catalytic site [active] 357804007606 putative glucosyl-3-phosphoglycerate synthase; Provisional; Region: PRK13915 357804007607 mannosyl-3-phosphoglycerate phosphatase; Reviewed; Region: PRK00192 357804007608 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 357804007609 active site 357804007610 motif I; other site 357804007611 motif II; other site 357804007612 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 357804007613 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 357804007614 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 357804007615 active site 357804007616 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 357804007617 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 357804007618 substrate binding site [chemical binding]; other site 357804007619 oxyanion hole (OAH) forming residues; other site 357804007620 trimer interface [polypeptide binding]; other site 357804007621 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804007622 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 357804007623 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 357804007624 3-ketoacyl-CoA thiolase; Reviewed; Region: fadI; PRK08963 357804007625 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 357804007626 dimer interface [polypeptide binding]; other site 357804007627 active site 357804007628 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 357804007629 AMP-binding enzyme; Region: AMP-binding; cl15778 357804007630 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 as...; Region: NfsA_FRP; cd02146 357804007631 dimer interface [polypeptide binding]; other site 357804007632 FMN binding site [chemical binding]; other site 357804007633 NADPH bind site [chemical binding]; other site 357804007634 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 357804007635 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 357804007636 nucleophilic elbow; other site 357804007637 catalytic triad; other site 357804007638 Protein of unknown function (DUF2960); Region: DUF2960; pfam11173 357804007639 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 357804007640 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 357804007641 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 357804007642 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 357804007643 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 357804007644 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 357804007645 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 357804007646 RNA binding surface [nucleotide binding]; other site 357804007647 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 357804007648 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 357804007649 alphaNTD homodimer interface [polypeptide binding]; other site 357804007650 alphaNTD - beta interaction site [polypeptide binding]; other site 357804007651 alphaNTD - beta' interaction site [polypeptide binding]; other site 357804007652 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 357804007653 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 357804007654 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 357804007655 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 357804007656 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804007657 Walker A/P-loop; other site 357804007658 ATP binding site [chemical binding]; other site 357804007659 Q-loop/lid; other site 357804007660 ABC transporter signature motif; other site 357804007661 Walker B; other site 357804007662 D-loop; other site 357804007663 H-loop/switch region; other site 357804007664 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 357804007665 Citrate synthase; Region: Citrate_synt; pfam00285 357804007666 oxalacetate binding site [chemical binding]; other site 357804007667 citrylCoA binding site [chemical binding]; other site 357804007668 coenzyme A binding site [chemical binding]; other site 357804007669 catalytic triad [active] 357804007670 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 357804007671 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 357804007672 putative substrate translocation pore; other site 357804007673 AMMECR1; Region: AMMECR1; cl00911 357804007674 Memo (mediator of ErbB2-driven cell motility) is co-precipitated with the C terminus of ErbB2, a protein involved in cell motility; Region: MEMO_like; cd07361 357804007675 putative ligand binding pocket/active site [active] 357804007676 putative metal binding site [ion binding]; other site 357804007677 chaperone protein DnaJ; Provisional; Region: PRK14299 357804007678 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 Hsp70s; Region: DnaJ; cd06257 357804007679 HSP70 interaction site [polypeptide binding]; other site 357804007680 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 357804007681 substrate binding site [polypeptide binding]; other site 357804007682 dimer interface [polypeptide binding]; other site 357804007683 L,D-transpeptidase; Provisional; Region: PRK10190 357804007684 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 357804007685 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 357804007686 Murein lipoprotein [Cell envelope biogenesis, outer membrane]; Region: COG4238; cl11539 357804007687 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 357804007688 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804007689 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 357804007690 dimer interface [polypeptide binding]; other site 357804007691 active site 357804007692 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; cl00756 357804007693 RecX family; Region: RecX; cl00936 357804007694 DNA repair protein RadA; Provisional; Region: PRK11823 357804007695 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804007696 Walker A motif; other site 357804007697 ATP binding site [chemical binding]; other site 357804007698 Walker B motif; other site 357804007699 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 357804007700 Domain of unknown function (DUF4389); Region: DUF4389; pfam14333 357804007701 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 357804007702 metal binding triad [ion binding]; metal-binding site 357804007703 thioredoxin 2; Provisional; Region: PRK10996 357804007704 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 357804007705 catalytic residues [active] 357804007706 Cupin domain; Region: Cupin_2; cl09118 357804007707 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 357804007708 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 357804007709 nucleotide binding site [chemical binding]; other site 357804007710 homotetrameric interface [polypeptide binding]; other site 357804007711 putative phosphate binding site [ion binding]; other site 357804007712 putative allosteric binding site; other site 357804007713 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; cl16911 357804007714 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804007715 Microcystin-dependent protein [Function unknown]; Region: MdpB; COG4675 357804007716 Phage Tail Collar Domain; Region: Collar; pfam07484 357804007717 Microcystin-dependent protein [Function unknown]; Region: MdpB; COG4675 357804007718 Phage Tail Collar Domain; Region: Collar; pfam07484 357804007719 PEP-CTERM protein sorting domain; Region: PEP_exosort; TIGR02595 357804007720 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 357804007721 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ACT14924; Region: LPLAT_ACT14924-like; cd07986 357804007722 putative acyl-acceptor binding pocket; other site 357804007723 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 357804007724 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 357804007725 homotrimer interaction site [polypeptide binding]; other site 357804007726 putative active site [active] 357804007727 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 357804007728 EamA-like transporter family; Region: EamA; cl01037 357804007729 EamA-like transporter family; Region: EamA; cl01037 357804007730 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 357804007731 Coenzyme A binding pocket [chemical binding]; other site 357804007732 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 357804007733 Major Facilitator Superfamily; Region: MFS_1; pfam07690 357804007734 putative substrate translocation pore; other site 357804007735 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 357804007736 PAS domain S-box; Region: sensory_box; TIGR00229 357804007737 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 357804007738 putative active site [active] 357804007739 heme pocket [chemical binding]; other site 357804007740 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804007741 metal binding site [ion binding]; metal-binding site 357804007742 active site 357804007743 I-site; other site 357804007744 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 357804007745 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 357804007746 Helix-turn-helix domains; Region: HTH; cl00088 357804007747 Helix-turn-helix domains; Region: HTH; cl00088 357804007748 Integrase core domain; Region: rve; cl01316 357804007749 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 357804007750 active site 357804007751 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 the...; Region: Asn_Synthase_B_C; cd01991 357804007752 Ligand Binding Site [chemical binding]; other site 357804007753 Molecular Tunnel; other site 357804007754 Predicted proline hydroxylase [Posttranslational modification, protein turnover, chaperones]; Region: EGL-9; COG3751 357804007755 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 357804007756 Coenzyme PQQ synthesis protein D (PqqD); Region: PqqD; cl05126 357804007757 HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent...; Region: HprK_C; cd01918 357804007758 active site 357804007759 AAA domain; Region: AAA_18; pfam13238 357804007760 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 357804007761 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 357804007762 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804007763 Walker A/P-loop; other site 357804007764 ATP binding site [chemical binding]; other site 357804007765 Q-loop/lid; other site 357804007766 ABC transporter signature motif; other site 357804007767 Walker B; other site 357804007768 D-loop; other site 357804007769 H-loop/switch region; other site 357804007770 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 357804007771 Transposase IS200 like; Region: Y1_Tnp; cl00848 357804007772 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 357804007773 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804007774 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 357804007775 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 industrial...; Region: Aldo_ket_red; cd06660 357804007776 active site 357804007777 catalytic tetrad [active] 357804007778 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 357804007779 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 industrial...; Region: Aldo_ket_red; cd06660 357804007780 active site 357804007781 catalytic tetrad [active] 357804007782 Transcriptional regulator [Transcription]; Region: LysR; COG0583 357804007783 Helix-turn-helix domains; Region: HTH; cl00088 357804007784 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 357804007785 putative effector binding pocket; other site 357804007786 dimerization interface [polypeptide binding]; other site 357804007787 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; cl02930 357804007788 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 357804007789 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 357804007790 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 357804007791 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 357804007792 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 357804007793 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 357804007794 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 357804007795 catalytic triad [active] 357804007796 Putative amidoligase enzyme; Region: Amidoligase_2; pfam12224 357804007797 Protein of unknown function (DUF1348); Region: DUF1348; pfam07080 357804007798 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 357804007799 atypical (a) SDRs, subgroup 5; Region: SDR_a5; cd05243 357804007800 NADH(P)-binding; Region: NAD_binding_10; pfam13460 357804007801 NAD(P) binding site [chemical binding]; other site 357804007802 putative active site [active] 357804007803 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 357804007804 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; cl15357 357804007805 transmembrane helices; other site 357804007806 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 357804007807 Coenzyme A binding pocket [chemical binding]; other site 357804007808 Predicted membrane protein (DUF2254); Region: DUF2254; pfam10011 357804007809 Domain of unknown function; Region: DUF331; cl01149 357804007810 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 357804007811 catalytic residue [active] 357804007812 N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; Region: PLDc_N_DEXD_b2; cd09204 357804007813 PLD-like domain; Region: PLDc_2; pfam13091 357804007814 putative homodimer interface [polypeptide binding]; other site 357804007815 putative active site [active] 357804007816 catalytic site [active] 357804007817 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 357804007818 ATP binding site [chemical binding]; other site 357804007819 putative Mg++ binding site [ion binding]; other site 357804007820 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 357804007821 nucleotide binding region [chemical binding]; other site 357804007822 ATP-binding site [chemical binding]; other site 357804007823 Domain of unknown function (DUF3427); Region: DUF3427; pfam11907 357804007824 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 357804007825 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 (EC...; Region: S24_LexA-like; cd06529 357804007826 Catalytic site [active] 357804007827 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 357804007828 active site 357804007829 8-oxo-dGMP binding site [chemical binding]; other site 357804007830 nudix motif; other site 357804007831 metal binding site [ion binding]; metal-binding site 357804007832 Restriction endonuclease; Region: Mrr_cat; cl00516 357804007833 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 357804007834 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 357804007835 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804007836 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 357804007837 Family description; Region: UvrD_C_2; cl15862 357804007838 Molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: DnaK; COG0443 357804007839 Predicted extracellular nuclease [General function prediction only]; Region: COG2374 357804007840 Lamin Tail Domain; Region: LTD; pfam00932 357804007841 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 357804007842 generic binding surface I; other site 357804007843 generic binding surface II; other site 357804007844 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 357804007845 putative catalytic site [active] 357804007846 putative metal binding site [ion binding]; other site 357804007847 putative phosphate binding site [ion binding]; other site 357804007848 bifunctional UDP-sugar hydrolase/5'-nucleotidase periplasmic precursor; Reviewed; Region: ushA; PRK09558 357804007849 Escherichia coli UshA and related proteins, N-terminal metallophosphatase domain; Region: MPP_UshA_N; cd07405 357804007850 active site 357804007851 metal binding site [ion binding]; metal-binding site 357804007852 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 357804007853 Membrane transport protein; Region: Mem_trans; cl09117 357804007854 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 357804007855 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 357804007856 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 357804007857 DNA-binding site [nucleotide binding]; DNA binding site 357804007858 RNA-binding motif; other site 357804007859 Helix-turn-helix domains; Region: HTH; cl00088 357804007860 Winged helix-turn helix; Region: HTH_29; pfam13551 357804007861 Helix-turn-helix domains; Region: HTH; cl00088 357804007862 Winged helix-turn helix; Region: HTH_33; pfam13592 357804007863 Integrase core domain; Region: rve; cl01316 357804007864 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 357804007865 30S subunit binding site; other site 357804007866 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 357804007867 DNA-binding site [nucleotide binding]; DNA binding site 357804007868 RNA-binding motif; other site 357804007869 NMT1/THI5 like; Region: NMT1; pfam09084 357804007870 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 inorganic...; Region: PBPb; cd00134 357804007871 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 357804007872 substrate binding pocket [chemical binding]; other site 357804007873 membrane-bound complex binding site; other site 357804007874 hinge residues; other site 357804007875 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804007876 metal binding site [ion binding]; metal-binding site 357804007877 active site 357804007878 I-site; other site 357804007879 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 357804007880 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 357804007881 active site 357804007882 motif I; other site 357804007883 motif II; other site 357804007884 PrkA family serine protein kinase; Provisional; Region: PRK15455 357804007885 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 357804007886 Uncharacterized conserved protein [Function unknown]; Region: COG2718 357804007887 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 357804007888 SpoVR family protein; Provisional; Region: PRK11767 357804007889 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 357804007890 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 357804007891 active site 357804007892 metal binding site [ion binding]; metal-binding site 357804007893 AAA domain; Region: AAA_33; pfam13671 357804007894 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804007895 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 357804007896 MatE; Region: MatE; cl10513 357804007897 UbiA prenyltransferase family; Region: UbiA; cl00337 357804007898 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 357804007899 SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring...; Region: SURF1; cd06662 357804007900 Cytochrome c oxidase subunit III. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_III; cd01665 357804007901 Subunit III/VIIa interface [polypeptide binding]; other site 357804007902 Phospholipid binding site [chemical binding]; other site 357804007903 Subunit I/III interface [polypeptide binding]; other site 357804007904 Subunit III/VIb interface [polypeptide binding]; other site 357804007905 Subunit III/VIa interface; other site 357804007906 Subunit III/Vb interface [polypeptide binding]; other site 357804007907 Cytochrome c oxidase assembly protein CtaG/Cox11; Region: CtaG_Cox11; cl01240 357804007908 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 357804007909 Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_I; cd01663 357804007910 Subunit I/III interface [polypeptide binding]; other site 357804007911 D-pathway; other site 357804007912 Subunit I/VIIc interface [polypeptide binding]; other site 357804007913 Subunit I/IV interface [polypeptide binding]; other site 357804007914 Subunit I/II interface [polypeptide binding]; other site 357804007915 Low-spin heme (heme a) binding site [chemical binding]; other site 357804007916 Subunit I/VIIa interface [polypeptide binding]; other site 357804007917 Subunit I/VIa interface [polypeptide binding]; other site 357804007918 Dimer interface; other site 357804007919 Putative water exit pathway; other site 357804007920 Binuclear center (heme a3/CuB) [ion binding]; other site 357804007921 K-pathway; other site 357804007922 Putative proton exit pathway; other site 357804007923 Subunit I/VIb interface; other site 357804007924 Subunit I/VIc interface [polypeptide binding]; other site 357804007925 Electron transfer pathway; other site 357804007926 Subunit I/VIIIb interface [polypeptide binding]; other site 357804007927 Subunit I/VIIb interface [polypeptide binding]; other site 357804007928 cytochrome c oxidase subunit II; Validated; Region: COX2; MTH00023 357804007929 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 357804007930 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 357804007931 Cytochrome c; Region: Cytochrom_C; cl11414 357804007932 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 357804007933 Cytochrome c; Region: Cytochrom_C; cl11414 357804007934 Protein of unknown function (DUF2750); Region: DUF2750; pfam11042 357804007935 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 357804007936 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 357804007937 DsbA family, FrnE subfamily; FrnE is a DsbA-like protein containing a CXXC motif. It is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins; Region: DsbA_FrnE; cd03024 357804007938 catalytic residues [active] 357804007939 Protein of unknown function (DUF496); Region: DUF496; cl09955 357804007940 Phosphopantetheinyl transferase [Coenzyme metabolism]; Region: Sfp; COG2091 357804007941 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 357804007942 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 triad...; Region: Tryp_SPc; cd00190 357804007943 cleavage site 357804007944 active site 357804007945 substrate binding sites [chemical binding]; other site 357804007946 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 357804007947 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 357804007948 ATP binding site [chemical binding]; other site 357804007949 Mg++ binding site [ion binding]; other site 357804007950 motif III; other site 357804007951 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 357804007952 nucleotide binding region [chemical binding]; other site 357804007953 ATP-binding site [chemical binding]; other site 357804007954 DbpA RNA binding domain; Region: DbpA; pfam03880 357804007955 PTS system glucose-specific transporter subunits IIBC; Provisional; Region: PRK11089 357804007956 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; cl00557 357804007957 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 family...; Region: PTS_IIB_glc; cd00212 357804007958 active site turn [active] 357804007959 phosphorylation site [posttranslational modification] 357804007960 glycine cleavage system aminomethyltransferase T; Provisional; Region: gcvT; PRK13579 357804007961 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 357804007962 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 357804007963 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 357804007964 non-specific DNA binding site [nucleotide binding]; other site 357804007965 salt bridge; other site 357804007966 sequence-specific DNA binding site [nucleotide binding]; other site 357804007967 Cupin domain; Region: Cupin_2; cl09118 357804007968 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...; Region: GCS_H; cd06848 357804007969 lipoyl attachment site [posttranslational modification]; other site 357804007970 glycine dehydrogenase; Provisional; Region: PRK05367 357804007971 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:2.1; Region: GDC-P; cd00613 357804007972 tetramer interface [polypeptide binding]; other site 357804007973 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804007974 catalytic residue [active] 357804007975 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:2.1; Region: GDC-P; cd00613 357804007976 tetramer interface [polypeptide binding]; other site 357804007977 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804007978 catalytic residue [active] 357804007979 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 357804007980 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804007981 metal binding site [ion binding]; metal-binding site 357804007982 active site 357804007983 I-site; other site 357804007984 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 357804007985 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804007986 metal binding site [ion binding]; metal-binding site 357804007987 active site 357804007988 I-site; other site 357804007989 Cation efflux family; Region: Cation_efflux; cl00316 357804007990 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 357804007991 Ligand Binding Site [chemical binding]; other site 357804007992 Transcriptional regulator [Transcription]; Region: LysR; COG0583 357804007993 Helix-turn-helix domains; Region: HTH; cl00088 357804007994 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 357804007995 dimerization interface [polypeptide binding]; other site 357804007996 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cl00184 357804007997 substrate binding pocket [chemical binding]; other site 357804007998 active site 357804007999 iron coordination sites [ion binding]; other site 357804008000 hydroxyglutarate oxidase; Provisional; Region: PRK11728 357804008001 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804008002 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 357804008003 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 357804008004 transcriptional regulator protein; Region: phnR; TIGR03337 357804008005 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 357804008006 DNA-binding site [nucleotide binding]; DNA binding site 357804008007 UTRA domain; Region: UTRA; cl01230 357804008008 putative 2-aminoethylphosphonate ABC transporter, permease protein; Region: PhnU2; TIGR03262 357804008009 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, and...; Region: TM_PBP2; cd06261 357804008010 dimer interface [polypeptide binding]; other site 357804008011 conserved gate region; other site 357804008012 putative PBP binding loops; other site 357804008013 ABC-ATPase subunit interface; other site 357804008014 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, and...; Region: TM_PBP2; cd06261 357804008015 dimer interface [polypeptide binding]; other site 357804008016 conserved gate region; other site 357804008017 putative PBP binding loops; other site 357804008018 ABC-ATPase subunit interface; other site 357804008019 putative 2-aminoethylphosphonate ABC transporter, ATP-binding protein; Region: PhnT2; TIGR03265 357804008020 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804008021 Walker A/P-loop; other site 357804008022 ATP binding site [chemical binding]; other site 357804008023 Q-loop/lid; other site 357804008024 ABC transporter signature motif; other site 357804008025 Walker B; other site 357804008026 D-loop; other site 357804008027 H-loop/switch region; other site 357804008028 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 357804008029 ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]; Region: TbpA; COG4143 357804008030 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 357804008031 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 357804008032 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 357804008033 catalytic residue [active] 357804008034 4-aminobutyrate aminotransferase; Provisional; Region: PRK06082 357804008035 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 357804008036 inhibitor-cofactor binding pocket; inhibition site 357804008037 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804008038 catalytic residue [active] 357804008039 phosphonoacetaldehyde hydrolase; Provisional; Region: PRK13478 357804008040 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 357804008041 motif II; other site 357804008042 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 357804008043 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804008044 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 357804008045 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804008046 6-phosphogluconate dehydrogenase; Validated; Region: PRK09287 357804008047 6-phosphogluconate dehydrogenase, C-terminal domain; Region: 6PGD; pfam00393 357804008048 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard...; Region: 6PGL; cd01400 357804008049 putative active site [active] 357804008050 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 357804008051 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 357804008052 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 357804008053 siroheme synthase, N-terminal domain; Region: cysG_Nterm; TIGR01470 357804008054 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804008055 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 357804008056 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 357804008057 Late embryogenesis abundant protein; Region: LEA_2; cl12118 