-- dump date 20120504_153841 -- class Genbank::misc_feature -- table misc_feature_note -- id note 323098000001 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 323098000002 DnaA N-terminal domain; Region: DnaA_N; pfam11638 323098000003 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 323098000004 Walker A motif; other site 323098000005 ATP binding site [chemical binding]; other site 323098000006 Walker B motif; other site 323098000007 arginine finger; other site 323098000008 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 323098000009 DnaA box-binding interface [nucleotide binding]; other site 323098000010 DNA polymerase III subunit beta; Validated; Region: PRK05643 323098000011 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 323098000012 putative DNA binding surface [nucleotide binding]; other site 323098000013 dimer interface [polypeptide binding]; other site 323098000014 beta-clamp/clamp loader binding surface; other site 323098000015 beta-clamp/translesion DNA polymerase binding surface; other site 323098000016 recombination protein F; Reviewed; Region: recF; PRK00064 323098000017 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098000018 Walker A/P-loop; other site 323098000019 ATP binding site [chemical binding]; other site 323098000020 Q-loop/lid; other site 323098000021 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098000022 ABC transporter signature motif; other site 323098000023 Walker B; other site 323098000024 D-loop; other site 323098000025 H-loop/switch region; other site 323098000026 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 323098000027 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 323098000028 Mg2+ binding site [ion binding]; other site 323098000029 G-X-G motif; other site 323098000030 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 323098000031 anchoring element; other site 323098000032 dimer interface [polypeptide binding]; other site 323098000033 ATP binding site [chemical binding]; other site 323098000034 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 323098000035 active site 323098000036 putative metal-binding site [ion binding]; other site 323098000037 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 323098000038 PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins, plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech...; Region: PAN_APPLE; cl00112 323098000039 Subfamily of PAN/APPLE-like domains; present in plasma prekallikrein/coagulation factor XI, microneme antigen proteins, and a few prokaryotic proteins. PAN/APPLE domains fulfill diverse biological functions by mediating protein-protein or...; Region: APPLE_Factor_XI_like; cd01100 323098000040 putative binding site; other site 323098000041 Transposase domain (DUF772); Region: DUF772; cl15789 323098000042 Transposase domain (DUF772); Region: DUF772; cl15789 323098000043 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 323098000044 Ligand Binding Site [chemical binding]; other site 323098000045 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; cl07364 323098000046 NifU-like domain; Region: NifU; cl00484 323098000047 Protein of unknown function (DUF2778); Region: DUF2778; pfam10908 323098000048 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 323098000049 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 323098000050 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 323098000051 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 323098000052 metal binding site 2 [ion binding]; metal-binding site 323098000053 putative DNA binding helix; other site 323098000054 metal binding site 1 [ion binding]; metal-binding site 323098000055 dimer interface [polypeptide binding]; other site 323098000056 structural Zn2+ binding site [ion binding]; other site 323098000057 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 323098000058 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 323098000059 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 323098000060 FeS/SAM binding site; other site 323098000061 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 323098000062 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 323098000063 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098000064 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 323098000065 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 323098000066 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 323098000067 Transporter associated domain; Region: CorC_HlyC; cl08393 323098000068 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 323098000069 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 323098000070 putative active site [active] 323098000071 catalytic triad [active] 323098000072 putative dimer interface [polypeptide binding]; other site 323098000073 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 323098000074 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 323098000075 non-specific DNA binding site [nucleotide binding]; other site 323098000076 salt bridge; other site 323098000077 sequence-specific DNA binding site [nucleotide binding]; other site 323098000078 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; cl15754 323098000079 Uncharacterized BCR, YhbC family COG0779; Region: DUF150; pfam02576 323098000080 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 323098000081 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 323098000082 Sm1 motif; other site 323098000083 D3 - B interaction site; other site 323098000084 D1 - D2 interaction site; other site 323098000085 Hfq - Hfq interaction site; other site 323098000086 RNA binding pocket [nucleotide binding]; other site 323098000087 Sm2 motif; other site 323098000088 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 323098000089 NusA N-terminal domain; Region: NusA_N; pfam08529 323098000090 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 323098000091 RNA binding site [nucleotide binding]; other site 323098000092 homodimer interface [polypeptide binding]; other site 323098000093 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 323098000094 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 323098000095 G-X-X-G motif; other site 323098000096 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 323098000097 hypothetical protein; Provisional; Region: PRK09190 323098000098 Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; structure revealed putative RNA binding cleft; proteins are encoded by an operon