357804008058 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 357804008059 MgtE intracellular N domain; Region: MgtE_N; cl15244 357804008060 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 357804008061 Divalent cation transporter; Region: MgtE; cl00786 357804008062 transcriptional regulator HdfR; Provisional; Region: PRK03601 357804008063 Helix-turn-helix domains; Region: HTH; cl00088 357804008064 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 357804008065 acetate kinase; Region: ackA; TIGR00016 357804008066 Acetokinase family; Region: Acetate_kinase; cl01029 357804008067 pyruvate phosphate dikinase; Provisional; Region: PRK09279 357804008068 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 357804008069 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 357804008070 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 357804008071 Mechanosensitive ion channel; Region: MS_channel; pfam00924 357804008072 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 357804008073 Predicted protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: COG3531 357804008074 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_4; cd06231 357804008075 putative active site [active] 357804008076 Zn binding site [ion binding]; other site 357804008077 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, testis; Region: BFIT_BACH; cd03442 357804008078 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 357804008079 mercuric reductase; Validated; Region: PRK06370 357804008080 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804008081 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 357804008082 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 357804008083 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 357804008084 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG4134 357804008085 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4135 357804008086 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, and...; Region: TM_PBP2; cd06261 357804008087 dimer interface [polypeptide binding]; other site 357804008088 conserved gate region; other site 357804008089 putative PBP binding loops; other site 357804008090 ABC-ATPase subunit interface; other site 357804008091 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: COG4136 357804008092 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804008093 Walker A/P-loop; other site 357804008094 ATP binding site [chemical binding]; other site 357804008095 Q-loop/lid; other site 357804008096 ABC transporter signature motif; other site 357804008097 Walker B; other site 357804008098 D-loop; other site 357804008099 H-loop/switch region; other site 357804008100 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 357804008101 Syd protein (SUKH-2); Region: Syd; cl06405 357804008102 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 357804008103 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 357804008104 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 357804008105 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 357804008106 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 357804008107 Domain of unknown function (DUF3412); Region: DUF3412; pfam11892 357804008108 flap endonuclease-like protein; Provisional; Region: PRK09482 357804008109 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 357804008110 active site 357804008111 metal binding site 1 [ion binding]; metal-binding site 357804008112 putative 5' ssDNA interaction site; other site 357804008113 metal binding site 3; metal-binding site 357804008114 metal binding site 2 [ion binding]; metal-binding site 357804008115 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 357804008116 putative DNA binding site [nucleotide binding]; other site 357804008117 putative metal binding site [ion binding]; other site 357804008118 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804008119 acetoin reductases; Region: 23BDH; TIGR02415 357804008120 NAD(P) binding site [chemical binding]; other site 357804008121 active site 357804008122 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 357804008123 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 357804008124 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 357804008125 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 357804008126 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 357804008127 E3 interaction surface; other site 357804008128 lipoyl attachment site [posttranslational modification]; other site 357804008129 e3 binding domain; Region: E3_binding; pfam02817 357804008130 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 357804008131 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 357804008132 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 357804008133 active site 357804008134 metal binding site [ion binding]; metal-binding site 357804008135 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 357804008136 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 357804008137 tetramer interface [polypeptide binding]; other site 357804008138 TPP-binding site [chemical binding]; other site 357804008139 heterodimer interface [polypeptide binding]; other site 357804008140 phosphorylation loop region [posttranslational modification] 357804008141 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 357804008142 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 357804008143 alpha subunit interface [polypeptide binding]; other site 357804008144 TPP binding site [chemical binding]; other site 357804008145 heterodimer interface [polypeptide binding]; other site 357804008146 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 357804008147 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 357804008148 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 357804008149 tetramerization interface [polypeptide binding]; other site 357804008150 NAD(P) binding site [chemical binding]; other site 357804008151 catalytic residues [active] 357804008152 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 357804008153 A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity...; Region: APP_MetAP; cd01066 357804008154 active site 357804008155 Transcriptional regulators [Transcription]; Region: PurR; COG1609 357804008156 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 357804008157 DNA binding site [nucleotide binding] 357804008158 domain linker motif; other site 357804008159 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 357804008160 dimerization interface [polypeptide binding]; other site 357804008161 ligand binding site [chemical binding]; other site 357804008162 Zinc ribbon domain; Region: CxxC_CxxC_SSSS; cl00993 357804008163 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 357804008164 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 hexoses...; Region: ABC_Carb_Monos_I; cd03216 357804008165 Walker A/P-loop; other site 357804008166 ATP binding site [chemical binding]; other site 357804008167 Q-loop/lid; other site 357804008168 ABC transporter signature motif; other site 357804008169 Walker B; other site 357804008170 D-loop; other site 357804008171 H-loop/switch region; other site 357804008172 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 357804008173 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 357804008174 TM-ABC transporter signature motif; other site 357804008175 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 357804008176 TM-ABC transporter signature motif; other site 357804008177 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Region: PBP1_ABC_sugar_binding_like_8; cd06317 357804008178 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 357804008179 putative ligand binding site [chemical binding]; other site 357804008180 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 357804008181 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 357804008182 ring oligomerisation interface [polypeptide binding]; other site 357804008183 ATP/Mg binding site [chemical binding]; other site 357804008184 stacking interactions; other site 357804008185 hinge regions; other site 357804008186 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 357804008187 2-hydroxyacid dehydrogenase; Provisional; Region: PRK08410 357804008188 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804008189 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 357804008190 HflC protein; Region: hflC; TIGR01932 357804008191 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 357804008192 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 357804008193 HflK protein; Region: hflK; TIGR01933 357804008194 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 357804008195 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 357804008196 Coenzyme A binding pocket [chemical binding]; other site 357804008197 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 357804008198 Major Facilitator Superfamily; Region: MFS_1; pfam07690 357804008199 putative substrate translocation pore; other site 357804008200 Transcriptional regulator [Transcription]; Region: LysR; COG0583 357804008201 Helix-turn-helix domains; Region: HTH; cl00088 357804008202 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 357804008203 dimerization interface [polypeptide binding]; other site 357804008204 osmolarity response regulator; Provisional; Region: ompR; PRK09468 357804008205 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 357804008206 active site 357804008207 phosphorylation site [posttranslational modification] 357804008208 intermolecular recognition site; other site 357804008209 dimerization interface [polypeptide binding]; other site 357804008210 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 and...; Region: trans_reg_C; cd00383 357804008211 DNA binding site [nucleotide binding] 357804008212 nucleoside triphosphate hydrolase domain-containing protein; Reviewed; Region: PRK09270 357804008213 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804008214 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804008215 active site 357804008216 Walker A/P-loop; other site 357804008217 ATP binding site [chemical binding]; other site 357804008218 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 357804008219 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Region: PBP1_ABC_sugar_binding_like_11; cd06321 357804008220 putative ligand binding site [chemical binding]; other site 357804008221 sensory histidine kinase AtoS; Provisional; Region: PRK11360 357804008222 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 357804008223 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...; Region: HisKA; cd00082 357804008224 dimer interface [polypeptide binding]; other site 357804008225 phosphorylation site [posttranslational modification] 357804008226 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 357804008227 ATP binding site [chemical binding]; other site 357804008228 G-X-G motif; other site 357804008229 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 357804008230 active site 357804008231 phosphorylation site [posttranslational modification] 357804008232 intermolecular recognition site; other site 357804008233 dimerization interface [polypeptide binding]; other site 357804008234 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 357804008235 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Region: PBP1_ABC_sugar_binding_like_11; cd06321 357804008236 putative ligand binding site [chemical binding]; other site 357804008237 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 357804008238 TM-ABC transporter signature motif; other site 357804008239 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 357804008240 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 hexoses...; Region: ABC_Carb_Monos_I; cd03216 357804008241 Walker A/P-loop; other site 357804008242 ATP binding site [chemical binding]; other site 357804008243 Q-loop/lid; other site 357804008244 ABC transporter signature motif; other site 357804008245 Walker B; other site 357804008246 D-loop; other site 357804008247 H-loop/switch region; other site 357804008248 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 357804008249 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 357804008250 catalytic core [active] 357804008251 Protein of unknown function (Duf2374); Region: DUF2374; cl09797 357804008252 MoxR-like ATPases [General function prediction only]; Region: COG0714 357804008253 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804008254 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 357804008255 Domain of unknown function (DUF4381); Region: DUF4381; pfam14316 357804008256 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 357804008257 metal ion-dependent adhesion site (MIDAS); other site 357804008258 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 357804008259 metal ion-dependent adhesion site (MIDAS); other site 357804008260 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 357804008261 binding surface 357804008262 Tetratricopeptide repeat; Region: TPR_16; pfam13432 357804008263 TPR motif; other site 357804008264 Oxygen tolerance; Region: BatD; pfam13584 357804008265 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 357804008266 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 inorganic...; Region: PBPb; cd00134 357804008267 substrate binding pocket [chemical binding]; other site 357804008268 membrane-bound complex binding site; other site 357804008269 hinge residues; other site 357804008270 ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]; Region: BatB; COG4597 357804008271 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, and...; Region: TM_PBP2; cl00427 357804008272 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, and...; Region: TM_PBP2; cd06261 357804008273 putative PBP binding loops; other site 357804008274 dimer interface [polypeptide binding]; other site 357804008275 ABC-ATPase subunit interface; other site 357804008276 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, and...; Region: TM_PBP2; cd06261 357804008277 dimer interface [polypeptide binding]; other site 357804008278 conserved gate region; other site 357804008279 putative PBP binding loops; other site 357804008280 ABC-ATPase subunit interface; other site 357804008281 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 357804008282 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. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 357804008283 Walker A/P-loop; other site 357804008284 ATP binding site [chemical binding]; other site 357804008285 Q-loop/lid; other site 357804008286 ABC transporter signature motif; other site 357804008287 Walker B; other site 357804008288 D-loop; other site 357804008289 H-loop/switch region; other site 357804008290 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 357804008291 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 inorganic...; Region: PBPb; cd00134 357804008292 substrate binding pocket [chemical binding]; other site 357804008293 membrane-bound complex binding site; other site 357804008294 hinge residues; other site 357804008295 ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]; Region: BatB; COG4597 357804008296 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, and...; Region: TM_PBP2; cl00427 357804008297 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, and...; Region: TM_PBP2; cd06261 357804008298 putative PBP binding loops; other site 357804008299 dimer interface [polypeptide binding]; other site 357804008300 ABC-ATPase subunit interface; other site 357804008301 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, and...; Region: TM_PBP2; cd06261 357804008302 dimer interface [polypeptide binding]; other site 357804008303 conserved gate region; other site 357804008304 putative PBP binding loops; other site 357804008305 ABC-ATPase subunit interface; other site 357804008306 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 357804008307 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. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 357804008308 Walker A/P-loop; other site 357804008309 ATP binding site [chemical binding]; other site 357804008310 Q-loop/lid; other site 357804008311 ABC transporter signature motif; other site 357804008312 Walker B; other site 357804008313 D-loop; other site 357804008314 H-loop/switch region; other site 357804008315 Putative ATP-dependant zinc protease; Region: Zn_protease; cl01682 357804008316 Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup; Region: M14_ASTE_ASPA_like_1; cd06251 357804008317 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 357804008318 putative active site [active] 357804008319 Zn binding site [ion binding]; other site 357804008320 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 357804008321 ATP-grasp domain; Region: ATP-grasp_4; cl03087 357804008322 Mechanosensitive ion channel; Region: MS_channel; pfam00924 357804008323 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 357804008324 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 357804008325 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, and...; Region: TM_PBP2; cd06261 357804008326 dimer interface [polypeptide binding]; other site 357804008327 conserved gate region; other site 357804008328 putative PBP binding loops; other site 357804008329 ABC-ATPase subunit interface; other site 357804008330 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 357804008331 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, and...; Region: TM_PBP2; cl00427 357804008332 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, and...; Region: TM_PBP2; cd06261 357804008333 ABC-ATPase subunit interface; other site 357804008334 putative PBP binding loops; other site 357804008335 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 357804008336 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 inorganic...; Region: PBPb; cd00134 357804008337 substrate binding pocket [chemical binding]; other site 357804008338 membrane-bound complex binding site; other site 357804008339 hinge residues; other site 357804008340 ABC-type histidine transport system, ATPase component [Amino acid transport and metabolism]; Region: HisP; COG4598 357804008341 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. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 357804008342 Walker A/P-loop; other site 357804008343 ATP binding site [chemical binding]; other site 357804008344 Q-loop/lid; other site 357804008345 ABC transporter signature motif; other site 357804008346 Walker B; other site 357804008347 D-loop; other site 357804008348 H-loop/switch region; other site 357804008349 GPR1/FUN34/yaaH family; Region: Grp1_Fun34_YaaH; cl00685 357804008350 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; cl16911 357804008351 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 357804008352 Acetyl-CoA carboxylase beta subunit [Lipid metabolism]; Region: AccD; COG0777 357804008353 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 357804008354 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 357804008355 ATP-grasp domain; Region: ATP-grasp_4; cl03087 357804008356 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 357804008357 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 357804008358 carboxyltransferase (CT) interaction site; other site 357804008359 biotinylation site [posttranslational modification]; other site 357804008360 Staphylococcal nuclease homologues; Region: SNc; smart00318 357804008361 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 357804008362 Catalytic site; other site 357804008363 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 357804008364 putative deacylase active site [active] 357804008365 Helix-turn-helix domains; Region: HTH; cl00088 357804008366 Glycosyl hydrolase family 1; Region: Glyco_hydro_1; cl01046 357804008367 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 357804008368 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, acyl; Region: Biotinyl_lipoyl_domains; cl11404 357804008369 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, acyl; Region: Biotinyl_lipoyl_domains; cl11404 357804008370 ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]; Region: SunT; COG2274 357804008371 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 357804008372 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 357804008373 Walker A/P-loop; other site 357804008374 ATP binding site [chemical binding]; other site 357804008375 Q-loop/lid; other site 357804008376 ABC transporter signature motif; other site 357804008377 Walker B; other site 357804008378 D-loop; other site 357804008379 H-loop/switch region; other site 357804008380 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 357804008381 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 357804008382 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 357804008383 binding surface 357804008384 TPR motif; other site 357804008385 Sulfotransferase family; Region: Sulfotransfer_3; cl14559 357804008386 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 357804008387 TPR repeat; Region: TPR_11; pfam13414 357804008388 binding surface 357804008389 TPR motif; other site 357804008390 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 357804008391 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 357804008392 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 357804008393 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 357804008394 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 357804008395 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 357804008396 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 357804008397 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 357804008398 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 357804008399 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 357804008400 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 357804008401 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 357804008402 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 357804008403 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 357804008404 Protein of unknown function (DUF3494); Region: DUF3494; pfam11999 357804008405 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 357804008406 DNA-binding site [nucleotide binding]; DNA binding site 357804008407 RNA-binding motif; other site 357804008408 Protein of unknown function (DUF1294); Region: DUF1294; cl01311 357804008409 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 357804008410 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 357804008411 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs); Region: APH_ChoK_like; cd05120 357804008412 active site 357804008413 ATP binding site [chemical binding]; other site 357804008414 Cupin domain; Region: Cupin_2; cl09118 357804008415 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 357804008416 catalytic triad [active] 357804008417 dimer interface [polypeptide binding]; other site 357804008418 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804008419 Flavin Reductases; Region: FlaRed; cl00801 357804008420 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 357804008421 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 357804008422 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 357804008423 Nucleoside recognition; Region: Gate; cl00486 357804008424 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 357804008425 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 357804008426 intersubunit interface [polypeptide binding]; other site 357804008427 active site 357804008428 catalytic residue [active] 357804008429 Sulfatase; Region: Sulfatase; cl10460 357804008430 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 357804008431 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 357804008432 thymidine phosphorylase; Reviewed; Region: deoA; PRK05820 357804008433 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 357804008434 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 357804008435 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; cl06734 357804008436 Bacterial inner membrane protein; Region: Imp-YgjV; pfam10688 357804008437 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 357804008438 active site 357804008439 catalytic motif [active] 357804008440 Zn binding site [ion binding]; other site 357804008441 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 357804008442 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 357804008443 primosome assembly protein PriA; Validated; Region: PRK05580 357804008444 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 357804008445 ATP binding site [chemical binding]; other site 357804008446 putative Mg++ binding site [ion binding]; other site 357804008447 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804008448 Stringent starvation protein B; Region: SspB; cl01120 357804008449 stringent starvation protein A; Provisional; Region: sspA; PRK09481 357804008450 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 357804008451 C-terminal domain interface [polypeptide binding]; other site 357804008452 putative GSH binding site (G-site) [chemical binding]; other site 357804008453 dimer interface [polypeptide binding]; other site 357804008454 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 357804008455 dimer interface [polypeptide binding]; other site 357804008456 N-terminal domain interface [polypeptide binding]; other site 357804008457 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 357804008458 cytochrome b; Provisional; Region: CYTB; MTH00145 357804008459 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 357804008460 Qi binding site; other site 357804008461 intrachain domain interface; other site 357804008462 interchain domain interface [polypeptide binding]; other site 357804008463 heme bH binding site [chemical binding]; other site 357804008464 heme bL binding site [chemical binding]; other site 357804008465 Qo binding site; other site 357804008466 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; cd00290 357804008467 interchain domain interface [polypeptide binding]; other site 357804008468 intrachain domain interface; other site 357804008469 Qi binding site; other site 357804008470 Qo binding site; other site 357804008471 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 357804008472 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 357804008473 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 357804008474 [2Fe-2S] cluster binding site [ion binding]; other site 357804008475 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 357804008476 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 357804008477 23S rRNA interface [nucleotide binding]; other site 357804008478 L3 interface [polypeptide binding]; other site 357804008479 Predicted ATPase [General function prediction only]; Region: COG1485 357804008480 pyruvate kinase; Provisional; Region: PRK09206 357804008481 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 357804008482 domain interfaces; other site 357804008483 active site 357804008484 periplasmic serine pepetdase DegS; Region: protease_degS; TIGR02038 357804008485 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 triad...; Region: Tryp_SPc; cl00149 357804008486 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...; Region: PDZ_serine_protease; cd00987 357804008487 protein binding site [polypeptide binding]; other site 357804008488 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 357804008489 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 357804008490 hinge; other site 357804008491 active site 357804008492 BolA-like protein; Region: BolA; cl00386 357804008493 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 357804008494 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; cl01074 357804008495 mce related protein; Region: MCE; pfam02470 357804008496 Permease; Region: Permease; cl00510 357804008497 putative ABC transporter ATP-binding protein YrbF; Provisional; Region: PRK11831 357804008498 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 357804008499 Walker A/P-loop; other site 357804008500 ATP binding site [chemical binding]; other site 357804008501 Q-loop/lid; other site 357804008502 ABC transporter signature motif; other site 357804008503 Walker B; other site 357804008504 D-loop; other site 357804008505 H-loop/switch region; other site 357804008506 Low specificity phosphatase (HAD superfamily) [General function prediction only]; Region: COG1778 357804008507 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 357804008508 active site 357804008509 motif I; other site 357804008510 motif II; other site 357804008511 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 357804008512 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 357804008513 OstA-like protein; Region: OstA; cl00844 357804008514 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 357804008515 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 357804008516 Walker A/P-loop; other site 357804008517 ATP binding site [chemical binding]; other site 357804008518 Q-loop/lid; other site 357804008519 ABC transporter signature motif; other site 357804008520 Walker B; other site 357804008521 D-loop; other site 357804008522 H-loop/switch region; other site 357804008523 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 357804008524 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 357804008525 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 357804008526 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 357804008527 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 357804008528 active site 357804008529 phosphorylation site [posttranslational modification] 357804008530 P-loop ATPase protein family; Region: ATP_bind_2; cl15794 357804008531 Predicted P-loop-containing kinase [General function prediction only]; Region: COG1660 357804008532 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 357804008533 dimerization domain swap beta strand [polypeptide binding]; other site 357804008534 regulatory protein interface [polypeptide binding]; other site 357804008535 active site 357804008536 regulatory phosphorylation site [posttranslational modification]; other site 357804008537 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 357804008538 MgtE intracellular N domain; Region: MgtE_N; cl15244 357804008539 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 357804008540 Divalent cation transporter; Region: MgtE; cl00786 357804008541 Uncharacterized protein family (UPF0231); Region: UPF0231; cl11474 357804008542 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 and...; Region: trans_reg_C; cd00383 357804008543 DNA binding site [nucleotide binding] 357804008544 Response regulator receiver domain; Region: Response_reg; pfam00072 357804008545 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 357804008546 active site 357804008547 phosphorylation site [posttranslational modification] 357804008548 intermolecular recognition site; other site 357804008549 dimerization interface [polypeptide binding]; other site 357804008550 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 357804008551 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 in...; Region: AcnB_Swivel; cd01576 357804008552 substrate binding site [chemical binding]; other site 357804008553 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 357804008554 substrate binding site [chemical binding]; other site 357804008555 ligand binding site [chemical binding]; other site 357804008556 Peptidase family M48; Region: Peptidase_M48; cl12018 357804008557 2-haloalkanoic acid dehalogenase, type II; Region: HAD_type_II; TIGR01428 357804008558 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 357804008559 motif II; other site 357804008560 putative S-transferase; Provisional; Region: PRK11752 357804008561 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 sources...; Region: GST_N_Ure2p_like; cd03048 357804008562 C-terminal domain interface [polypeptide binding]; other site 357804008563 GSH binding site (G-site) [chemical binding]; other site 357804008564 dimer interface [polypeptide binding]; other site 357804008565 C-terminal, alpha helical domain of Escherichia coli Yghu Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YghU_like; cd10292 357804008566 dimer interface [polypeptide binding]; other site 357804008567 N-terminal domain interface [polypeptide binding]; other site 357804008568 active site 357804008569 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 357804008570 Helix-turn-helix domains; Region: HTH; cl00088 357804008571 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 357804008572 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional; Region: PRK13289 357804008573 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 357804008574 heme-binding site [chemical binding]; other site 357804008575 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 357804008576 FAD binding pocket [chemical binding]; other site 357804008577 FAD binding motif [chemical binding]; other site 357804008578 phosphate binding motif [ion binding]; other site 357804008579 beta-alpha-beta structure motif; other site 357804008580 NAD binding pocket [chemical binding]; other site 357804008581 Domain of unknown function DUF302; Region: DUF302; cl01364 357804008582 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 357804008583 Alpha amylase catalytic domain found in Sucrose isomerases, oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase), dextran glucosidase (also called glucan 1,6-alpha-glucosidase), and related proteins; Region: AmyAc_SI_OligoGlu_DGase; cd11333 357804008584 Ca binding site [ion binding]; other site 357804008585 active site 357804008586 catalytic site [active] 357804008587 Domain of unknown function (DUF3459); Region: DUF3459; pfam11941 357804008588 Transcriptional regulators [Transcription]; Region: PurR; COG1609 357804008589 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 357804008590 DNA binding site [nucleotide binding] 357804008591 domain linker motif; other site 357804008592 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; Region: PBP1_LacI_like_3; cd06279 357804008593 putative dimerization interface [polypeptide binding]; other site 357804008594 putative ligand binding site [chemical binding]; other site 357804008595 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 357804008596 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 357804008597 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, and...; Region: TM_PBP2; cd06261 357804008598 dimer interface [polypeptide binding]; other site 357804008599 conserved gate region; other site 357804008600 putative PBP binding loops; other site 357804008601 ABC-ATPase subunit interface; other site 357804008602 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, and...; Region: TM_PBP2; cd06261 357804008603 dimer interface [polypeptide binding]; other site 357804008604 conserved gate region; other site 357804008605 putative PBP binding loops; other site 357804008606 ABC-ATPase subunit interface; other site 357804008607 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 357804008608 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 357804008609 Walker A/P-loop; other site 357804008610 ATP binding site [chemical binding]; other site 357804008611 Q-loop/lid; other site 357804008612 ABC transporter signature motif; other site 357804008613 Walker B; other site 357804008614 D-loop; other site 357804008615 H-loop/switch region; other site 357804008616 TOBE domain; Region: TOBE_2; cl01440 357804008617 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804008618 metal binding site [ion binding]; metal-binding site 357804008619 active site 357804008620 I-site; other site 357804008621 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 357804008622 LysE type translocator; Region: LysE; cl00565 357804008623 F plasmid transfer operon, TraF, protein; Region: TraF_2; pfam13729 357804008624 putative phosphatase; Provisional; Region: PRK11587 357804008625 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 357804008626 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804008627 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 357804008628 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 357804008629 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 357804008630 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 357804008631 E3 interaction surface; other site 357804008632 lipoyl attachment site [posttranslational modification]; other site 357804008633 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 357804008634 E3 interaction surface; other site 357804008635 lipoyl attachment site [posttranslational modification]; other site 357804008636 e3 binding domain; Region: E3_binding; pfam02817 357804008637 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 357804008638 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 357804008639 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 357804008640 dimer interface [polypeptide binding]; other site 357804008641 TPP-binding site [chemical binding]; other site 357804008642 transcriptional regulator PdhR; Reviewed; Region: pdhR; PRK09464 357804008643 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 357804008644 DNA-binding site [nucleotide binding]; DNA binding site 357804008645 FCD domain; Region: FCD; cl11656 357804008646 gluconate operon transcriptional regulator; Provisional; Region: PRK14987 357804008647 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 357804008648 DNA binding site [nucleotide binding] 357804008649 domain linker motif; other site 357804008650 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 357804008651 putative ligand binding site [chemical binding]; other site 357804008652 putative dimerization interface [polypeptide binding]; other site 357804008653 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 357804008654 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 357804008655 active site 357804008656 intersubunit interface [polypeptide binding]; other site 357804008657 catalytic residue [active] 357804008658 Dehydratase family; Region: ILVD_EDD; cl00340 357804008659 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 357804008660 Gluconate kinase [Carbohydrate transport and metabolism]; Region: GntK; COG3265 357804008661 ATP-binding site [chemical binding]; other site 357804008662 Gluconate-6-phosphate binding site [chemical binding]; other site 357804008663 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 357804008664 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 357804008665 DctM-like transporters; Region: DctM; pfam06808 357804008666 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 357804008667 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 357804008668 Gluconate kinase [Carbohydrate transport and metabolism]; Region: GntK; COG3265 357804008669 ATP-binding site [chemical binding]; other site 357804008670 Gluconate-6-phosphate binding site [chemical binding]; other site 357804008671 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804008672 6-phosphogluconate dehydrogenase; Validated; Region: PRK09287 357804008673 6-phosphogluconate dehydrogenase, C-terminal domain; Region: 6PGD; pfam00393 357804008674 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 357804008675 Amidase; Region: Amidase; cl11426 357804008676 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 357804008677 amidase catalytic site [active] 357804008678 Zn binding residues [ion binding]; other site 357804008679 substrate binding site [chemical binding]; other site 357804008680 MBOAT, membrane-bound O-acyltransferase family; Region: MBOAT; cl00738 357804008681 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 357804008682 active site 357804008683 catalytic residues [active] 357804008684 DNA binding site [nucleotide binding] 357804008685 Int/Topo IB signature motif; other site 357804008686 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 357804008687 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 357804008688 active site 357804008689 catalytic residues [active] 357804008690 DNA binding site [nucleotide binding] 357804008691 Int/Topo IB signature motif; other site 357804008692 GMP synthase; Reviewed; Region: guaA; PRK00074 357804008693 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 357804008694 AMP/PPi binding site [chemical binding]; other site 357804008695 candidate oxyanion hole; other site 357804008696 catalytic triad [active] 357804008697 potential glutamine specificity residues [chemical binding]; other site 357804008698 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 357804008699 ATP Binding subdomain [chemical binding]; other site 357804008700 Ligand Binding sites [chemical binding]; other site 357804008701 Dimerization subdomain; other site 357804008702 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 357804008703 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 357804008704 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 357804008705 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 guanine...; Region: IMPDH; cd00381 357804008706 active site 357804008707 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 357804008708 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...; Region: ExoVII_LU_OBF; cd04489 357804008709 generic binding surface II; other site 357804008710 generic binding surface I; other site 357804008711 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 357804008712 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 357804008713 putative catalytic cysteine [active] 357804008714 gamma-glutamyl kinase; Provisional; Region: PRK05429 357804008715 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 357804008716 nucleotide binding site [chemical binding]; other site 357804008717 homotetrameric interface [polypeptide binding]; other site 357804008718 putative phosphate binding site [ion binding]; other site 357804008719 putative allosteric binding site; other site 357804008720 PUA domain; Region: PUA; cl00607 357804008721 Transcriptional regulator Crl; Region: Crl; cl11653 357804008722 fermentation/respiration switch protein; Reviewed; Region: frsA; PRK05077 357804008723 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 357804008724 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 357804008725 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 357804008726 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 357804008727 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804008728 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; cl15357 357804008729 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 357804008730 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 357804008731 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 357804008732 Walker A/P-loop; other site 357804008733 ATP binding site [chemical binding]; other site 357804008734 Q-loop/lid; other site 357804008735 ABC transporter signature motif; other site 357804008736 Walker B; other site 357804008737 D-loop; other site 357804008738 H-loop/switch region; other site 357804008739 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 357804008740 active site 357804008741 catalytic triad [active] 357804008742 oxyanion hole [active] 357804008743 switch loop; other site 357804008744 tRNA(Ile)-lysidine synthetase; Provisional; Region: tilS; PRK10660 357804008745 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 357804008746 Ligand Binding Site [chemical binding]; other site 357804008747 TilS substrate binding domain; Region: TilS; pfam09179 357804008748 B3/4 domain; Region: B3_4; cl11458 357804008749 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 357804008750 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 357804008751 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 contains...; Region: DnaE_OBF; cd04485 357804008752 generic binding surface II; other site 357804008753 generic binding surface I; other site 357804008754 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 357804008755 RNA/DNA hybrid binding site [nucleotide binding]; other site 357804008756 active site 357804008757 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 357804008758 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 357804008759 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 357804008760 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 biosynthetic...; Region: LbH_UDP-GlcNAc_AT; cd03351 357804008761 active site 357804008762 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 357804008763 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 357804008764 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 357804008765 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; Region: LbH_LpxD; cd03352 357804008766 trimer interface [polypeptide binding]; other site 357804008767 active site 357804008768 UDP-GlcNAc binding site [chemical binding]; other site 357804008769 lipid binding site [chemical binding]; lipid-binding site 357804008770 periplasmic chaperone; Provisional; Region: PRK10780 357804008771 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 357804008772 outer membrane protein assembly factor YaeT; Provisional; Region: PRK11067 357804008773 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 357804008774 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 357804008775 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 357804008776 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 357804008777 Surface antigen; Region: Bac_surface_Ag; cl03097 357804008778 zinc metallopeptidase RseP; Provisional; Region: PRK10779 357804008779 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 357804008780 active site 357804008781 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 PDZ...; Region: PDZ_metalloprotease; cd00989 357804008782 protein binding site [polypeptide binding]; other site 357804008783 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 357804008784 putative substrate binding region [chemical binding]; other site 357804008785 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 357804008786 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 357804008787 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 357804008788 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 357804008789 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 357804008790 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 357804008791 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 357804008792 catalytic residue [active] 357804008793 putative FPP diphosphate binding site; other site 357804008794 putative FPP binding hydrophobic cleft; other site 357804008795 dimer interface [polypeptide binding]; other site 357804008796 putative IPP diphosphate binding site; other site 357804008797 ribosome recycling factor; Reviewed; Region: frr; PRK00083 357804008798 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 357804008799 hinge region; other site 357804008800 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 and...; Region: AAK_UMPK-PyrH-Ec; cd04254 357804008801 putative nucleotide binding site [chemical binding]; other site 357804008802 uridine monophosphate binding site [chemical binding]; other site 357804008803 homohexameric interface [polypeptide binding]; other site 357804008804 elongation factor Ts; Provisional; Region: tsf; PRK09377 357804008805 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 357804008806 Elongation factor TS; Region: EF_TS; pfam00889 357804008807 Elongation factor TS; Region: EF_TS; pfam00889 357804008808 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 357804008809 rRNA interaction site [nucleotide binding]; other site 357804008810 S8 interaction site; other site 357804008811 putative laminin-1 binding site; other site 357804008812 Protein of unknown function DUF262; Region: DUF262; cl14890 357804008813 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cl00195 357804008814 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 357804008815 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 357804008816 DNA-binding site [nucleotide binding]; DNA binding site 357804008817 FCD domain; Region: FCD; cl11656 357804008818 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 357804008819 active site 357804008820 phosphorylation site [posttranslational modification] 357804008821 intermolecular recognition site; other site 357804008822 dimerization interface [polypeptide binding]; other site 357804008823 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. Many...; Region: LuxR_C_like; cd06170 357804008824 DNA binding residues [nucleotide binding] 357804008825 dimerization interface [polypeptide binding]; other site 357804008826 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 357804008827 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...; Region: HisKA; cd00082 357804008828 dimer interface [polypeptide binding]; other site 357804008829 phosphorylation site [posttranslational modification] 357804008830 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 357804008831 ATP binding site [chemical binding]; other site 357804008832 Mg2+ binding site [ion binding]; other site 357804008833 G-X-G motif; other site 357804008834 Response regulator receiver domain; Region: Response_reg; pfam00072 357804008835 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 357804008836 active site 357804008837 phosphorylation site [posttranslational modification] 357804008838 intermolecular recognition site; other site 357804008839 dimerization interface [polypeptide binding]; other site 357804008840 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 357804008841 Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF); Region: PBP1_FmdD_like; cd06355 357804008842 putative ligand binding site [chemical binding]; other site 357804008843 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 357804008844 TM-ABC transporter signature motif; other site 357804008845 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 357804008846 TM-ABC transporter signature motif; other site 357804008847 urea ABC transporter, ATP-binding protein UrtD; Region: urea_trans_UrtD; TIGR03411 357804008848 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 357804008849 Walker A/P-loop; other site 357804008850 ATP binding site [chemical binding]; other site 357804008851 Q-loop/lid; other site 357804008852 ABC transporter signature motif; other site 357804008853 Walker B; other site 357804008854 D-loop; other site 357804008855 H-loop/switch region; other site 357804008856 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 357804008857 urea ABC transporter, ATP-binding protein UrtE; Region: urea_trans_UrtE; TIGR03410 357804008858 Walker A/P-loop; other site 357804008859 ATP binding site [chemical binding]; other site 357804008860 Q-loop/lid; other site 357804008861 ABC transporter signature motif; other site 357804008862 Walker B; other site 357804008863 D-loop; other site 357804008864 H-loop/switch region; other site 357804008865 UreD urease accessory protein; Region: UreD; cl00530 357804008866 Urease gamma-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use...; Region: Urease_gamma; cd00390 357804008867 alpha-gamma subunit interface [polypeptide binding]; other site 357804008868 beta-gamma subunit interface [polypeptide binding]; other site 357804008869 Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of...; Region: Urease_beta; cd00407 357804008870 gamma-beta subunit interface [polypeptide binding]; other site 357804008871 alpha-beta subunit interface [polypeptide binding]; other site 357804008872 urease subunit alpha; Reviewed; Region: ureC; PRK13207 357804008873 Urease alpha-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, fungi and plants. Their primary role is to allow the use of...; Region: Urease_alpha; cd00375 357804008874 subunit interactions [polypeptide binding]; other site 357804008875 active site 357804008876 flap region; other site 357804008877 urease accessory protein UreE; Provisional; Region: PRK14113 357804008878 UreE urease accessory protein. UreE is a metallochaperone assisting the insertion of a Ni2+ ion in the active site of urease, an important step in the in vivo assembly of urease, an enzyme that hydrolyses urea into ammonia and carbamic acid. The...; Region: UreE; cd00571 357804008879 dimer interface [polypeptide binding]; other site 357804008880 catalytic residues [active] 357804008881 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 357804008882 UreF; Region: UreF; pfam01730 357804008883 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804008884 Transposase IS200 like; Region: Y1_Tnp; cl00848 357804008885 Inorganic H+ pyrophosphatase; Region: H_PPase; pfam03030 357804008886 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 357804008887 Zn2+ binding site [ion binding]; other site 357804008888 Mg2+ binding site [ion binding]; other site 357804008889 shikimate 5-dehydrogenase; Reviewed; Region: PRK12550 357804008890 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 357804008891 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 357804008892 shikimate binding site; other site 357804008893 NAD(P) binding site [chemical binding]; other site 357804008894 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 357804008895 active site 357804008896 PII uridylyl-transferase; Provisional; Region: PRK05007 357804008897 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 357804008898 metal binding triad; other site 357804008899 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 357804008900 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 357804008901 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 357804008902 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 357804008903 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 357804008904 ABC Carbohydrate and Solute Transporters-like subgroup. This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family...; Region: ABC_Carb_Solutes_like; cd03259 357804008905 Walker A/P-loop; other site 357804008906 ATP binding site [chemical binding]; other site 357804008907 Q-loop/lid; other site 357804008908 ABC transporter signature motif; other site 357804008909 Walker B; other site 357804008910 D-loop; other site 357804008911 H-loop/switch region; other site 357804008912 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 357804008913 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, and...; Region: TM_PBP2; cd06261 357804008914 dimer interface [polypeptide binding]; other site 357804008915 conserved gate region; other site 357804008916 putative PBP binding loops; other site 357804008917 ABC-ATPase subunit interface; other site 357804008918 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, and...; Region: TM_PBP2; cl00427 357804008919 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 357804008920 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 357804008921 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 357804008922 putative active site [active] 357804008923 putative catalytic site [active] 357804008924 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 357804008925 active site 357804008926 dimer interface [polypeptide binding]; other site 357804008927 tetratricopeptide repeat protein; Provisional; Region: PRK11788 357804008928 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 357804008929 binding surface 357804008930 TPR motif; other site 357804008931 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 357804008932 binding surface 357804008933 TPR motif; other site 357804008934 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804008935 Protein of unknown function (DUF1049); Region: DUF1049; cl01539 357804008936 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...; Region: HU_IHF; cd00591 357804008937 IHF dimer interface [polypeptide binding]; other site 357804008938 IHF - DNA interface [nucleotide binding]; other site 357804008939 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 357804008940 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 consists...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 357804008941 RNA binding site [nucleotide binding]; other site 357804008942 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 consists...