that includes other proteins involved in transcription and/or translation; Region: YlxR; cd00279 323098000099 putative RNA binding cleft [nucleotide binding]; other site 323098000100 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 323098000101 translation initiation factor IF-2; Region: IF-2; TIGR00487 323098000102 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 323098000103 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 323098000104 G1 box; other site 323098000105 putative GEF interaction site [polypeptide binding]; other site 323098000106 GTP/Mg2+ binding site [chemical binding]; other site 323098000107 Switch I region; other site 323098000108 G2 box; other site 323098000109 G3 box; other site 323098000110 Switch II region; other site 323098000111 G4 box; other site 323098000112 G5 box; other site 323098000113 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 323098000114 Translation-initiation factor 2; Region: IF-2; pfam11987 323098000115 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 323098000116 Ribosome-binding factor A; Region: RBFA; cl00542 323098000117 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05389 323098000118 PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific...; Region: PseudoU_synth_EcTruB; cd02573 323098000119 RNA binding site [nucleotide binding]; other site 323098000120 active site 323098000121 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 323098000122 16S/18S rRNA binding site [nucleotide binding]; other site 323098000123 S13e-L30e interaction site [polypeptide binding]; other site 323098000124 25S rRNA binding site [nucleotide binding]; other site 323098000125 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 323098000126 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 323098000127 RNase E interface [polypeptide binding]; other site 323098000128 trimer interface [polypeptide binding]; other site 323098000129 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 323098000130 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 323098000131 RNase E interface [polypeptide binding]; other site 323098000132 trimer interface [polypeptide binding]; other site 323098000133 active site 323098000134 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 323098000135 putative nucleic acid binding region [nucleotide binding]; other site 323098000136 G-X-X-G motif; other site 323098000137 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 323098000138 RNA binding site [nucleotide binding]; other site 323098000139 domain interface; other site 323098000140 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 323098000141 Helix-turn-helix domains; Region: HTH; cl00088 323098000142 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 323098000143 dimerization interface [polypeptide binding]; other site 323098000144 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 323098000145 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 323098000146 dimer interface [polypeptide binding]; other site 323098000147 active site 323098000148 heme binding site [chemical binding]; other site 323098000149 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 323098000150 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 323098000151 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved...; Region: GST_N_GTT1_like; cd03046 323098000152 putative GSH binding site (G-site) [chemical binding]; other site 323098000153 putative C-terminal domain interface [polypeptide binding]; other site 323098000154 C-terminal, alpha helical domain of an unknown subfamily 8 of Glutathione S-transferases; Region: GST_C_8; cd03207 323098000155 dimer interface [polypeptide binding]; other site 323098000156 N-terminal domain interface [polypeptide binding]; other site 323098000157 putative substrate binding pocket (H-site) [chemical binding]; other site 323098000158 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06505 323098000159 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 323098000160 NAD binding site [chemical binding]; other site 323098000161 homotetramer interface [polypeptide binding]; other site 323098000162 homodimer interface [polypeptide binding]; other site 323098000163 substrate binding site [chemical binding]; other site 323098000164 active site 323098000165 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 323098000166 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 323098000167 dimer interface [polypeptide binding]; other site 323098000168 active site 323098000169 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 323098000170 active site 2 [active] 323098000171 active site 1 [active] 323098000172 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 323098000173 metal binding site 2 [ion binding]; metal-binding site 323098000174 putative DNA binding helix; other site 323098000175 metal binding site 1 [ion binding]; metal-binding site 323098000176 dimer interface [polypeptide binding]; other site 323098000177 structural Zn2+ binding site [ion binding]; other site 323098000178 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3807 323098000179 Bacterial SH3 domain; Region: SH3_3; cl02551 323098000180 Bacterial SH3 domain; Region: SH3_3; cl02551 323098000181 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 323098000182 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098000183 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 323098000184 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 323098000185 ATP binding site [chemical binding]; other site 323098000186 substrate interface [chemical binding]; other site 323098000187 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 323098000188 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 323098000189 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 323098000190 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 323098000191 DNA binding site [nucleotide binding] 323098000192 catalytic residue [active] 323098000193 H2TH interface [polypeptide binding]; other site 323098000194 putative catalytic residues [active] 323098000195 turnover-facilitating residue; other site 323098000196 intercalation triad [nucleotide binding]; other site 323098000197 8OG recognition residue [nucleotide binding]; other site 323098000198 putative reading head residues; other site 323098000199 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 323098000200 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 323098000201 