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 357804008943 RNA binding site [nucleotide binding]; other site 357804008944 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 357804008945 RNA binding site [nucleotide binding]; other site 357804008946 S1_RPS1_repeat_ec4: 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_ec4; cd05689 357804008947 RNA binding site [nucleotide binding]; other site 357804008948 S1_RPS1_repeat_ec5: 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_ec5; cd05690 357804008949 RNA binding site [nucleotide binding]; other site 357804008950 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 357804008951 RNA binding site [nucleotide binding]; other site 357804008952 cytidylate kinase; Provisional; Region: cmk; PRK00023 357804008953 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 357804008954 CMP-binding site; other site 357804008955 The sites determining sugar specificity; other site 357804008956 VacJ like lipoprotein; Region: VacJ; cl01073 357804008957 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 357804008958 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 357804008959 Cytochrome C biogenesis protein; Region: CcmH; cl01179 357804008960 thiol:disulfide interchange protein DsbE; Provisional; Region: PRK15412 357804008961 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 357804008962 catalytic residues [active] 357804008963 central insert; other site 357804008964 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 357804008965 CcmE; Region: CcmE; cl00994 357804008966 Heme exporter protein D (CcmD); Region: CcmD; cl11475 357804008967 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 357804008968 CcmB protein; Region: CcmB; cl01016 357804008969 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13538 357804008970 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). CcmE...; Region: ABC_CcmA_heme_exporter; cd03231 357804008971 Walker A/P-loop; other site 357804008972 ATP binding site [chemical binding]; other site 357804008973 Q-loop/lid; other site 357804008974 ABC transporter signature motif; other site 357804008975 Walker B; other site 357804008976 D-loop; other site 357804008977 H-loop/switch region; other site 357804008978 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 357804008979 Nitrogen regulatory protein P-II; Region: P-II; cl00412 357804008980 Nitrogen regulatory protein P-II; Region: P-II; smart00938 357804008981 D-alanyl-D-alanine carboxypeptidase fraction A; Provisional; Region: PRK10793 357804008982 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 357804008983 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; cl06814 357804008984 Protein of unknown function (DUF493); Region: DUF493; cl01102 357804008985 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 357804008986 lipoyl synthase; Provisional; Region: PRK05481 357804008987 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 357804008988 FeS/SAM binding site; other site 357804008989 1-aminocyclopropane-1-carboxylate deaminase [Amino acid transport and metabolism]; Region: Acd; COG2515 357804008990 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), tryptophan...; Region: Trp-synth-beta_II; cl00342 357804008991 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 357804008992 catalytic residue [active] 357804008993 16S ribosomal RNA m2G1207 methyltransferase; Provisional; Region: rsmC; PRK09489 357804008994 Methyltransferase small domain N-terminal; Region: MTS_N; pfam08468 357804008995 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 357804008996 S-adenosylmethionine binding site [chemical binding]; other site 357804008997 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00844 357804008998 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 357804008999 ligand binding site; other site 357804009000 oligomer interface; other site 357804009001 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...; Region: LbH_G1P_AT_C; cd04651 357804009002 N-terminal domain interface [polypeptide binding]; other site 357804009003 sulfate 1 binding site; other site 357804009004 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00844 357804009005 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 357804009006 ligand binding site; other site 357804009007 oligomer interface; other site 357804009008 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...; Region: LbH_G1P_AT_C; cd04651 357804009009 dimer interface [polypeptide binding]; other site 357804009010 N-terminal domain interface [polypeptide binding]; other site 357804009011 sulfate 1 binding site; other site 357804009012 glycogen synthase; Provisional; Region: glgA; PRK00654 357804009013 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 357804009014 ADP-binding pocket [chemical binding]; other site 357804009015 homodimer interface [polypeptide binding]; other site 357804009016 helicase 45; Provisional; Region: PTZ00424 357804009017 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 357804009018 ATP binding site [chemical binding]; other site 357804009019 Mg++ binding site [ion binding]; other site 357804009020 motif III; other site 357804009021 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 357804009022 nucleotide binding region [chemical binding]; other site 357804009023 ATP-binding site [chemical binding]; other site 357804009024 Protein of unknown function (DUF328); Region: DUF328; cl01143 357804009025 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 357804009026 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804009027 Walker A motif; other site 357804009028 ATP binding site [chemical binding]; other site 357804009029 Walker B motif; other site 357804009030 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 357804009031 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 357804009032 Walker A motif; other site 357804009033 ATP binding site [chemical binding]; other site 357804009034 Walker B motif; other site 357804009035 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 357804009036 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 357804009037 catalytic residue [active] 357804009038 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 357804009039 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804009040 YGGT family; Region: YGGT; cl00508 357804009041 YGGT family; Region: YGGT; cl00508 357804009042 Uncharacterized ACR, YggU family COG1872; Region: DUF167; cl00811 357804009043 Domain of unknown function (DUF4426); Region: DUF4426; pfam14467 357804009044 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...; Region: HAM1; cd00515 357804009045 active site 357804009046 dimerization interface [polypeptide binding]; other site 357804009047 HemN family oxidoreductase; Provisional; Region: PRK05660 357804009048 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 357804009049 FeS/SAM binding site; other site 357804009050 HemN C-terminal domain; Region: HemN_C; pfam06969 357804009051 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 357804009052 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 357804009053 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804009054 Mechanosensitive ion channel; Region: MS_channel; pfam00924 357804009055 Hydroxypyruvate isomerase [Carbohydrate transport and metabolism]; Region: Hfi; COG3622 357804009056 putative fimbrial outer membrane usher protein SteB; Provisional; Region: PRK15273 357804009057 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 357804009058 Protein of unknown function (DUF3308); Region: DUF3308; cl14675 357804009059 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 357804009060 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 357804009061 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 357804009062 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 357804009063 Probable transposase; Region: OrfB_IS605; pfam01385 357804009064 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 357804009065 putative fimbrial protein TcfA; Provisional; Region: PRK15308 357804009066 fimbrial outer membrane usher protein TcfC; Provisional; Region: PRK15310 357804009067 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 357804009068 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 357804009069 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 357804009070 N-terminal Early set domain associated with the catalytic domain of Glycogen debranching enzyme and bacterial isoamylase (also called glycogen 6-glucanohydrolase); Region: E_set_GDE_Isoamylase_N; cd02856 357804009071 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 357804009072 active site 357804009073 catalytic site [active] 357804009074 Uncharacterized ACR, YggU family COG1872; Region: DUF167; cl00811 357804009075 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 357804009076 putative acyl-acceptor binding pocket; other site 357804009077 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 357804009078 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct...; Region: Trunc_globin; cd00454 357804009079 apolar tunnel; other site 357804009080 heme binding site [chemical binding]; other site 357804009081 dimerization interface [polypeptide binding]; other site 357804009082 CHASE3 domain; Region: CHASE3; cl05000 357804009083 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 357804009084 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804009085 metal binding site [ion binding]; metal-binding site 357804009086 active site 357804009087 I-site; other site 357804009088 Transthyretin-like family; Region: DUF290; pfam01060 357804009089 Lipid A 3-O-deacylase (PagL); Region: PagL; pfam09411 357804009090 MiaE tRNA-modifying nonheme diiron monooxygenase, ferritin-like diiron-binding domain; Region: MiaE; cd07910 357804009091 active site 357804009092 dinuclear metal binding site [ion binding]; other site 357804009093 dimerization interface [polypeptide binding]; other site 357804009094 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804009095 metal binding site [ion binding]; metal-binding site 357804009096 active site 357804009097 I-site; other site 357804009098 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG3687 357804009099 Predicted metal-dependent hydrolase; Region: Metal_hydrol; pfam10118 357804009100 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 357804009101 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family; Region: PQQ_membr_DH; TIGR03074 357804009102 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 357804009103 Membrane-bound PQQ-dependent glucose dehydrogenase; Region: PQQ_mGDH; cd10280 357804009104 Trp docking motif [polypeptide binding]; other site 357804009105 putative active site [active] 357804009106 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 357804009107 FMN binding site [chemical binding]; other site 357804009108 active site 357804009109 substrate binding site [chemical binding]; other site 357804009110 catalytic residue [active] 357804009111 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 357804009112 Helix-turn-helix domains; Region: HTH; cl00088 357804009113 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804009114 metal binding site [ion binding]; metal-binding site 357804009115 active site 357804009116 I-site; other site 357804009117 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 357804009118 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 357804009119 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 357804009120 putative substrate translocation pore; other site 357804009121 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 357804009122 Sensors of blue-light using FAD; Region: BLUF; cl04855 357804009123 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 357804009124 DNA-binding site [nucleotide binding]; DNA binding site 357804009125 RNA-binding motif; other site 357804009126 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 357804009127 Major Facilitator Superfamily; Region: MFS_1; pfam07690 357804009128 putative substrate translocation pore; other site 357804009129 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 357804009130 DNA-binding site [nucleotide binding]; DNA binding site 357804009131 RNA-binding motif; other site 357804009132 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 357804009133 Predicted ATPase [General function prediction only]; Region: COG3899 357804009134 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804009135 Tetratricopeptide repeat; Region: TPR_12; pfam13424 357804009136 TniQ; Region: TniQ; pfam06527 357804009137 AAA domain; Region: AAA_22; pfam13401 357804009138 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804009139 Integrase core domain; Region: rve; cl01316 357804009140 TnsA endonuclease N terminal; Region: Tn7_Tnp_TnsA_N; cl07370 357804009141 HNH endonuclease; Region: HNH_5; pfam14279 357804009142 Superfamily II RNA helicase [DNA replication, recombination, and repair]; Region: COG4581 357804009143 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 357804009144 ATP binding site [chemical binding]; other site 357804009145 putative Mg++ binding site [ion binding]; other site 357804009146 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804009147 Domain of unknown function (DUF1837); Region: DUF1837; pfam08878 357804009148 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 357804009149 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 357804009150 HI0933-like protein; Region: HI0933_like; pfam03486 357804009151 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804009152 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK10902 357804009153 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 357804009154 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 357804009155 SlyX; Region: SlyX; cl01090 357804009156 PilX N-terminal; Region: PilX_N; pfam14341 357804009157 acetyl-CoA synthetase; Provisional; Region: PRK00174 357804009158 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 357804009159 AMP-binding enzyme; Region: AMP-binding; cl15778 357804009160 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 357804009161 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 357804009162 active site 357804009163 trimer interface [polypeptide binding]; other site 357804009164 dimer interface [polypeptide binding]; other site 357804009165 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 357804009166 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 357804009167 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 also...; Region: DUS_like_FMN; cd02801 357804009168 FMN binding site [chemical binding]; other site 357804009169 active site 357804009170 catalytic residues [active] 357804009171 substrate binding site [chemical binding]; other site 357804009172 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 ABC; Region: AAA; cd00009 357804009173 Walker A motif; other site 357804009174 ATP binding site [chemical binding]; other site 357804009175 Walker B motif; other site 357804009176 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 357804009177 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 357804009178 Transposase; Region: DEDD_Tnp_IS110; pfam01548 357804009179 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 357804009180 CheB methylesterase; Region: CheB_methylest; pfam01339 357804009181 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 357804009182 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 357804009183 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; cl16911 357804009184 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 357804009185 Protein of unknown function (DUF904); Region: DUF904; cl11531 357804009186 PAS domain; Region: PAS_10; pfam13596 357804009187 PAS domain S-box; Region: sensory_box; TIGR00229 357804009188 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 357804009189 PAS domain; Region: PAS_9; pfam13426 357804009190 putative active site [active] 357804009191 heme pocket [chemical binding]; other site 357804009192 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804009193 metal binding site [ion binding]; metal-binding site 357804009194 active site 357804009195 I-site; other site 357804009196 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 357804009197 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; cl00159 357804009198 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 357804009199 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 357804009200 Protein of unknown function, DUF462; Region: DUF462; cl01190 357804009201 YfcL protein; Region: YfcL; pfam08891 357804009202 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 357804009203 PAS domain; Region: PAS_9; pfam13426 357804009204 putative active site [active] 357804009205 heme pocket [chemical binding]; other site 357804009206 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804009207 metal binding site [ion binding]; metal-binding site 357804009208 active site 357804009209 I-site; other site 357804009210 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 357804009211 riboflavin synthase subunit alpha; Provisional; Region: PRK13020 357804009212 Lumazine binding domain; Region: Lum_binding; pfam00677 357804009213 Lumazine binding domain; Region: Lum_binding; pfam00677 357804009214 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_12; cd04670 357804009215 nudix motif; other site 357804009216 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 357804009217 DctM-like transporters; Region: DctM; pfam06808 357804009218 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 357804009219 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT1; COG4663 357804009220 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 357804009221 Membrane transport protein; Region: Mem_trans; cl09117 357804009222 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4676 357804009223 Uncharacterized protein conserved in bacteria (DUF2135); Region: DUF2135; pfam09906 357804009224 short chain dehydrogenase; Validated; Region: PRK06182 357804009225 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 357804009226 NADP binding site [chemical binding]; other site 357804009227 active site 357804009228 steroid binding site; other site 357804009229 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 357804009230 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 357804009231 catalytic residues [active] 357804009232 hinge region; other site 357804009233 alpha helical domain; other site 357804009234 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 357804009235 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 357804009236 Walker A/P-loop; other site 357804009237 ATP binding site [chemical binding]; other site 357804009238 Q-loop/lid; other site 357804009239 ABC transporter signature motif; other site 357804009240 Walker B; other site 357804009241 D-loop; other site 357804009242 H-loop/switch region; other site 357804009243 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 357804009244 Walker A/P-loop; other site 357804009245 ATP binding site [chemical binding]; other site 357804009246 Q-loop/lid; other site 357804009247 ABC transporter signature motif; other site 357804009248 Walker B; other site 357804009249 D-loop; other site 357804009250 H-loop/switch region; other site 357804009251 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 357804009252 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 357804009253 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, and...; Region: TM_PBP2; cd06261 357804009254 dimer interface [polypeptide binding]; other site 357804009255 conserved gate region; other site 357804009256 putative PBP binding loops; other site 357804009257 ABC-ATPase subunit interface; other site 357804009258 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 357804009259 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, and...; Region: TM_PBP2; cl00427 357804009260 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 357804009261 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 357804009262 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_4; cd08500 357804009263 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 357804009264 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 357804009265 Uncharacterized proteins of the AP superfamily [General function prediction only]; Region: COG1524 357804009266 DOMON-like domain of an uncharacterized protein family; Region: DOMON_like_cytochrome; cd09625 357804009267 putative ligand binding site [chemical binding]; other site 357804009268 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-terminal...; Region: MIP; cl00200 357804009269 Asn-Pro-Ala signature motifs; other site 357804009270 glycerol kinase; Provisional; Region: glpK; PRK00047 357804009271 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 357804009272 N- and C-terminal domain interface [polypeptide binding]; other site 357804009273 active site 357804009274 MgATP binding site [chemical binding]; other site 357804009275 catalytic site [active] 357804009276 metal binding site [ion binding]; metal-binding site 357804009277 glycerol binding site [chemical binding]; other site 357804009278 homotetramer interface [polypeptide binding]; other site 357804009279 homodimer interface [polypeptide binding]; other site 357804009280 FBP binding site [chemical binding]; other site 357804009281 protein IIAGlc interface [polypeptide binding]; other site 357804009282 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 357804009283 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 357804009284 Predicted small integral membrane protein (DUF2160); Region: DUF2160; cl02294 357804009285 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 357804009286 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, and...; Region: TM_PBP2; cd06261 357804009287 dimer interface [polypeptide binding]; other site 357804009288 conserved gate region; other site 357804009289 putative PBP binding loops; other site 357804009290 ABC-ATPase subunit interface; other site 357804009291 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 357804009292 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, and...; Region: TM_PBP2; cd06261 357804009293 putative PBP binding loops; other site 357804009294 dimer interface [polypeptide binding]; other site 357804009295 ABC-ATPase subunit interface; other site 357804009296 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 357804009297 ABC Carbohydrate and Solute Transporters-like subgroup. This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family...; Region: ABC_Carb_Solutes_like; cd03259 357804009298 Walker A/P-loop; other site 357804009299 ATP binding site [chemical binding]; other site 357804009300 Q-loop/lid; other site 357804009301 ABC transporter signature motif; other site 357804009302 Walker B; other site 357804009303 D-loop; other site 357804009304 H-loop/switch region; other site 357804009305 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 357804009306 ABC Carbohydrate and Solute Transporters-like subgroup. This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family...; Region: ABC_Carb_Solutes_like; cd03259 357804009307 Walker A/P-loop; other site 357804009308 ATP binding site [chemical binding]; other site 357804009309 Q-loop/lid; other site 357804009310 ABC transporter signature motif; other site 357804009311 Walker B; other site 357804009312 D-loop; other site 357804009313 H-loop/switch region; other site 357804009314 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 357804009315 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and 4-amino-4-deoxychorismate...; Region: PLPDE_IV; cl00224 357804009316 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 ABC; Region: AAA; cd00009 357804009317 Walker A motif; other site 357804009318 ATP binding site [chemical binding]; other site 357804009319 Walker B motif; other site 357804009320 arginine finger; other site 357804009321 Helix-turn-helix domains; Region: HTH; cl00088 357804009322 DNA-binding transcriptional repressor GlpR; Provisional; Region: PRK10906 357804009323 Helix-turn-helix domains; Region: HTH; cl00088 357804009324 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 357804009325 glycerophosphodiester phosphodiesterase; Provisional; Region: glpQ; PRK11143 357804009326 Glycerophosphodiester phosphodiesterase domain of Escherichia coli (GlpQ) and similar proteins; Region: GDPD_EcGlpQ_like; cd08600 357804009327 active site 357804009328 catalytic site [active] 357804009329 metal binding site [ion binding]; metal-binding site 357804009330 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 357804009331 active site 357804009332 metal binding site [ion binding]; metal-binding site 357804009333 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 357804009334 metal binding site 2 [ion binding]; metal-binding site 357804009335 putative DNA binding helix; other site 357804009336 metal binding site 1 [ion binding]; metal-binding site 357804009337 dimer interface [polypeptide binding]; other site 357804009338 structural Zn2+ binding site [ion binding]; other site 357804009339 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 357804009340 active site 357804009341 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 357804009342 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, acyl; Region: Biotinyl_lipoyl_domains; cl11404 357804009343 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 357804009344 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, acyl; Region: Biotinyl_lipoyl_domains; cl11404 357804009345 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, acyl; Region: Biotinyl_lipoyl_domains; cl11404 357804009346 Domain of unknown function (DUF4347); Region: DUF4347; pfam14252 357804009347 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 357804009348 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, acyl; Region: Biotinyl_lipoyl_domains; cl11404 357804009349 Outer membrane efflux protein; Region: OEP; pfam02321 357804009350 Outer membrane efflux protein; Region: OEP; pfam02321 357804009351 DNA polymerase I; Provisional; Region: PRK05755 357804009352 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 357804009353 active site 357804009354 metal binding site 1 [ion binding]; metal-binding site 357804009355 putative 5' ssDNA interaction site; other site 357804009356 metal binding site 3; metal-binding site 357804009357 metal binding site 2 [ion binding]; metal-binding site 357804009358 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 357804009359 putative DNA binding site [nucleotide binding]; other site 357804009360 putative metal binding site [ion binding]; other site 357804009361 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 357804009362 active site 357804009363 catalytic site [active] 357804009364 substrate binding site [chemical binding]; other site 357804009365 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 357804009366 active site 357804009367 DNA binding site [nucleotide binding] 357804009368 catalytic site [active] 357804009369 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 357804009370 putative acyl-acceptor binding pocket; other site 357804009371 FMN reductase; Validated; Region: fre; PRK08051 357804009372 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, FMN; Region: flavin_oxioreductase; cd06189 357804009373 FAD binding pocket [chemical binding]; other site 357804009374 FAD binding motif [chemical binding]; other site 357804009375 phosphate binding motif [ion binding]; other site 357804009376 beta-alpha-beta structure motif; other site 357804009377 NAD binding pocket [chemical binding]; other site 357804009378 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 357804009379 transcription termination factor Rho; Provisional; Region: rho; PRK09376 357804009380 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 357804009381 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 mRNA...; Region: Rho_CSD; cd04459 357804009382 RNA binding site [nucleotide binding]; other site 357804009383 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 the...; Region: rho_factor; cd01128 357804009384 multimer interface [polypeptide binding]; other site 357804009385 Walker A motif; other site 357804009386 ATP binding site [chemical binding]; other site 357804009387 Walker B motif; other site 357804009388 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 357804009389 catalytic residues [active] 357804009390 ATP-dependent RNA helicase RhlB; Provisional; Region: PRK04837 357804009391 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 357804009392 ATP binding site [chemical binding]; other site 357804009393 Mg++ binding site [ion binding]; other site 357804009394 motif III; other site 357804009395 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 357804009396 nucleotide binding region [chemical binding]; other site 357804009397 ATP-binding site [chemical binding]; other site 357804009398 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 357804009399 Helix-turn-helix domains; Region: HTH; cl00088 357804009400 Winged helix-turn helix; Region: HTH_29; pfam13551 357804009401 Helix-turn-helix domains; Region: HTH; cl00088 357804009402 Winged helix-turn helix; Region: HTH_33; pfam13592 357804009403 Integrase core domain; Region: rve; cl01316 357804009404 Protein of unknown function (DUF1255); Region: DUF1255; cl01202 357804009405 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 357804009406 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804009407 Walker A/P-loop; other site 357804009408 ATP binding site [chemical binding]; other site 357804009409 Q-loop/lid; other site 357804009410 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 facilitated...; Region: ABCF_EF-3; cd03221 357804009411 ABC transporter; Region: ABC_tran_2; pfam12848 357804009412 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 facilitated...; Region: ABCF_EF-3; cd03221 357804009413 Probable metal-binding protein (DUF2387); Region: DUF2387; cl01410 357804009414 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 357804009415 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 357804009416 pimelyl-[acyl-carrier protein] methyl ester esterase; Region: bioH; TIGR01738 357804009417 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 357804009418 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 