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 323098000202 S-adenosylmethionine binding site [chemical binding]; other site 323098000203 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 323098000204 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 323098000205 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 323098000206 active site 323098000207 ATP binding site [chemical binding]; other site 323098000208 bifunctional SbtC-like/phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Provisional; Region: PRK13982 323098000209 Flavoprotein; Region: Flavoprotein; cl08021 323098000210 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 323098000211 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 323098000212 trimer interface [polypeptide binding]; other site 323098000213 active site 323098000214 dUTPase; Provisional; Region: PHA03124 323098000215 PAS fold; Region: PAS_7; pfam12860 323098000216 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 323098000217 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 323098000218 dimer interface [polypeptide binding]; other site 323098000219 phosphorylation site [posttranslational modification] 323098000220 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 323098000221 ATP binding site [chemical binding]; other site 323098000222 Mg2+ binding site [ion binding]; other site 323098000223 G-X-G motif; other site 323098000224 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 323098000225 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 323098000226 PilZ domain; Region: PilZ; cl01260 323098000227 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 323098000228 Substrate binding site; other site 323098000229 metal-binding site 323098000230 Inactivated superfamily I helicase [DNA replication, recombination, and repair]; Region: COG3893 323098000231 double-strand break repair protein AddB, alphaproteobacterial type; Region: addB_alphas; TIGR02786 323098000232 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 323098000233 double-strand break repair helicase AddA, alphaproteobacterial type; Region: addA_alphas; TIGR02784 323098000234 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098000235 Family description; Region: UvrD_C_2; cl15862 323098000236 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 323098000237 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 323098000238 catalytic residues [active] 323098000239 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 323098000240 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 323098000241 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 323098000242 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 323098000243 substrate binding site [chemical binding]; other site 323098000244 active site 323098000245 catalytic residues [active] 323098000246 heterodimer interface [polypeptide binding]; other site 323098000247 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 323098000248 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 323098000249 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098000250 catalytic residue [active] 323098000251 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 323098000252 active site 323098000253 Protein of unknown function (DUF1049); Region: DUF1049; cl01539 323098000254 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 323098000255 IHF dimer interface [polypeptide binding]; other site 323098000256 IHF - DNA interface [nucleotide binding]; other site 323098000257 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 323098000258 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 323098000259 tandem repeat interface [polypeptide binding]; other site 323098000260 oligomer interface [polypeptide binding]; other site 323098000261 active site residues [active] 323098000262 Etoposide-induced protein 2.4 (EI24); Region: EI24; cl01126 323098000263 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 323098000264 catalytic residues [active] 323098000265 Orthopoxvirus protein of unknown function (DUF830); Region: DUF830; cl13998 323098000266 Flavin containing amine oxidoreductase; Region: Amino_oxidase; pfam01593 323098000267 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098000268 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098000269 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_IV; cd01994 323098000270 Ligand Binding Site [chemical binding]; other site 323098000271 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 323098000272 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 323098000273 putative tRNA-binding site [nucleotide binding]; other site 323098000274 B3/4 domain; Region: B3_4; cl11458 323098000275 tRNA synthetase B5 domain; Region: B5; cl08394 323098000276 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 323098000277 dimer interface [polypeptide binding]; other site 323098000278 motif 1; other site 323098000279 motif 3; other site 323098000280 motif 2; other site 323098000281 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 323098000282 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 323098000283 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 323098000284 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 323098000285 dimer interface [polypeptide binding]; other site 323098000286 motif 1; other site 323098000287 active site 323098000288 motif 2; other site 323098000289 motif 3; other site 323098000290 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 323098000291 23S rRNA binding site [nucleotide binding]; other site 323098000292 L21 binding site [polypeptide binding]; other site 323098000293 L13 binding site [polypeptide binding]; other site 323098000294 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 323098000295 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 323098000296 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 323098000297 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 323098000298 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 323098000299 Uncharacterized conserved protein (DUF2235); Region: DUF2235; cl01480 323098000300 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 323098000301 PAS domain; Region: PAS_9; pfam13426 323098000302 putative active site [active] 323098000303 heme pocket [chemical binding]; other site 323098000304 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 323098000305 PAS domain; Region: PAS_9; pfam13426 323098000306 