357804009419 active site 357804009420 Fe/S biogenesis protein NfuA; Provisional; Region: PRK11190 357804009421 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 357804009422 NifU-like domain; Region: NifU; cl00484 357804009423 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 357804009424 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 357804009425 ATP binding site [chemical binding]; other site 357804009426 Mg++ binding site [ion binding]; other site 357804009427 motif III; other site 357804009428 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 357804009429 nucleotide binding region [chemical binding]; other site 357804009430 ATP-binding site [chemical binding]; other site 357804009431 DbpA RNA binding domain; Region: DbpA; pfam03880 357804009432 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK09451 357804009433 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 357804009434 Substrate binding site; other site 357804009435 Mg++ binding site; other site 357804009436 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 357804009437 active site 357804009438 substrate binding site [chemical binding]; other site 357804009439 CoA binding site [chemical binding]; other site 357804009440 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 NAD...; Region: NAD_synthase; cd00553 357804009441 NAD synthase; Region: NAD_synthase; pfam02540 357804009442 NAD binding pocket [chemical binding]; other site 357804009443 ATP binding pocket [chemical binding]; other site 357804009444 Mg binding site [ion binding]; other site 357804009445 active-site loop [active] 357804009446 homodimer interface [polypeptide binding]; other site 357804009447 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 357804009448 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804009449 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 357804009450 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 357804009451 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804009452 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 357804009453 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 357804009454 SecA binding site; other site 357804009455 Preprotein binding site; other site 357804009456 Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the...; Region: GRX_GRXb_1_3_like; cd03418 357804009457 GSH binding site [chemical binding]; other site 357804009458 catalytic residues [active] 357804009459 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 357804009460 active site residue [active] 357804009461 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 357804009462 Sulfatase; Region: Sulfatase; cl10460 357804009463 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 357804009464 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 357804009465 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 357804009466 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; cl16911 357804009467 tRNA-dihydrouridine synthase B; Provisional; Region: PRK10415 357804009468 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 also...; Region: DUS_like_FMN; cd02801 357804009469 FMN binding site [chemical binding]; other site 357804009470 active site 357804009471 catalytic residues [active] 357804009472 substrate binding site [chemical binding]; other site 357804009473 Helix-turn-helix domains; Region: HTH; cl00088 357804009474 Protein of unknown function (DUF416); Region: DUF416; cl01166 357804009475 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...; Region: HU_IHF; cd00591 357804009476 IHF dimer interface [polypeptide binding]; other site 357804009477 IHF - DNA interface [nucleotide binding]; other site 357804009478 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 357804009479 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 357804009480 ATP-grasp domain; Region: ATP-grasp_4; cl03087 357804009481 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 357804009482 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 357804009483 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...; Region: IMPCH; cd01421 357804009484 purine monophosphate binding site [chemical binding]; other site 357804009485 dimer interface [polypeptide binding]; other site 357804009486 putative catalytic residues [active] 357804009487 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 357804009488 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 357804009489 methyltransferase, MtaA/CmuA family; Region: mtaA_cmuA; TIGR01463 357804009490 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 reaction...; Region: URO-D; cd00717 357804009491 substrate binding site [chemical binding]; other site 357804009492 active site 357804009493 NADH pyrophosphatase; Reviewed; Region: nudC; PRK00241 357804009494 NADH pyrophosphatase-like rudimentary NUDIX domain; Region: NUDIX-like; pfam09296 357804009495 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 357804009496 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 357804009497 putative NADH binding site [chemical binding]; other site 357804009498 putative active site [active] 357804009499 nudix motif; other site 357804009500 putative metal binding site [ion binding]; other site 357804009501 Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ; Region: Rsd_AlgQ; cl11478 357804009502 putative peptidase; Provisional; Region: PRK11649 357804009503 S-adenosylmethionine synthetase; Validated; Region: PRK05250 357804009504 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 357804009505 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 357804009506 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 357804009507 hypothetical protein; Provisional; Region: PRK04860 357804009508 SprT homologues; Region: SprT; cl01182 357804009509 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 357804009510 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 357804009511 ribosomal-protein-alanine N-acetyltransferase; Provisional; Region: rimI; PRK09491 357804009512 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 357804009513 Coenzyme A binding pocket [chemical binding]; other site 357804009514 DNA polymerase III psi subunit; Region: DNA_III_psi; cl11436 357804009515 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GlpA; COG0578 357804009516 trehalose repressor; Provisional; Region: treR; PRK09492 357804009517 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 357804009518 DNA binding site [nucleotide binding] 357804009519 domain linker motif; other site 357804009520 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 357804009521 dimerization interface [polypeptide binding]; other site 357804009522 ligand binding site [chemical binding]; other site 357804009523 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 357804009524 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...; Region: AdSS; cd03108 357804009525 GDP-binding site [chemical binding]; other site 357804009526 ACT binding site; other site 357804009527 IMP binding site; other site 357804009528 FtsH protease regulator HflC; Provisional; Region: PRK11029 357804009529 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 357804009530 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 357804009531 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 357804009532 HflK protein; Region: hflK; TIGR01933 357804009533 GTPase HflX; Provisional; Region: PRK11058 357804009534 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 357804009535 HflX GTPase family; Region: HflX; cd01878 357804009536 G1 box; other site 357804009537 GTP/Mg2+ binding site [chemical binding]; other site 357804009538 Switch I region; other site 357804009539 G2 box; other site 357804009540 G3 box; other site 357804009541 Switch II region; other site 357804009542 G4 box; other site 357804009543 G5 box; other site 357804009544 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 357804009545 Sm1 motif; other site 357804009546 intra - hexamer interaction site; other site 357804009547 inter - hexamer interaction site [polypeptide binding]; other site 357804009548 nucleotide binding pocket [chemical binding]; other site 357804009549 Sm2 motif; other site 357804009550 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 357804009551 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804009552 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 357804009553 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 357804009554 ATP binding site [chemical binding]; other site 357804009555 Mg2+ binding site [ion binding]; other site 357804009556 G-X-G motif; other site 357804009557 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 357804009558 ATP binding site [chemical binding]; other site 357804009559 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 357804009560 AMIN domain; Region: AMIN; pfam11741 357804009561 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 357804009562 active site 357804009563 metal binding site [ion binding]; metal-binding site 357804009564 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 357804009565 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 357804009566 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 357804009567 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 357804009568 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 357804009569 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 357804009570 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 357804009571 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 357804009572 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 357804009573 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 357804009574 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 357804009575 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 357804009576 putative carbohydrate kinase; Provisional; Region: PRK10565 357804009577 YjeF-related protein N-terminus; Region: YjeF_N; cl00318 357804009578 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 357804009579 putative substrate binding site [chemical binding]; other site 357804009580 putative ATP binding site [chemical binding]; other site 357804009581 Uncharacterized Fe-S protein [Energy production and conversion]; Region: COG1600 357804009582 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 357804009583 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 357804009584 Protein of unknown function (DUF2750); Region: DUF2750; pfam11042 357804009585 Helix-turn-helix domains; Region: HTH; cl00088 357804009586 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 357804009587 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 357804009588 dimerization interface [polypeptide binding]; other site 357804009589 PilX N-terminal; Region: PilX_N; pfam14341 357804009590 Protein of unknown function (DUF3494); Region: DUF3494; pfam11999 357804009591 PilX N-terminal; Region: PilX_N; pfam14341 357804009592 PilX N-terminal; Region: PilX_N; pfam14341 357804009593 Protein of unknown function (DUF3494); Region: DUF3494; pfam11999 357804009594 PilX N-terminal; Region: PilX_N; pfam14341 357804009595 Protein of unknown function (DUF3494); Region: DUF3494; pfam11999 357804009596 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 357804009597 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 357804009598 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 357804009599 Tfp pilus assembly protein PilV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilV; COG4967 357804009600 Type II transport protein GspH; Region: GspH; pfam12019 357804009601 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 357804009602 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 357804009603 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 357804009604 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 357804009605 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 357804009606 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 357804009607 LabA_like proteins; Region: LabA; cd10911 357804009608 putative metal binding site [ion binding]; other site 357804009609 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 357804009610 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 357804009611 ATP binding site [chemical binding]; other site 357804009612 Mg++ binding site [ion binding]; other site 357804009613 motif III; other site 357804009614 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 357804009615 nucleotide binding region [chemical binding]; other site 357804009616 ATP-binding site [chemical binding]; other site 357804009617 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 357804009618 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804009619 Walker A/P-loop; other site 357804009620 ATP binding site [chemical binding]; other site 357804009621 Q-loop/lid; other site 357804009622 ABC transporter signature motif; other site 357804009623 Walker B; other site 357804009624 D-loop; other site 357804009625 H-loop/switch region; other site 357804009626 ABC transporter; Region: ABC_tran_2; pfam12848 357804009627 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 facilitated...; Region: ABCF_EF-3; cd03221 357804009628 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 357804009629 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 industrial...; Region: Aldo_ket_red; cd06660 357804009630 active site 357804009631 catalytic tetrad [active] 357804009632 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 357804009633 Clp amino terminal domain; Region: Clp_N; pfam02861 357804009634 Clp amino terminal domain; Region: Clp_N; pfam02861 357804009635 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 ABC; Region: AAA; cd00009 357804009636 Walker A motif; other site 357804009637 ATP binding site [chemical binding]; other site 357804009638 Walker B motif; other site 357804009639 arginine finger; other site 357804009640 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 ABC; Region: AAA; cd00009 357804009641 Walker A motif; other site 357804009642 ATP binding site [chemical binding]; other site 357804009643 Walker B motif; other site 357804009644 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 357804009645 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 357804009646 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 357804009647 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 357804009648 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 357804009649 RNA binding surface [nucleotide binding]; other site 357804009650 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 357804009651 active site 357804009652 Outer membrane lipoprotein; Region: YfiO; pfam13525 357804009653 Nitrogen regulatory protein P-II; Region: P-II; cl00412 357804009654 Nitrogen regulatory protein P-II; Region: P-II; smart00938 357804009655 LytB protein; Region: LYTB; cl00507 357804009656 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 357804009657 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 357804009658 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 357804009659 lipoprotein signal peptidase; Provisional; Region: PRK14787 357804009660 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 357804009661 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 357804009662 active site 357804009663 HIGH motif; other site 357804009664 nucleotide binding site [chemical binding]; other site 357804009665 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 357804009666 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 357804009667 active site 357804009668 KMSKS motif; other site 357804009669 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 357804009670 tRNA binding surface [nucleotide binding]; other site 357804009671 anticodon binding site; other site 357804009672 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 357804009673 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 357804009674 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 357804009675 active site 357804009676 Riboflavin kinase; Region: Flavokinase; cl03312 357804009677 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 357804009678 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 357804009679 Domain of unknown function (DUF4404); Region: DUF4404; pfam14357 357804009680 poxB regulator PoxA; Provisional; Region: PRK09350 357804009681 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 attaches...; Region: class_II_aaRS-like_core; cl00268 357804009682 motif 1; other site 357804009683 dimer interface [polypeptide binding]; other site 357804009684 active site 357804009685 motif 2; other site 357804009686 motif 3; other site 357804009687 fumarate reductase flavoprotein subunit; Validated; Region: PRK09231 357804009688 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804009689 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 357804009690 fumarate reductase iron-sulfur subunit; Provisional; Region: PRK12385 357804009691 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; cl00159 357804009692 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 357804009693 D-subunit interface [polypeptide binding]; other site 357804009694 Iron-sulfur protein interface; other site 357804009695 proximal quinone binding site [chemical binding]; other site 357804009696 distal quinone binding site [chemical binding]; other site 357804009697 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 357804009698 Iron-sulfur protein interface; other site 357804009699 proximal quinone binding site [chemical binding]; other site 357804009700 C-subunit interface; other site 357804009701 distal quinone binding site; other site 357804009702 elongation factor P; Validated; Region: PRK00529 357804009703 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 357804009704 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...; Region: S1_EF-P_repeat_1; cd04470 357804009705 RNA binding site [nucleotide binding]; other site 357804009706 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...; Region: S1_EF-P_repeat_2; cd05794 357804009707 RNA binding site [nucleotide binding]; other site 357804009708 Lysine 2,3-aminomutase [Amino acid transport and metabolism]; Region: KamA; COG1509 357804009709 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; cl15377 357804009710 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 357804009711 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 357804009712 active site 357804009713 motif I; other site 357804009714 motif II; other site 357804009715 outer membrane lipoprotein; Reviewed; Region: rcsF; PRK10781 357804009716 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 357804009717 homodimer interaction site [polypeptide binding]; other site 357804009718 cofactor binding site; other site 357804009719 Rhomboid family; Region: Rhomboid; cl11446 357804009720 prolyl-tRNA synthetase; Provisional; Region: PRK09194 357804009721 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 of...; Region: ProRS_core_prok; cd00779 357804009722 dimer interface [polypeptide binding]; other site 357804009723 motif 1; other site 357804009724 active site 357804009725 motif 2; other site 357804009726 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...; Region: ProRS-INS; cd04334 357804009727 putative deacylase active site [active] 357804009728 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 attaches...; Region: class_II_aaRS-like_core; cl00268 357804009729 active site 357804009730 motif 3; other site 357804009731 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-binding; Region: ProRS_anticodon_short; cd00861 357804009732 anticodon binding site; other site 357804009733 lysophospholipase L2; Provisional; Region: PRK10749 357804009734 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 357804009735 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 357804009736 putative hydrolase; Provisional; Region: PRK10976 357804009737 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 357804009738 active site 357804009739 motif I; other site 357804009740 motif II; other site 357804009741 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 357804009742 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 357804009743 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 4) [Cell envelope biogenesis, outer membrane]; Region: DacB; COG2027 357804009744 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 357804009745 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 357804009746 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804009747 aspartate carbamoyltransferase regulatory subunit; Reviewed; Region: PRK00893 357804009748 Aspartate carbamoyltransferase regulatory chain, allosteric domain; Region: PyrI; pfam01948 357804009749 Aspartate carbamoyltransferase regulatory chain, metal binding domain; Region: PyrI_C; pfam02748 357804009750 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 357804009751 Protein of unknown function (DUF904); Region: DUF904; cl11531 357804009752 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 357804009753 serine acetyltransferase; Provisional; Region: cysE; PRK11132 357804009754 Serine acetyltransferase, N-terminal; Region: SATase_N; cl05762 357804009755 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...; Region: LbH_SAT; cd03354 357804009756 trimer interface [polypeptide binding]; other site 357804009757 active site 357804009758 substrate binding site [chemical binding]; other site 357804009759 CoA binding site [chemical binding]; other site 357804009760 Cation efflux family; Region: Cation_efflux; cl00316 357804009761 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 357804009762 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 357804009763 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 357804009764 DHH family; Region: DHH; pfam01368 357804009765 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 357804009766 active site 357804009767 DHHA1 domain; Region: DHHA1; pfam02272 357804009768 protein disulfide isomerase II DsbC; Provisional; Region: PRK10877 357804009769 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 bonds...; Region: DsbA_DsbC_DsbG; cd03020 357804009770 dimerization domain [polypeptide binding]; other site 357804009771 dimer interface [polypeptide binding]; other site 357804009772 catalytic residues [active] 357804009773 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 357804009774 XerD and XerC integrases, DNA breaking-rejoining enzymes, 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...; Region: INT_XerDC; cd00798 357804009775 active site 357804009776 Int/Topo IB signature motif; other site 357804009777 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 357804009778 Formate/nitrite transporter; Region: Form_Nir_trans; cl00927 357804009779 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 357804009780 Pyruvate formate lyase 1; Region: PFL1; cd01678 357804009781 coenzyme A binding site [chemical binding]; other site 357804009782 active site 357804009783 catalytic residues [active] 357804009784 glycine loop; other site 357804009785 pyruvate formate lyase-activating enzyme 1; Provisional; Region: pflA; PRK11145 357804009786 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 357804009787 FeS/SAM binding site; other site 357804009788 23S rRNA methyltransferase A; Provisional; Region: rrmA; PRK11088 357804009789 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 357804009790 S-adenosylmethionine binding site [chemical binding]; other site 357804009791 Protein of unknown function, DUF412; Region: DUF412; cl01183 357804009792 acetate kinase; Region: ackA; TIGR00016 357804009793 Acetokinase family; Region: Acetate_kinase; cl01029 357804009794 phosphate acetyltransferase; Reviewed; Region: PRK05632 357804009795 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804009796 DRTGG domain; Region: DRTGG; cl12147 357804009797 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 357804009798 S-adenosylmethionine-dependent methyltransferase; Region: Methyltrans_SAM; pfam10672 357804009799 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 357804009800 S-adenosylmethionine binding site [chemical binding]; other site 357804009801 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 357804009802 bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional; Region: PRK13805 357804009803 Coenzyme A acylating aldehyde dehydrogenase (ACDH), ALDH family 20-like; Region: ALDH_F20_ACDH; cd07122 357804009804 putative catalytic cysteine [active] 357804009805 C-terminal alcohol dehydrogenase domain of the acetaldehyde dehydrogenase-alcohol dehydrogenase bifunctional two-domain protein (AAD); Region: AAD_C; cd08178 357804009806 putative active site [active] 357804009807 metal binding site [ion binding]; metal-binding site 357804009808 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 357804009809 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 357804009810 Catalytic domain, repeat 1, of Escherichia coli cardiolipin synthase and similar proteins; Region: PLDc_EcCLS_like_1; cd09152 357804009811 putative active site [active] 357804009812 catalytic site [active] 357804009813 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase and similar proteins; Region: PLDc_EcCLS_like_2; cd09158 357804009814 putative active site [active] 357804009815 catalytic site [active] 357804009816 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 357804009817 PAS fold; Region: PAS_4; pfam08448 357804009818 aerobic respiration control sensor protein ArcB; Provisional; Region: PRK11091 357804009819 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 357804009820 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 357804009821 PAS domain; Region: PAS_9; pfam13426 357804009822 putative active site [active] 357804009823 heme pocket [chemical binding]; other site 357804009824 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804009825 metal binding site [ion binding]; metal-binding site 357804009826 active site 357804009827 I-site; other site 357804009828 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 357804009829 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 357804009830 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 357804009831 dimerization interface [polypeptide binding]; other site 357804009832 ATP binding site [chemical binding]; other site 357804009833 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 357804009834 dimerization interface [polypeptide binding]; other site 357804009835 ATP binding site [chemical binding]; other site 357804009836 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 357804009837 putative active site [active] 357804009838 catalytic triad [active] 357804009839 membrane-bound lytic transglycosylase F; Provisional; Region: PRK10859 357804009840 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 inorganic...; Region: PBPb; cd00134 357804009841 substrate binding pocket [chemical binding]; other site 357804009842 membrane-bound complex binding site; other site 357804009843 hinge residues; other site 357804009844 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 357804009845 N-acetyl-D-glucosamine binding site [chemical binding]; other site 357804009846 catalytic residue [active] 357804009847 HEAT repeats; Region: HEAT_2; pfam13646 357804009848 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(II)...; Region: Pep_deformylase; cd00487 357804009849 active site 357804009850 catalytic residues [active] 357804009851 metal binding site [ion binding]; metal-binding site 357804009852 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 357804009853 nucleoside/Zn binding site; other site 357804009854 dimer interface [polypeptide binding]; other site 357804009855 catalytic motif [active] 357804009856 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 357804009857 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 357804009858 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 357804009859 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 357804009860 active site 357804009861 multimer interface [polypeptide binding]; other site 357804009862 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 357804009863 Response regulator receiver domain; Region: Response_reg; pfam00072 357804009864 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 357804009865 active site 357804009866 phosphorylation site [posttranslational modification] 357804009867 intermolecular recognition site; other site 357804009868 dimerization interface [polypeptide binding]; other site 357804009869 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804009870 metal binding site [ion binding]; metal-binding site 357804009871 active site 357804009872 I-site; other site 357804009873 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 357804009874 Cache domain; Region: Cache_2; cl07034 357804009875 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4564 357804009876 