putative active site [active] 323098000307 heme pocket [chemical binding]; other site 323098000308 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 323098000309 PAS domain; Region: PAS_9; pfam13426 323098000310 putative active site [active] 323098000311 heme pocket [chemical binding]; other site 323098000312 PAS domain; Region: PAS_9; pfam13426 323098000313 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 323098000314 putative active site [active] 323098000315 heme pocket [chemical binding]; other site 323098000316 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 323098000317 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 323098000318 Uncharacterized protein, similar to the N-terminal domain of Lon protease [General function prediction only]; Region: COG2802 323098000319 Trm112p-like protein; Region: Trm112p; cl01066 323098000320 Nitrogen regulatory protein P-II; Region: P-II; cl00412 323098000321 Nitrogen regulatory protein P-II; Region: P-II; smart00938 323098000322 Domain of unknown function (DUF4339); Region: DUF4339; pfam14237 323098000323 Bacterial protein of unknown function (DUF898); Region: DUF898; cl01738 323098000324 Acyl-CoA thioesterase [Lipid metabolism]; Region: TesB; COG1946 323098000325 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 323098000326 active site 323098000327 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 323098000328 catalytic triad [active] 323098000329 dimer interface [polypeptide binding]; other site 323098000330 2-octaprenyl-6-methoxyphenyl hydroxylase; Provisional; Region: PRK07333 323098000331 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098000332 Transposase zinc-ribbon domain; Region: Zn_Tnp_IS1595; pfam12760 323098000333 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 323098000334 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; cl01481 323098000335 succinyldiaminopimelate transaminase; Region: DapC_gpp; TIGR03538 323098000336 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 323098000337 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098000338 homodimer interface [polypeptide binding]; other site 323098000339 catalytic residue [active] 323098000340 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 323098000341 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098000342 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 323098000343 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 323098000344 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 323098000345 putative phosphate binding site [ion binding]; other site 323098000346 putative catalytic site [active] 323098000347 active site 323098000348 metal binding site A [ion binding]; metal-binding site 323098000349 DNA binding site [nucleotide binding] 323098000350 putative AP binding site [nucleotide binding]; other site 323098000351 putative metal binding site B [ion binding]; other site 323098000352 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 323098000353 ligand binding site [chemical binding]; other site 323098000354 flexible hinge region; other site 323098000355 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 323098000356 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 323098000357 active site 323098000358 phosphorylation site [posttranslational modification] 323098000359 intermolecular recognition site; other site 323098000360 dimerization interface [polypeptide binding]; other site 323098000361 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 323098000362 DNA binding site [nucleotide binding] 323098000363 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 323098000364 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 323098000365 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 323098000366 catalytic residue [active] 323098000367 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 323098000368 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 323098000369 C-terminal domain interface [polypeptide binding]; other site 323098000370 GSH binding site (G-site) [chemical binding]; other site 323098000371 dimer interface [polypeptide binding]; other site 323098000372 C-terminal, alpha helical domain of Ure2p and related Glutathione S-transferase-like proteins; Region: GST_C_Ure2p_like; cd03178 323098000373 dimer interface [polypeptide binding]; other site 323098000374 N-terminal domain interface [polypeptide binding]; other site 323098000375 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 323098000376 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 323098000377 HIGH motif; other site 323098000378 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 323098000379 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 323098000380 active site 323098000381 KMSKS motif; other site 323098000382 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 323098000383 tRNA binding surface [nucleotide binding]; other site 323098000384 Lipopolysaccharide-assembly; Region: LptE; cl01125 323098000385 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 323098000386 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 323098000387 ParB-like partition proteins; Region: parB_part; TIGR00180 323098000388 ParB-like nuclease domain; Region: ParBc; cl02129 323098000389 KorB domain; Region: KorB; pfam08535 323098000390 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 323098000391 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 323098000392 P-loop; other site 323098000393 Magnesium ion binding site [ion binding]; other site 323098000394 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; cl15754 323098000395 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 323098000396 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098000397 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 323098000398 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 323098000399 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 323098000400 trmE is a tRNA modification GTPase; Region: trmE; cd04164 323098000401 G1 box; other site 323098000402 GTP/Mg2+ binding site [chemical binding]; other site 323098000403 Switch I region; other site 323098000404 G2 box; other site 323098000405 Switch II region; other site 323098000406 G3 box; other site 323098000407 G4 box; other site 323098000408 G5 box; other site 323098000409 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 323098000410 Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones]; Region: COG1331 