Histidine kinase, Adenylyl cyclase, 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...; Region: HAMP; cl01054 357804009877 dimerization interface [polypeptide binding]; other site 357804009878 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...; Region: HisKA; cd00082 357804009879 dimer interface [polypeptide binding]; other site 357804009880 phosphorylation site [posttranslational modification] 357804009881 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 357804009882 ATP binding site [chemical binding]; other site 357804009883 Mg2+ binding site [ion binding]; other site 357804009884 G-X-G motif; other site 357804009885 Response regulator receiver domain; Region: Response_reg; pfam00072 357804009886 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 357804009887 active site 357804009888 phosphorylation site [posttranslational modification] 357804009889 intermolecular recognition site; other site 357804009890 dimerization interface [polypeptide binding]; other site 357804009891 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 357804009892 putative binding surface; other site 357804009893 active site 357804009894 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 357804009895 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 357804009896 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 357804009897 Major Facilitator Superfamily; Region: MFS_1; pfam07690 357804009898 putative substrate translocation pore; other site 357804009899 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 357804009900 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 357804009901 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 357804009902 catalytic site [active] 357804009903 putative active site [active] 357804009904 putative substrate binding site [chemical binding]; other site 357804009905 dimer interface [polypeptide binding]; other site 357804009906 GTPase RsgA; Reviewed; Region: PRK12288 357804009907 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 357804009908 RNA binding site [nucleotide binding]; other site 357804009909 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 357804009910 GTPase/Zn-binding domain interface [polypeptide binding]; other site 357804009911 GTP/Mg2+ binding site [chemical binding]; other site 357804009912 G4 box; other site 357804009913 G5 box; other site 357804009914 G1 box; other site 357804009915 Switch I region; other site 357804009916 G2 box; other site 357804009917 G3 box; other site 357804009918 Switch II region; other site 357804009919 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 357804009920 threonine dehydratase; Reviewed; Region: PRK09224 357804009921 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 357804009922 tetramer interface [polypeptide binding]; other site 357804009923 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804009924 catalytic residue [active] 357804009925 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 357804009926 putative Ile/Val binding site [chemical binding]; other site 357804009927 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 357804009928 putative Ile/Val binding site [chemical binding]; other site 357804009929 Ion channel; Region: Ion_trans_2; cl11596 357804009930 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 357804009931 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 357804009932 N-terminal plug; other site 357804009933 ligand-binding site [chemical binding]; other site 357804009934 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 between...; Region: TroA-like; cl00262 357804009935 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 357804009936 intersubunit interface [polypeptide binding]; other site 357804009937 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 of...; Region: TM_ABC_iron-siderophores_like; cd06550 357804009938 ABC-ATPase subunit interface; other site 357804009939 dimer interface [polypeptide binding]; other site 357804009940 putative PBP binding regions; other site 357804009941 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 357804009942 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 357804009943 Walker A/P-loop; other site 357804009944 ATP binding site [chemical binding]; other site 357804009945 Q-loop/lid; other site 357804009946 ABC transporter signature motif; other site 357804009947 Walker B; other site 357804009948 D-loop; other site 357804009949 H-loop/switch region; other site 357804009950 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 357804009951 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 357804009952 Gram-negative bacterial tonB protein; Region: TonB; cl10048 357804009953 SapC; Region: SapC; pfam07277 357804009954 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 357804009955 Prostaglandin dehydrogenases; Region: PGDH; cd05288 357804009956 NAD(P) binding site [chemical binding]; other site 357804009957 substrate binding site [chemical binding]; other site 357804009958 dimer interface [polypeptide binding]; other site 357804009959 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]; Region: COG1979 357804009960 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 357804009961 dimer interface [polypeptide binding]; other site 357804009962 active site 357804009963 metal binding site [ion binding]; metal-binding site 357804009964 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein; Region: GATase1_Hsp31_like; cd03141 357804009965 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 357804009966 potential catalytic triad [active] 357804009967 conserved cys residue [active] 357804009968 transcriptional regulator; Provisional; Region: PRK10632 357804009969 Helix-turn-helix domains; Region: HTH; cl00088 357804009970 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 357804009971 putative effector binding pocket; other site 357804009972 dimerization interface [polypeptide binding]; other site 357804009973 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 357804009974 Helix-turn-helix domains; Region: HTH; cl00088 357804009975 AsnC family; Region: AsnC_trans_reg; pfam01037 357804009976 2-isopropylmalate synthase; Validated; Region: PRK03739 357804009977 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 357804009978 active site 357804009979 catalytic residues [active] 357804009980 metal binding site [ion binding]; metal-binding site 357804009981 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 357804009982 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 357804009983 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 357804009984 ATP binding site [chemical binding]; other site 357804009985 Mg2+ binding site [ion binding]; other site 357804009986 G-X-G motif; other site 357804009987 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 357804009988 anchoring element; other site 357804009989 dimer interface [polypeptide binding]; other site 357804009990 ATP binding site [chemical binding]; other site 357804009991 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 357804009992 active site 357804009993 metal binding site [ion binding]; metal-binding site 357804009994 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 357804009995 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 357804009996 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804009997 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 357804009998 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 357804009999 Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; Region: MPP_GpdQ; cd07402 357804010000 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 357804010001 active site 357804010002 metal binding site [ion binding]; metal-binding site 357804010003 hexamer interface [polypeptide binding]; other site 357804010004 ADP-ribose pyrophosphatase NudF; Provisional; Region: nudF; PRK10729 357804010005 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 Mg2+; Region: ADPRase_NUDT5; cd03424 357804010006 dimer interface [polypeptide binding]; other site 357804010007 ADP-ribose binding site [chemical binding]; other site 357804010008 active site 357804010009 nudix motif; other site 357804010010 metal binding site [ion binding]; metal-binding site 357804010011 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 357804010012 bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase; Provisional; Region: PRK11316 357804010013 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 357804010014 putative ribose interaction site [chemical binding]; other site 357804010015 putative ADP binding site [chemical binding]; other site 357804010016 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 357804010017 active site 357804010018 nucleotide binding site [chemical binding]; other site 357804010019 HIGH motif; other site 357804010020 KMSKS motif; other site 357804010021 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 357804010022 ligand binding site [chemical binding]; other site 357804010023 flexible hinge region; other site 357804010024 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...; Region: HisKA; cl00080 357804010025 dimer interface [polypeptide binding]; other site 357804010026 phosphorylation site [posttranslational modification] 357804010027 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]; Region: COG4251 357804010028 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 357804010029 ATP binding site [chemical binding]; other site 357804010030 Mg2+ binding site [ion binding]; other site 357804010031 G-X-G motif; other site 357804010032 Protein of unknown function (DUF454); Region: DUF454; cl01063 357804010033 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 357804010034 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 357804010035 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 357804010036 RimM N-terminal domain; Region: RimM; pfam01782 357804010037 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 produce...; Region: PRCH; cl09959 357804010038 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 357804010039 signal recognition particle protein; Provisional; Region: PRK10867 357804010040 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 357804010041 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 357804010042 P loop; other site 357804010043 GTP binding site [chemical binding]; other site 357804010044 Signal peptide binding domain; Region: SRP_SPB; pfam02978 357804010045 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 357804010046 hypothetical protein; Provisional; Region: PRK11573 357804010047 Domain of unknown function DUF21; Region: DUF21; pfam01595 357804010048 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 357804010049 Transporter associated domain; Region: CorC_HlyC; cl08393 357804010050 S-Ribosylhomocysteinase (LuxS); Region: LuxS; cl00802 357804010051 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 357804010052 Glutamate-cysteine ligase family 2(GCS2); Region: GCS2; cl00954 357804010053 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 357804010054 Na+-transporting oxaloacetate decarboxylase beta subunit; Region: OAD_beta; cl00816 357804010055 oxaloacetate decarboxylase; Provisional; Region: PRK14040 357804010056 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 357804010057 active site 357804010058 catalytic residues [active] 357804010059 metal binding site [ion binding]; metal-binding site 357804010060 homodimer binding site [polypeptide binding]; other site 357804010061 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 357804010062 carboxyltransferase (CT) interaction site; other site 357804010063 biotinylation site [posttranslational modification]; other site 357804010064 Oxaloacetate decarboxylase, gamma chain; Region: OAD_gamma; cl01458 357804010065 Global regulator protein family; Region: CsrA; cl00670 357804010066 aspartate kinase; Reviewed; Region: PRK06635 357804010067 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 357804010068 putative nucleotide binding site [chemical binding]; other site 357804010069 putative catalytic residues [active] 357804010070 putative Mg ion binding site [ion binding]; other site 357804010071 putative aspartate binding site [chemical binding]; other site 357804010072 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 357804010073 putative allosteric regulatory site; other site 357804010074 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 357804010075 putative allosteric regulatory residue; other site 357804010076 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 357804010077 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 of...; Region: AlaRS_core; cd00673 357804010078 motif 1; other site 357804010079 active site 357804010080 motif 2; other site 357804010081 motif 3; other site 357804010082 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 357804010083 DHHA1 domain; Region: DHHA1; pfam02272 357804010084 recombinase A; Provisional; Region: recA; PRK09354 357804010085 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 357804010086 hexamer interface [polypeptide binding]; other site 357804010087 Walker A motif; other site 357804010088 ATP binding site [chemical binding]; other site 357804010089 Walker B motif; other site 357804010090 Competence-damaged protein; Region: CinA; cl00666 357804010091 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 357804010092 MutS domain I; Region: MutS_I; pfam01624 357804010093 MutS domain II; Region: MutS_II; pfam05188 357804010094 MutS family domain IV; Region: MutS_IV; pfam05190 357804010095 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 357804010096 Walker A/P-loop; other site 357804010097 ATP binding site [chemical binding]; other site 357804010098 Q-loop/lid; other site 357804010099 ABC transporter signature motif; other site 357804010100 Walker B; other site 357804010101 D-loop; other site 357804010102 H-loop/switch region; other site 357804010103 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cd00051 357804010104 EF-hand domain pair; Region: EF_hand_5; pfam13499 357804010105 Ca2+ binding site [ion binding]; other site 357804010106 Transcriptional regulator [Transcription]; Region: LysR; COG0583 357804010107 Helix-turn-helix domains; Region: HTH; cl00088 357804010108 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 357804010109 dimerization interface [polypeptide binding]; other site 357804010110 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 357804010111 CIMS - Cobalamine-independent methonine synthase, or MetE, 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...; Region: CIMS_N_terminal_like; cd03312 357804010112 THF binding site; other site 357804010113 CIMS - Cobalamine-independent methonine synthase, or MetE, 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...; Region: CIMS_C_terminal_like; cd03311 357804010114 substrate binding site [chemical binding]; other site 357804010115 THF binding site; other site 357804010116 zinc-binding site [ion binding]; other site 357804010117 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Deinococcus radiodurans DR2231 protein and its bacterial homologs; Region: NTP-PPase_DR2231_like; cd11530 357804010118 metal binding site [ion binding]; metal-binding site 357804010119 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 357804010120 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 357804010121 Major Facilitator Superfamily; Region: MFS_1; pfam07690 357804010122 putative substrate translocation pore; other site 357804010123 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 357804010124 dimer interface [polypeptide binding]; other site 357804010125 ssDNA binding site [nucleotide binding]; other site 357804010126 tetramer (dimer of dimers) interface [polypeptide binding]; other site 357804010127 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 357804010128 PAS domain S-box; Region: sensory_box; TIGR00229 357804010129 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804010130 metal binding site [ion binding]; metal-binding site 357804010131 active site 357804010132 I-site; other site 357804010133 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 357804010134 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 357804010135 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 357804010136 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 357804010137 Zn2+ binding site [ion binding]; other site 357804010138 Mg2+ binding site [ion binding]; other site 357804010139 Type I (cytosolic) bacterial L-asparaginase; Region: L-asparaginase_I; cd08963 357804010140 active site 357804010141 homodimer interface [polypeptide binding]; other site 357804010142 Alternative oxidase, ferritin-like diiron-binding domain; Region: AOX; cd01053 357804010143 diiron binding motif [ion binding]; other site 357804010144 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 357804010145 ATP binding site [chemical binding]; other site 357804010146 putative Mg++ binding site [ion binding]; other site 357804010147 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 357804010148 nucleotide binding region [chemical binding]; other site 357804010149 ATP-binding site [chemical binding]; other site 357804010150 DTW domain; Region: DTW; cl01221 357804010151 putative hydrolase; Provisional; Region: PRK10976 357804010152 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 357804010153 active site 357804010154 motif I; other site 357804010155 motif II; other site 357804010156 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 357804010157 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 357804010158 Walker A motif; other site 357804010159 LysE type translocator; Region: LysE; cl00565 357804010160 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 industrial...; Region: Aldo_ket_red; cd06660 357804010161 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 357804010162 active site 357804010163 catalytic tetrad [active] 357804010164 Protein of unknown function (DUF3996); Region: DUF3996; pfam13161 357804010165 putative rhodanese-related sulfurtransferase; Provisional; Region: PRK00142 357804010166 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 357804010167 active site residue [active] 357804010168 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 357804010169 dimer interface [polypeptide binding]; other site 357804010170 Alkaline phosphatase homologues; Region: alkPPc; smart00098 357804010171 active site 357804010172 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 357804010173 dimer interface [polypeptide binding]; other site 357804010174 Alkaline phosphatase homologues; Region: alkPPc; smart00098 357804010175 active site 357804010176 hypothetical protein; Provisional; Region: PRK09040 357804010177 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 357804010178 ligand binding site [chemical binding]; other site 357804010179 exoribonuclease R; Provisional; Region: PRK11642 357804010180 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 357804010181 RNB domain; Region: RNB; pfam00773 357804010182 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 important...; Region: S1_RNase_R; cd04471 357804010183 RNA binding site [nucleotide binding]; other site 357804010184 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 357804010185 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 357804010186 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 357804010187 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 357804010188 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 357804010189 dimer interface [polypeptide binding]; other site 357804010190 ssDNA binding site [nucleotide binding]; other site 357804010191 tetramer (dimer of dimers) interface [polypeptide binding]; other site 357804010192 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 357804010193 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 357804010194 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 357804010195 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 357804010196 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 357804010197 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 357804010198 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, and...; Region: TM_PBP2; cd06261 357804010199 dimer interface [polypeptide binding]; other site 357804010200 conserved gate region; other site 357804010201 putative PBP binding loops; other site 357804010202 ABC-ATPase subunit interface; other site 357804010203 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, and...; Region: TM_PBP2; cd06261 357804010204 dimer interface [polypeptide binding]; other site 357804010205 conserved gate region; other site 357804010206 putative PBP binding loops; other site 357804010207 ABC-ATPase subunit interface; other site 357804010208 This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these...; Region: ABC_Pro_Gly_Bertaine; cd03294 357804010209 ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]; Region: OpuBA; COG1125 357804010210 Walker A/P-loop; other site 357804010211 ATP binding site [chemical binding]; other site 357804010212 Q-loop/lid; other site 357804010213 ABC transporter signature motif; other site 357804010214 Walker B; other site 357804010215 D-loop; other site 357804010216 H-loop/switch region; other site 357804010217 NMT1-like family; Region: NMT1_2; cl15260 357804010218 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 357804010219 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 357804010220 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-loop; Region: LysRS_N; cd04322 357804010221 dimer interface [polypeptide binding]; other site 357804010222 putative anticodon binding site; other site 357804010223 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 357804010224 motif 1; other site 357804010225 active site 357804010226 motif 2; other site 357804010227 motif 3; other site 357804010228 peptide chain release factor 2; Provisional; Region: PRK08787 357804010229 RF-1 domain; Region: RF-1; cl02875 357804010230 RF-1 domain; Region: RF-1; cl02875 357804010231 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06466 357804010232 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 357804010233 PYR/PP interface [polypeptide binding]; other site 357804010234 dimer interface [polypeptide binding]; other site 357804010235 TPP binding site [chemical binding]; other site 357804010236 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 357804010237 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 357804010238 TPP-binding site [chemical binding]; other site 357804010239 dimer interface [polypeptide binding]; other site 357804010240 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 357804010241 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 357804010242 putative valine binding site [chemical binding]; other site 357804010243 dimer interface [polypeptide binding]; other site 357804010244 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 357804010245 Protein of unknown function (DUF461); Region: DUF461; cl01071 357804010246 outer membrane protein; Region: OMP_w_GlyGly; TIGR04219 357804010247 sulfite reductase [NADPH] flavoprotein, alpha-component; Region: cysJ; TIGR01931 357804010248 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 357804010249 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 357804010250 FAD binding pocket [chemical binding]; other site 357804010251 FAD binding motif [chemical binding]; other site 357804010252 catalytic residues [active] 357804010253 NAD binding pocket [chemical binding]; other site 357804010254 phosphate binding motif [ion binding]; other site 357804010255 beta-alpha-beta structure motif; other site 357804010256 sulfite reductase subunit beta; Provisional; Region: PRK13504 357804010257 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 357804010258 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 357804010259 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 357804010260 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 357804010261 Active Sites [active] 357804010262 elongation factor Tu; Reviewed; Region: PRK00049 357804010263 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 357804010264 G1 box; other site 357804010265 GEF interaction site [polypeptide binding]; other site 357804010266 GTP/Mg2+ binding site [chemical binding]; other site 357804010267 Switch I region; other site 357804010268 G2 box; other site 357804010269 G3 box; other site 357804010270 Switch II region; other site 357804010271 G4 box; other site 357804010272 G5 box; other site 357804010273 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 357804010274 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 357804010275 Antibiotic Binding Site [chemical binding]; other site 357804010276 elongation factor G; Reviewed; Region: PRK00007 357804010277 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 357804010278 G1 box; other site 357804010279 putative GEF interaction site [polypeptide binding]; other site 357804010280 GTP/Mg2+ binding site [chemical binding]; other site 357804010281 Switch I region; other site 357804010282 G2 box; other site 357804010283 G3 box; other site 357804010284 Switch II region; other site 357804010285 G4 box; other site 357804010286 G5 box; other site 357804010287 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 synthesis...; Region: EFG_mtEFG_II; cd04088 357804010288 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 2...; Region: EFG_mtEFG1_IV; cd01434 357804010289 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 2...; Region: EFG_mtEFG_C; cd03713 357804010290 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 357804010291 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 357804010292 S17 interaction site [polypeptide binding]; other site 357804010293 S8 interaction site; other site 357804010294 16S rRNA interaction site [nucleotide binding]; other site 357804010295 streptomycin interaction site [chemical binding]; other site 357804010296 23S rRNA interaction site [nucleotide binding]; other site 357804010297 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 357804010298 DsrE/DsrF-like family; Region: DrsE; cl00672 357804010299 DsrE/DsrF-like family; Region: DrsE; cl00672 357804010300 DsrE/DsrF-like family; Region: DrsE; cl00672 357804010301 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 357804010302 homotrimer interaction site [polypeptide binding]; other site 357804010303 putative active site [active] 357804010304 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 357804010305 DNA-directed RNA polymerase, beta' subunit, predominant form; Region: rpoC_TIGR; TIGR02386 357804010306 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 357804010307 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 357804010308 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 357804010309 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 357804010310 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 357804010311 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 357804010312 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 357804010313 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 357804010314 DNA binding site [nucleotide binding] 357804010315 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 357804010316 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 357804010317 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 357804010318 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 357804010319 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 357804010320 RPB11 interaction site [polypeptide binding]; other site 357804010321 RPB12 interaction site [polypeptide binding]; other site 357804010322 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 357804010323 RPB3 interaction site [polypeptide binding]; other site 357804010324 RPB1 interaction site [polypeptide binding]; other site 357804010325 RPB11 interaction site [polypeptide binding]; other site 357804010326 RPB10 interaction site [polypeptide binding]; other site 357804010327 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 357804010328 core dimer interface [polypeptide binding]; other site 357804010329 peripheral dimer interface [polypeptide binding]; other site 357804010330 L10 interface [polypeptide binding]; other site 357804010331 L11 interface [polypeptide binding]; other site 357804010332 putative EF-Tu interaction site [polypeptide binding]; other site 357804010333 putative EF-G interaction site [polypeptide binding]; other site 357804010334 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 protein...; Region: Ribosomal_L10; cd05797 357804010335 23S rRNA interface [nucleotide binding]; other site 357804010336 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 357804010337 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 binds...; Region: Ribosomal_L1; cd00403 357804010338 mRNA/rRNA interface [nucleotide binding]; other site 357804010339 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 357804010340 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 357804010341 23S rRNA interface [nucleotide binding]; other site 357804010342 L7/L12 interface [polypeptide binding]; other site 357804010343 putative thiostrepton binding site; other site 357804010344 L25 interface [polypeptide binding]; other site 357804010345 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 357804010346 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 357804010347 putative homodimer interface [polypeptide binding]; other site 357804010348 KOW motif; Region: KOW; cl00354 357804010349 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 357804010350 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11160 357804010351 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804010352 Walker A/P-loop; other site 357804010353 ATP binding site [chemical binding]; other site 357804010354 Q-loop/lid; other site 357804010355 ABC transporter signature motif; other site 357804010356 Walker B; other site 357804010357 D-loop; other site 357804010358 H-loop/switch region; other site 357804010359 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11174 357804010360 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 357804010361 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804010362 Walker A/P-loop; other site 357804010363 ATP binding site [chemical binding]; other site 357804010364 Q-loop/lid; other site 357804010365 ABC transporter signature motif; other site 357804010366 Walker B; other site 357804010367 D-loop; other site 357804010368 H-loop/switch region; other site 357804010369 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 357804010370 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 357804010371 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 357804010372 NAD(P) binding site [chemical binding]; other site 357804010373 homodimer interface [polypeptide binding]; other site 357804010374 substrate binding site [chemical binding]; other site 357804010375 active site 357804010376 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 357804010377 UDP-glucose 4 epimerase, subgroup 4, extended (e) SDRs; Region: UDP_G4E_4_SDR_e; cd05232 357804010378 putative NAD(P) binding site [chemical binding]; other site 357804010379 active site 357804010380 putative substrate binding site [chemical binding]; other site 357804010381 Bacterial sugar transferase; Region: Bac_transf; cl00939 357804010382 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 357804010383 active site 357804010384 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 357804010385 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; cl16911 357804010386 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 357804010387 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cl01298 357804010388 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 357804010389 ABC_KpsT_Wzt The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export. Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides, and...; Region: ABC_KpsT_Wzt; cd03220 357804010390 Walker A/P-loop; other site 357804010391 ATP binding site [chemical binding]; other site 357804010392 Q-loop/lid; other site 357804010393 ABC transporter signature motif; other site 357804010394 Walker B; other site 357804010395 D-loop; other site 357804010396 H-loop/switch region; other site 357804010397 C-Terminal domain of O-antigenic polysaccharide transporter protein Wzt and related proteins; Region: Wzt_C-like; cd10147 357804010398 putative carbohydrate binding site [chemical binding]; other site 357804010399 ABC-2 type transporter; Region: ABC2_membrane; cl11417 357804010400 Cupin domain; Region: Cupin_2; cl09118 357804010401 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 357804010402 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 357804010403 NADP binding site [chemical binding]; other site 357804010404 active site 357804010405 putative substrate binding site [chemical binding]; other site 357804010406 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 357804010407 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 357804010408 substrate binding site; other site 357804010409 tetramer interface; other site 357804010410 dTDP-glucose 4,6 dehydratase; Provisional; Region: PRK10084 357804010411 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 357804010412 NAD binding site [chemical binding]; other site 357804010413 substrate binding site [chemical binding]; other site 357804010414 homodimer interface [polypeptide binding]; other site 357804010415 active site 357804010416 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; Region: NGN_SP_RfaH; cd09892 357804010417 transcriptional activator RfaH; Provisional; Region: rfaH; PRK09014 357804010418 Protein of unknown function (DUF3582); Region: DUF3582; pfam12122 357804010419 rhomboid family protease GlpG; Region: rhombo_GlpG; TIGR04239 357804010420 Rhomboid family; Region: Rhomboid; cl11446 357804010421 UTRA domain; Region: UTRA; cl01230 357804010422 UbiA prenyltransferase family; Region: UbiA; cl00337 357804010423 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 357804010424 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 357804010425 dihydrolipoamide dehydrogenase; Validated; Region: PRK06292 357804010426 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 357804010427 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 357804010428 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 357804010429 catalytic triad [active] 357804010430 dimer interface [polypeptide binding]; other site 357804010431 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 357804010432 ATP-dependent DNA helicase Rep; Provisional; Region: PRK10919 357804010433 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804010434 Family description; Region: UvrD_C_2; cl15862 357804010435 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 357804010436 Helix-turn-helix domains; Region: HTH; cl00088 357804010437 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 357804010438 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, acyl; Region: Biotinyl_lipoyl_domains; cl11404 357804010439 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, acyl; Region: Biotinyl_lipoyl_domains; cl11404 357804010440 multidrug efflux protein; Reviewed; Region: PRK09579 357804010441 Protein export membrane protein; Region: SecD_SecF; cl14618 357804010442 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 357804010443 UDP-glucose 4-epimerase; Region: PLN02240 357804010444 NAD binding site [chemical binding]; other site 357804010445 homodimer interface [polypeptide binding]; other site 357804010446 active site 357804010447 substrate binding site [chemical binding]; other site 357804010448 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 357804010449 active site 357804010450 ribonuclease PH; Reviewed; Region: rph; PRK00173 357804010451 Ribonuclease PH; Region: RNase_PH_bact; cd11362 357804010452 hexamer interface [polypeptide binding]; other site 357804010453 active site 357804010454 protease3; Provisional; Region: PRK15101 357804010455 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 357804010456 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 357804010457 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 357804010458 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 not...; Region: Dtyr_deacylase; cd00563 357804010459 putative active site [active] 357804010460 dimerization interface [polypeptide binding]; other site 357804010461 putative tRNAtyr binding site [nucleotide binding]; other site 357804010462 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 357804010463 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 357804010464 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 357804010465 G1 box; other site 357804010466 putative GEF interaction site [polypeptide binding]; other site 357804010467 GTP/Mg2+ binding site [chemical binding]; other site 357804010468 Switch I region; other site 357804010469 G2 box; other site 357804010470 G3 box; other site 357804010471 Switch II region; other site 357804010472 G4 box; other site 357804010473 G5 box; other site 357804010474 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 357804010475 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 highly...; Region: BipA_TypA_C; cd03710 357804010476 glutamine synthetase; Provisional; Region: glnA; PRK09469 357804010477 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 357804010478 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 357804010479 Uncharacterized protein related to glutamine synthetase [General function prediction only]; Region: COG3968 357804010480 Glutamine synthetase type III N terminal; Region: GSIII_N; pfam12437 357804010481 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 357804010482 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 357804010483 nitrogen regulation protein NR(II); Provisional; Region: glnL; PRK11073 357804010484 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 357804010485 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...; Region: HisKA; cd00082 357804010486 dimer interface [polypeptide binding]; other site 357804010487 phosphorylation site [posttranslational modification] 357804010488 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 357804010489 ATP binding site [chemical binding]; other site 357804010490 Mg2+ binding site [ion binding]; other site 357804010491 G-X-G motif; other site 357804010492 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 357804010493 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 357804010494 active site 357804010495 phosphorylation site [posttranslational modification] 357804010496 intermolecular recognition site; other site 357804010497 dimerization interface [polypeptide binding]; other site 357804010498 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 ABC; Region: AAA; cd00009 357804010499 Walker A motif; other site 357804010500 ATP binding site [chemical binding]; other site 357804010501 Walker B motif; other site 357804010502 arginine finger; other site 357804010503 Helix-turn-helix domains; Region: HTH; cl00088 357804010504 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 357804010505 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 357804010506 Na binding site [ion binding]; other site 357804010507 AsmA family; Region: AsmA; pfam05170 357804010508 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 357804010509 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...; Region: RecG_wedge_OBF; cd04488 357804010510 generic binding surface II; other site 357804010511 ssDNA binding site; other site 357804010512 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 357804010513 ATP binding site [chemical binding]; other site 357804010514 putative Mg++ binding site [ion binding]; other site 357804010515 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 357804010516 nucleotide binding region [chemical binding]; other site 357804010517 ATP-binding site [chemical binding]; other site 357804010518 The outer membrane phospholipase A (OMPLA) is an integral membrane enzyme that catalyses the hydrolysis of acylester bonds in phospholipids using calcium as a cofactor. The enzyme has a fold of transmembrane beta-barrels and is widespread among...; Region: OMPLA; cd00541 357804010519 dimerization interface [polypeptide binding]; other site 357804010520 substrate binding site [chemical binding]; other site 357804010521 active site 357804010522 calcium binding site [ion binding]; other site 357804010523 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804010524 G1 box; other site 357804010525 GTP/Mg2+ binding site [chemical binding]; other site 357804010526 G2 box; other site 357804010527 Switch I region; other site 357804010528 G3 box; other site 357804010529 Switch II region; other site 357804010530 Domain of unknown function (DUF3482); Region: DUF3482; pfam11981 357804010531 Protein of unknown function (DUF2868); Region: DUF2868; pfam11067 357804010532 tRNA guanosine-2'-O-methyltransferase; Provisional; Region: PRK11081 357804010533 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 357804010534 SpoU, rRNA methylase, C-terminal; Region: SpoU_methylas_C; pfam12105 357804010535 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 357804010536 Helix-turn-helix domains; Region: HTH; cl00088 357804010537 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 357804010538 dimerization interface [polypeptide binding]; other site 357804010539 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 357804010540 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 357804010541 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 357804010542 alphaNTD homodimer interface [polypeptide binding]; other site 357804010543 alphaNTD - beta interaction site [polypeptide binding]; other site 357804010544 alphaNTD - beta' interaction site [polypeptide binding]; other site 357804010545 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 357804010546 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 357804010547 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 357804010548 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 357804010549 RNA binding surface [nucleotide binding]; other site 357804010550 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 357804010551 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 357804010552 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 357804010553 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 357804010554 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 357804010555 SecY translocase; Region: SecY; pfam00344 357804010556 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 357804010557 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 that...; Region: Ribosomal_L30; cd01658 357804010558 23S rRNA binding site [nucleotide binding]; other site 357804010559 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 357804010560 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 357804010561 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 357804010562 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 357804010563 5S rRNA interface [nucleotide binding]; other site 357804010564 L5 interface [polypeptide binding]; other site 357804010565 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 357804010566 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 357804010567 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 357804010568 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 357804010569 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 357804010570 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 357804010571 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 357804010572 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 357804010573 KOW motif; Region: KOW; cl00354 357804010574 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 357804010575 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 357804010576 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 it...; Region: Ribosomal_L29_HIP; cd00427 357804010577 23S rRNA interface [nucleotide binding]; other site 357804010578 putative translocon interaction site; other site 357804010579 signal recognition particle (SRP54) interaction site; other site 357804010580 L23 interface [polypeptide binding]; other site 357804010581 trigger factor interaction site; other site 357804010582 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 357804010583 23S rRNA interface [nucleotide binding]; other site 357804010584 5S rRNA interface [nucleotide binding]; other site 357804010585 putative antibiotic binding site [chemical binding]; other site 357804010586 L25 interface [polypeptide binding]; other site 357804010587 L27 interface [polypeptide binding]; other site 357804010588 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 357804010589 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 KH...; Region: 30S_S3_KH; cd02412 357804010590 G-X-X-G motif; other site 357804010591 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 357804010592 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 357804010593 putative translocon binding site; other site 357804010594 protein-rRNA interface [nucleotide binding]; other site 357804010595 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 357804010596 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 357804010597 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 357804010598 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 357804010599 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 357804010600 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 357804010601 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 357804010602 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 357804010603 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]; Region: COG1444 357804010604 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804010605 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 357804010606 Coenzyme A binding pocket [chemical binding]; other site 357804010607 Possible tRNA binding domain; Region: tRNA_bind_2; pfam13725 357804010608 16S rRNA pseudouridylate synthase A; Provisional; Region: PRK10839 357804010609 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 357804010610 RNA binding surface [nucleotide binding]; other site 357804010611 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 357804010612 active site 357804010613 uracil binding [chemical binding]; other site 357804010614 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 357804010615 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 357804010616 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 357804010617 motif II; other site 357804010618 LysR family transcriptional regulator; Provisional; Region: PRK14997 357804010619 Helix-turn-helix domains; Region: HTH; cl00088 357804010620 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 357804010621 dimerization interface [polypeptide binding]; other site 357804010622 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 357804010623 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase; Region: adh_III_F_hyde; TIGR02818 357804010624 substrate binding site [chemical binding]; other site 357804010625 catalytic Zn binding site [ion binding]; other site 357804010626 NAD binding site [chemical binding]; other site 357804010627 structural Zn binding site [ion binding]; other site 357804010628 dimer interface [polypeptide binding]; other site 357804010629 Predicted esterase [General function prediction only]; Region: COG0627 357804010630 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 357804010631 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 357804010632 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 357804010633 putative metal binding site [ion binding]; other site 357804010634 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 357804010635 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 357804010636 Coenzyme A binding pocket [chemical binding]; other site 357804010637 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 357804010638 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804010639 NMT1-like family; Region: NMT1_2; cl15260 357804010640 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, and...; Region: TM_PBP2; cd06261 357804010641 dimer interface [polypeptide binding]; other site 357804010642 conserved gate region; other site 357804010643 ABC-ATPase subunit interface; other site 357804010644 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 357804010645 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. ABC...; Region: ABC_MetN_methionine_transporter; cd03258 357804010646 Walker A/P-loop; other site 357804010647 ATP binding site [chemical binding]; other site 357804010648 Q-loop/lid; other site 357804010649 ABC transporter signature motif; other site 357804010650 Walker B; other site 357804010651 D-loop; other site 357804010652 H-loop/switch region; other site 357804010653 NIL domain; Region: NIL; cl09633 357804010654 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 357804010655 active site 357804010656 Protein of unknown function, DUF479; Region: DUF479; cl01203 357804010657 The SYLF domain (also called DUF500), a novel lipid-binding module; Region: SYLF; cd11524 357804010658 putative amphipathic alpha helix; other site 357804010659 Arginate lyase and other MDR family members; Region: AL_MDR; cd08252 357804010660 zinc-binding alcohol dehydrogenase family protein; Region: adh_fam_1; TIGR02817 357804010661 putative NAD(P) binding site [chemical binding]; other site 357804010662 dimer interface [polypeptide binding]; other site 357804010663 Helix-turn-helix domains; Region: HTH; cl00088 357804010664 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 357804010665 DctM-like transporters; Region: DctM; pfam06808 357804010666 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 357804010667 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 357804010668 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 357804010669 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 357804010670 LamB/YcsF family of lactam utilization protein; Region: LamB_YcsF_like; cd10787 357804010671 putative active site [active] 357804010672 Allophanate hydrolase subunit 1; Region: AHS1; pfam02682 357804010673 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; cl00896 357804010674 Allophanate hydrolase subunit 2; Region: AHS2; cl00865 357804010675 DNA-binding transcriptional regulator FruR; Provisional; Region: PRK11303 357804010676 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 357804010677 DNA binding site [nucleotide binding] 357804010678 domain linker motif; other site 357804010679 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 357804010680 bifunctional PTS system fructose-specific transporter subunit IIA/HPr protein; Provisional; Region: PRK11109 357804010681 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 357804010682 active site 357804010683 phosphorylation site [posttranslational modification] 357804010684 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; cl00163 357804010685 active site 357804010686 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 357804010687 dimerization domain swap beta strand [polypeptide binding]; other site 357804010688 regulatory protein interface [polypeptide binding]; other site 357804010689 active site 357804010690 regulatory phosphorylation site [posttranslational modification]; other site 357804010691 Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]; Region: FruK; COG1105 357804010692 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 357804010693 putative substrate binding site [chemical binding]; other site 357804010694 putative ATP binding site [chemical binding]; other site 357804010695 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 and...; Region: PTS_IIB_fructose; cd05569 357804010696 active site 357804010697 P-loop; other site 357804010698 phosphorylation site [posttranslational modification] 357804010699 PTS system fructose-specific transporter subunits IIBC; Provisional; Region: PRK10712 357804010700 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 and...; Region: PTS_IIB_fructose; cd05569 357804010701 active site 357804010702 P-loop; other site 357804010703 phosphorylation site [posttranslational modification] 357804010704 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; cl00557 357804010705 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 357804010706 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; Region: FBPase; cd00354 357804010707 AMP binding site [chemical binding]; other site 357804010708 metal binding site [ion binding]; metal-binding site 357804010709 active site 357804010710 Lipocalin / cytosolic fatty-acid binding protein family; Region: Lipocalin; cl01150 357804010711 Protein of unknown function (DUF2860); Region: DUF2860; pfam11059 357804010712 SAF-like; Region: SAF_2; pfam13144 357804010713 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 357804010714 Domains similar to fish antifreeze type III protein; Region: SAF; cl00555 357804010715 StbA protein; Region: StbA; pfam06406 357804010716 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 357804010717 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 357804010718 Walker A motif/ATP binding site; other site 357804010719 Walker B motif; other site 357804010720 flagellar assembly protein H; Provisional; Region: fliH; PRK13386 357804010721 Essential protein Yae1, N terminal; Region: Yae1_N; pfam09811 357804010722 Flagellar assembly protein FliH; Region: FliH; pfam02108 357804010723 flagellar motor switch protein G; Reviewed; Region: fliG; PRK07194 357804010724 FliG C-terminal domain; Region: FliG_C; pfam01706 357804010725 flagellar MS-ring protein; Reviewed; Region: fliF; PRK07193 357804010726 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 357804010727 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 357804010728 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 357804010729 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 357804010730 ligand binding site [chemical binding]; other site 357804010731 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK07192 357804010732 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 357804010733 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK07191 357804010734 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 357804010735 Rod binding protein; Region: Rod-binding; cl01626 357804010736 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 357804010737 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 357804010738 Flagellar L-ring protein; Region: FlgH; cl00905 357804010739 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 357804010740 Flagella basal body rod protein; Region: Flg_bb_rod; cl16922 357804010741 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 357804010742 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 357804010743 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 357804010744 flagellar hook protein FlgE; Validated; Region: flgE; PRK06803 357804010745 Flagella basal body rod protein; Region: Flg_bb_rod; cl16922 357804010746 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 357804010747 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 357804010748 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK09619 357804010749 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 357804010750 FlgD Ig-like domain; Region: FlgD_ig; cl15790 357804010751 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK06802 357804010752 Flagella basal body rod protein; Region: Flg_bb_rod; cl16922 357804010753 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 357804010754 Flagella basal body rod protein; Region: Flg_bb_rod; cl16922 357804010755 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK12685 357804010756 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 357804010757 hypothetical protein; Validated; Region: PRK06778 357804010758 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 357804010759 ligand binding site [chemical binding]; other site 357804010760 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 357804010761 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 357804010762 flagellar biosynthesis sigma factor; Provisional; Region: PRK12427 357804010763 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 357804010764 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 357804010765 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 357804010766 Flagellar hook-length control protein FliK; Region: Flg_hook; cl15269 357804010767 Flagellar protein FliS; Region: FliS; cl00654 357804010768 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 357804010769 Flagellar capping protein [Cell motility and secretion]; Region: FliD; COG1345 357804010770 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 357804010771 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 357804010772 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 357804010773 flagellin; Reviewed; Region: PRK08869 357804010774 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 357804010775 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 357804010776 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 357804010777 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 357804010778 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 357804010779 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 357804010780 FliP family; Region: FliP; cl00593 357804010781 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 357804010782 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 357804010783 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 357804010784 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 357804010785 flagellar biosynthesis protein FlhA; Validated; Region: flhA; cl07980 357804010786 FHIPEP family; Region: FHIPEP; pfam00771 357804010787 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 357804010788 FlgN protein; Region: FlgN; cl09176 357804010789 acetyl-CoA synthetase; Provisional; Region: PRK04319 357804010790 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 357804010791 AMP-binding enzyme; Region: AMP-binding; cl15778 357804010792 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 357804010793 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 357804010794 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 357804010795 tetramer interface [polypeptide binding]; other site 357804010796 TPP-binding site [chemical binding]; other site 357804010797 heterodimer interface [polypeptide binding]; other site 357804010798 phosphorylation loop region [posttranslational modification] 357804010799 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 357804010800 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 357804010801 alpha subunit interface [polypeptide binding]; other site 357804010802 TPP binding site [chemical binding]; other site 357804010803 heterodimer interface [polypeptide binding]; other site 357804010804 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 357804010805 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 357804010806 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 357804010807 E3 interaction surface; other site 357804010808 lipoyl attachment site [posttranslational modification]; other site 357804010809 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 357804010810 Phosphopantetheine attachment site; Region: PP-binding; cl09936 357804010811 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 357804010812 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; cl15379 357804010813 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804010814 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 357804010815 Helix-turn-helix domains; Region: HTH; cl00088 357804010816 AsnC family; Region: AsnC_trans_reg; pfam01037 357804010817 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 357804010818 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 357804010819 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 357804010820 DsbD alpha interface [polypeptide binding]; other site 357804010821 catalytic residues [active] 357804010822 Ribosomal protein L34; Region: Ribosomal_L34; cl00370 357804010823 Ribonuclease P; Region: Ribonuclease_P; cl00457 357804010824 Haemolytic domain; Region: Haemolytic; cl00506 357804010825 membrane protein insertase; Provisional; Region: PRK01318 357804010826 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 357804010827 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 357804010828 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 357804010829 trmE is a tRNA modification GTPase; Region: trmE; cd04164 357804010830 G1 box; other site 357804010831 GTP/Mg2+ binding site [chemical binding]; other site 357804010832 Switch I region; other site 357804010833 G2 box; other site 357804010834 Switch II region; other site 357804010835 G3 box; other site 357804010836 G4 box; other site 357804010837 G5 box; other site 357804010838 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 357804010839 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. Trimers...; Region: gram_neg_porins; cd00342 357804010840 trimer interface [polypeptide binding]; other site 357804010841 eyelet of channel; other site 357804010842 atypical (a) SDRs, subgroup 8; Region: SDR_a8; cd05242 357804010843 TIGR01777 family protein; Region: yfcH 357804010844 putative NAD(P) binding site [chemical binding]; other site 357804010845 putative active site [active] 357804010846 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 357804010847 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 357804010848 glutamine binding [chemical binding]; other site 357804010849 catalytic triad [active] 357804010850 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein; Reviewed; Region: argD; PRK05093 357804010851 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 357804010852 inhibitor-cofactor binding pocket; inhibition site 357804010853 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804010854 catalytic residue [active] 357804010855 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 357804010856 putative active site [active] 357804010857 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 357804010858 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 357804010859 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 357804010860 Phosphotransferase enzyme family; Region: APH; pfam01636 357804010861 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 357804010862 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 357804010863 catalytic residues [active] 357804010864 hinge region; other site 357804010865 alpha helical domain; other site 357804010866 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804010867 active site 357804010868 pantothenate kinase; Provisional; Region: PRK05439 357804010869 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 357804010870 ATP-binding site [chemical binding]; other site 357804010871 CoA-binding site [chemical binding]; other site 357804010872 Mg2+-binding site [ion binding]; other site 357804010873 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 357804010874 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 guanosine...; Region: GMPK; cd00071 357804010875 catalytic site [active] 357804010876 G-X2-G-X-G-K; other site 357804010877 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 357804010878 putative calcium/sodium:proton antiporter; Provisional; Region: PRK10734 357804010879 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 357804010880 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 357804010881 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 357804010882 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804010883 NAD(P) binding site [chemical binding]; other site 357804010884 active site 357804010885 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 357804010886 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 357804010887 CoA-disulfide reductase; Region: CoA_CoA_reduc; TIGR03385 357804010888 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 357804010889 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 357804010890 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...; Region: RHOD_Pyr_redox; cd01524 357804010891 active site residue [active] 357804010892 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 357804010893 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 357804010894 dimerization interface [polypeptide binding]; other site 357804010895 putative DNA binding site [nucleotide binding]; other site 357804010896 putative Zn2+ binding site [ion binding]; other site 357804010897 Domain of unknown function (DUF4341); Region: DUF4341; pfam14241 357804010898 Predicted transporter component [General function prediction only]; Region: COG2391 357804010899 Predicted transporter component [General function prediction only]; Region: COG2391 357804010900 Sulphur transport; Region: Sulf_transp; cl01018 357804010901 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 357804010902 Predicted permeases [General function prediction only]; Region: COG0701 357804010903 Predicted permease; Region: DUF318; pfam03773 357804010904 Predicted permease; Region: DUF318; pfam03773 357804010905 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 357804010906 putative substrate translocation pore; other site 357804010907 glyceraldehyde-3-phosphate dehydrogenase; Validated; Region: PRK08955 357804010908 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804010909 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 357804010910 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 357804010911 dimerization interface [polypeptide binding]; other site 357804010912 putative DNA binding site [nucleotide binding]; other site 357804010913 putative Zn2+ binding site [ion binding]; other site 357804010914 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 357804010915 Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]; Region: HemY; COG3071 357804010916 HemY protein N-terminus; Region: HemY_N; pfam07219 357804010917 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 357804010918 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 357804010919 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 in...; Region: HemD; cd06578 357804010920 active site 357804010921 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 357804010922 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 357804010923 domain interfaces; other site 357804010924 active site 357804010925 Protein of unknown function (DUF3820); Region: DUF3820; cl01411 357804010926 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK06084 357804010927 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 357804010928 homodimer interface [polypeptide binding]; other site 357804010929 substrate-cofactor binding pocket; other site 357804010930 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804010931 catalytic residue [active] 357804010932 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 357804010933 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 357804010934 Coenzyme A binding pocket [chemical binding]; other site 357804010935 MAPEG family; Region: MAPEG; cl09190 357804010936 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 357804010937 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 357804010938 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 357804010939 dihydrodipicolinate reductase; Provisional; Region: PRK00048 357804010940 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804010941 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 357804010942 Protein of unknown function (DUF2956); Region: DUF2956; pfam11169 357804010943 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 basis...; Region: HIT_like; cl00228 357804010944 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 357804010945 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804010946 hypothetical protein; Provisional; Region: PRK11820 357804010947 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 357804010948 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 357804010949 Protein with unknown function (DUF469); Region: DUF469; cl01237 357804010950 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 357804010951 Acyl transferase domain; Region: Acyl_transf_1; cl08282 357804010952 Phosphoribosyl-dephospho-CoA transferase MdcG; Region: MdcG; cl07913 357804010953 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 357804010954 Malonate decarboxylase delta subunit (MdcD); Region: ACP; cl06082 357804010955 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 357804010956 ATP:dephospho-CoA triphosphoribosyl transferase; Region: CitG; cl00768 357804010957 malonate decarboxylase, alpha subunit; Region: mdcA; TIGR01110 357804010958 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 357804010959 Transcriptional regulator [Transcription]; Region: LysR; COG0583 357804010960 Helix-turn-helix domains; Region: HTH; cl00088 357804010961 The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold; Region: PBP2_MdcR; cd08416 357804010962 putative dimerization interface [polypeptide binding]; other site 357804010963 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 Mg2+; Region: ADPRase_NUDT5; cd03424 357804010964 dimer interface [polypeptide binding]; other site 357804010965 ADP-ribose binding site [chemical binding]; other site 357804010966 active site 357804010967 nudix motif; other site 357804010968 metal binding site [ion binding]; metal-binding site 357804010969 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 a...; Region: metallo-dependent_hydrolases; cl00281 357804010970 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 357804010971 Transcriptional regulators [Transcription]; Region: GntR; COG1802 357804010972 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 357804010973 DNA-binding site [nucleotide binding]; DNA binding site 357804010974 FCD domain; Region: FCD; cl11656 357804010975 putative transposase OrfB; Reviewed; Region: PHA02517 357804010976 HTH-like domain; Region: HTH_21; pfam13276 357804010977 Integrase core domain; Region: rve; cl01316 357804010978 Integrase core domain; Region: rve_3; cl15866 357804010979 Helix-turn-helix domains; Region: HTH; cl00088 357804010980 Transposase IS200 like; Region: Y1_Tnp; cl00848 357804010981 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 357804010982 DctM-like transporters; Region: DctM; pfam06808 357804010983 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 357804010984 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 357804010985 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 357804010986 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 357804010987 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 357804010988 Integrase core domain; Region: rve; cl01316 357804010989 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 Mg2+; Region: ADPRase_NUDT5; cd03424 357804010990 dimer interface [polypeptide binding]; other site 357804010991 ADP-ribose binding site [chemical binding]; other site 357804010992 active site 357804010993 nudix motif; other site 357804010994 metal binding site [ion binding]; metal-binding site 357804010995 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 357804010996 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 357804010997 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 357804010998 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804010999 phosphonate metabolism protein PhnM; Provisional; Region: PRK15446 357804011000 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 a...; Region: metallo-dependent_hydrolases; cl00281 357804011001 PhnM is believed to be a subunit of the membrane associated C-P lyase complex. C-P lyase is thought to catalyze the direct cleavage of inactivated C-P bonds to yield inorganic phosphate and the corresponding hydrocarbons. It is responsible for cleavage...; Region: PhnM; cd01306 357804011002 active site 357804011003 phosphonate C-P lyase system protein PhnL; Region: CP_lyasePhnL; TIGR02324 357804011004 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804011005 Walker A/P-loop; other site 357804011006 ATP binding site [chemical binding]; other site 357804011007 Q-loop/lid; other site 357804011008 ABC transporter signature motif; other site 357804011009 Walker B; other site 357804011010 D-loop; other site 357804011011 H-loop/switch region; other site 357804011012 phosphonate C-P lyase system protein PhnK; Provisional; Region: phnK; PRK11701 357804011013 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 357804011014 Walker A/P-loop; other site 357804011015 ATP binding site [chemical binding]; other site 357804011016 Q-loop/lid; other site 357804011017 ABC transporter signature motif; other site 357804011018 Walker B; other site 357804011019 D-loop; other site 357804011020 H-loop/switch region; other site 357804011021 Phosphonate metabolism protein PhnJ; Region: PhnJ; cl01457 357804011022 Bacterial phosphonate metabolism protein (PhnI); Region: PhnI; cl01456 357804011023 Bacterial phosphonate metabolism protein (PhnH); Region: PhnH; cl01455 357804011024 Phosphonate metabolism protein PhnG; Region: PhnG; cl01454 357804011025 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, and...; Region: TM_PBP2; cd06261 357804011026 dimer interface [polypeptide binding]; other site 357804011027 conserved gate region; other site 357804011028 putative PBP binding loops; other site 357804011029 ABC-ATPase subunit interface; other site 357804011030 phosphonate ABC transporter, ATP-binding protein; Region: ABC_phnC; TIGR02315 357804011031 ABC-type phosphate/phosphonate transport system. Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all...; Region: ABC_PhnC_transporter; cd03256 357804011032 Walker A/P-loop; other site 357804011033 ATP binding site [chemical binding]; other site 357804011034 Q-loop/lid; other site 357804011035 ABC transporter signature motif; other site 357804011036 Walker B; other site 357804011037 D-loop; other site 357804011038 H-loop/switch region; other site 357804011039 phosphate/phosphite/phosphonate ABC transporters, periplasmic binding protein; Region: 3A0109s03R; TIGR01098 357804011040 NMT1-like family; Region: NMT1_2; cl15260 357804011041 phosphonates metabolism transcriptional regulator PhnF; Region: C_P_lyase_phnF; TIGR02325 357804011042 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 357804011043 DNA-binding site [nucleotide binding]; DNA binding site 357804011044 UTRA domain; Region: UTRA; cl01230 357804011045 EamA-like transporter family; Region: EamA; cl01037 357804011046 Predicted permeases [General function prediction only]; Region: RarD; COG2962 357804011047 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 357804011048 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 357804011049 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 357804011050 dimer interface [polypeptide binding]; other site 357804011051 N-terminal domain interface [polypeptide binding]; other site 357804011052 substrate binding pocket (H-site) [chemical binding]; other site 357804011053 putative transcriptional regulator; Provisional; Region: PRK11640 357804011054 Helix-turn-helix domains; Region: HTH; cl00088 357804011055 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 357804011056 Sel1 repeat; Region: Sel1; cl02723 357804011057 Sel1 repeat; Region: Sel1; cl02723 357804011058 Sel1 repeat; Region: Sel1; cl02723 357804011059 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 357804011060 Sel1 repeat; Region: Sel1; cl02723 357804011061 Sel1 repeat; Region: Sel1; cl02723 357804011062 Sel1 repeat; Region: Sel1; cl02723 357804011063 Sel1 repeat; Region: Sel1; cl02723 357804011064 Sel1 repeat; Region: Sel1; cl02723 357804011065 Sel1 repeat; Region: Sel1; cl02723 357804011066 Sel1 repeat; Region: Sel1; cl02723 357804011067 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 357804011068 DNA-binding site [nucleotide binding]; DNA binding site 357804011069 RNA-binding motif; other site 357804011070 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 357804011071 catalytic residues [active] 357804011072 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 357804011073 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 357804011074 FtsX-like permease family; Region: FtsX; cl15850 357804011075 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 357804011076 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 357804011077 FtsX-like permease family; Region: FtsX; cl15850 357804011078 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 357804011079 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 357804011080 Walker A/P-loop; other site 357804011081 ATP binding site [chemical binding]; other site 357804011082 Q-loop/lid; other site 357804011083 ABC transporter signature motif; other site 357804011084 Walker B; other site 357804011085 D-loop; other site 357804011086 H-loop/switch region; other site 357804011087 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 357804011088 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, acyl; Region: Biotinyl_lipoyl_domains; cl11404 357804011089 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, acyl; Region: Biotinyl_lipoyl_domains; cl11404 357804011090 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 357804011091 Sulfate transporter family; Region: Sulfate_transp; cl15842 357804011092 Sulfate transporter family; Region: Sulfate_transp; cl15842 357804011093 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 357804011094 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 357804011095 DnaA N-terminal domain; Region: DnaA_N; pfam11638 357804011096 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 ABC; Region: AAA; cd00009 357804011097 Walker A motif; other site 357804011098 ATP binding site [chemical binding]; other site 357804011099 Walker B motif; other site 357804011100 arginine finger; other site 357804011101 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 357804011102 DnaA box-binding interface [nucleotide binding]; other site 357804011103 DNA polymerase III subunit beta; Validated; Region: PRK05643 357804011104 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 trimeric...; Region: beta_clamp; cd00140 357804011105 putative DNA binding surface [nucleotide binding]; other site 357804011106 dimer interface [polypeptide binding]; other site 357804011107 beta-clamp/clamp loader binding surface; other site 357804011108 beta-clamp/translesion DNA polymerase binding surface; other site 357804011109 recombination protein F; Reviewed; Region: recF; PRK00064 357804011110 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804011111 Walker A/P-loop; other site 357804011112 ATP binding site [chemical binding]; other site 357804011113 Q-loop/lid; other site 357804011114 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 357804011115 ABC transporter signature motif; other site 357804011116 Walker B; other site 357804011117 D-loop; other site 357804011118 H-loop/switch region; other site 357804011119 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 357804011120 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 357804011121 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 357804011122 anchoring element; other site 357804011123 dimer interface [polypeptide binding]; other site 357804011124 ATP binding site [chemical binding]; other site 357804011125 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 the...; Region: TOPRIM_TopoIIA_GyrB; cd03366 357804011126 active site 357804011127 putative metal-binding site [ion binding]; other site 357804011128 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 357804011129 CHASE3 domain; Region: CHASE3; cl05000 357804011130 Histidine kinase, Adenylyl cyclase, 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...; Region: HAMP; cd06225 357804011131 dimerization interface [polypeptide binding]; other site 357804011132 GAF domain; Region: GAF_2; pfam13185 357804011133 GAF domain; Region: GAF; cl15785 357804011134 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...; Region: HisKA; cd00082 357804011135 dimer interface [polypeptide binding]; other site 357804011136 phosphorylation site [posttranslational modification] 357804011137 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 357804011138 ATP binding site [chemical binding]; other site 357804011139 Mg2+ binding site [ion binding]; other site 357804011140 G-X-G motif; other site 357804011141 Response regulator receiver domain; Region: Response_reg; pfam00072 357804011142 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 357804011143 active site 357804011144 phosphorylation site [posttranslational modification] 357804011145 intermolecular recognition site; other site 357804011146 dimerization interface [polypeptide binding]; other site 357804011147 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 357804011148 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 357804011149 active site 357804011150 phosphorylation site [posttranslational modification] 357804011151 intermolecular recognition site; other site 357804011152 Response regulator receiver domain; Region: Response_reg; pfam00072 357804011153 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 357804011154 active site 357804011155 phosphorylation site [posttranslational modification] 357804011156 intermolecular recognition site; other site 357804011157 dimerization interface [polypeptide binding]; other site 357804011158 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 357804011159 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 357804011160 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; cl16911 357804011161 CheB methylesterase; Region: CheB_methylest; pfam01339 357804011162 Response regulator receiver domain; Region: Response_reg; pfam00072 357804011163 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 357804011164 active site 357804011165 phosphorylation site [posttranslational modification] 357804011166 intermolecular recognition site; other site 357804011167 dimerization interface [polypeptide binding]; other site 357804011168 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 357804011169 PAS domain; Region: PAS_9; pfam13426 357804011170 putative active site [active] 357804011171 heme pocket [chemical binding]; other site 357804011172 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 357804011173 metal binding site [ion binding]; metal-binding site 357804011174 active site 357804011175 I-site; other site 357804011176 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 357804011177 Branched-chain amino acid transport protein (AzlD); Region: AzlD; cl00735 357804011178 AzlC protein; Region: AzlC; cl00570 357804011179 valine--pyruvate transaminase; Provisional; Region: avtA; PRK09440 357804011180 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 357804011181 pyridoxal 5'-phosphate binding site [chemical binding]; other site 357804011182 homodimer interface [polypeptide binding]; other site 357804011183 catalytic residue [active] 357804011184 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 357804011185 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 357804011186 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 357804011187 dimer interface [polypeptide binding]; other site 357804011188 motif 1; other site 357804011189 active site 357804011190 motif 2; other site 357804011191 motif 3; other site 357804011192 Uncharacterized conserved protein (DUF2161); Region: DUF2161; cl02298 357804011193 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 357804011194 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 357804011195 ATP synthase, Delta/Epsilon chain, long alpha-helix domain; Region: ATP-synt_DE; pfam00401 357804011196 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 357804011197 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 357804011198 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 357804011199 alpha subunit interaction interface [polypeptide binding]; other site 357804011200 Walker A motif; other site 357804011201 ATP binding site [chemical binding]; other site 357804011202 Walker B motif; other site 357804011203 inhibitor binding site; inhibition site 357804011204 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 357804011205 ATP synthase; Region: ATP-synt; cl00365 357804011206 F0F1 ATP synthase subunit gamma; Provisional; Region: PRK13422 357804011207 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 357804011208 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 357804011209 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 357804011210 beta subunit interaction interface [polypeptide binding]; other site 357804011211 Walker A motif; other site 357804011212 ATP binding site [chemical binding]; other site 357804011213 Walker B motif; other site 357804011214 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 357804011215 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 357804011216 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 357804011217 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 357804011218 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 357804011219 ATP synthase subunit C; Region: ATP-synt_C; cl00466 357804011220 ATP synthase A chain; Region: ATP-synt_A; cl00413 357804011221 ATP synthase I chain; Region: ATP_synt_I; cl09170 357804011222 ParB-like partition proteins; Region: parB_part; TIGR00180 357804011223 ParB-like nuclease domain; Region: ParBc; cl02129 357804011224 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 357804011225 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 357804011226 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 the...; Region: ParA; cd02042 357804011227 P-loop; other site 357804011228 Magnesium ion binding site [ion binding]; other site 357804011229 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 the...; Region: ParA; cd02042 357804011230 Magnesium ion binding site [ion binding]; other site 357804011231 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; cl16911 357804011232 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 357804011233 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 357804011234 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 357804011235 NADPH-dependent FMN reductase; Region: FMN_red; cl00438