323098000411 TRX domain, SSP411 protein family; members of this family are highly conserved proteins present in eukaryotes, bacteria and archaea, about 600-800 amino acids in length, which contain a TRX domain with a redox active CXXC motif. The human/rat protein; Region: SSP411; cd02955 323098000412 catalytic residues [active] 323098000413 AGE domain; N-acyl-D-glucosamine 2-epimerase domain; Responsible for intermediate epimerization during biosynthesis of N-acetylneuraminic acid. Catalytic mechanism is believed to be via nucleotide elimination and readdition and is ATP modulated. AGE is...; Region: AGE; cl00183 323098000414 transcription termination factor Rho; Provisional; Region: rho; PRK09376 323098000415 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 323098000416 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 323098000417 RNA binding site [nucleotide binding]; other site 323098000418 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 323098000419 multimer interface [polypeptide binding]; other site 323098000420 Walker A motif; other site 323098000421 ATP binding site [chemical binding]; other site 323098000422 Walker B motif; other site 323098000423 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 323098000424 Kinase/pyrophosphorylase; Region: Kinase-PPPase; cl00780 323098000425 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 323098000426 active site 323098000427 dimer interface [polypeptide binding]; other site 323098000428 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 323098000429 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 323098000430 CoA-binding site [chemical binding]; other site 323098000431 ATP-binding [chemical binding]; other site 323098000432 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 323098000433 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 323098000434 active site 323098000435 substrate binding site [chemical binding]; other site 323098000436 catalytic site [active] 323098000437 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; cl00251 323098000438 SecA binding site; other site 323098000439 Preprotein binding site; other site 323098000440 Tim44-like domain; Region: Tim44; cl09208 323098000441 Membrane-bound lytic murein transglycosylase [Cell envelope biogenesis, outer membrane]; Region: MltA; COG2821 323098000442 MltA specific insert domain; Region: MltA; cl08398 323098000443 3D domain; Region: 3D; cl01439 323098000444 Smr domain; Region: Smr; cl02619 323098000445 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 323098000446 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 323098000447 ATP binding site [chemical binding]; other site 323098000448 Mg2+ binding site [ion binding]; other site 323098000449 G-X-G motif; other site 323098000450 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 323098000451 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 323098000452 active site 323098000453 phosphorylation site [posttranslational modification] 323098000454 intermolecular recognition site; other site 323098000455 dimerization interface [polypeptide binding]; other site 323098000456 Helix-turn-helix domains; Region: HTH; cl00088 323098000457 Protein of unknown function (DUF1052); Region: DUF1052; cl02197 323098000458 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 323098000459 PAS fold; Region: PAS_3; pfam08447 323098000460 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 323098000461 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 323098000462 putative active site [active] 323098000463 PAS fold; Region: PAS_3; pfam08447 323098000464 heme pocket [chemical binding]; other site 323098000465 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 323098000466 PAS domain; Region: PAS_9; pfam13426 323098000467 putative active site [active] 323098000468 heme pocket [chemical binding]; other site 323098000469 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 323098000470 dimer interface [polypeptide binding]; other site 323098000471 phosphorylation site [posttranslational modification] 323098000472 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 323098000473 ATP binding site [chemical binding]; other site 323098000474 Mg2+ binding site [ion binding]; other site 323098000475 G-X-G motif; other site 323098000476 Response regulator receiver domain; Region: Response_reg; pfam00072 323098000477 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 323098000478 active site 323098000479 phosphorylation site [posttranslational modification] 323098000480 intermolecular recognition site; other site 323098000481 dimerization interface [polypeptide binding]; other site 323098000482 Predicted methyltransferases [General function prediction only]; Region: COG0313 323098000483 Restriction endonuclease; Region: Mrr_cat; cl00516 323098000484 glutathione synthetase; Provisional; Region: PRK05246 323098000485 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 323098000486 ATP-grasp domain; Region: ATP-grasp_4; cl03087 323098000487 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 323098000488 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 323098000489 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098000490 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 323098000491 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 323098000492 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 323098000493 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 323098000494 dimer interface [polypeptide binding]; other site 323098000495 phosphorylation site [posttranslational modification] 323098000496 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 323098000497 ATP binding site [chemical binding]; other site 323098000498 Mg2+ binding site [ion binding]; other site 323098000499 G-X-G motif; other site 323098000500 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 323098000501 active site 323098000502 phosphorylation site [posttranslational modification] 323098000503 intermolecular recognition site; other site 323098000504 dimerization interface [polypeptide binding]; other site 323098000505 Response regulator receiver domain; Region: Response_reg; pfam00072 323098000506 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 323098000507 active site 323098000508 phosphorylation site [posttranslational modification] 323098000509 intermolecular recognition site; other site 323098000510 dimerization interface [polypeptide binding]; other site 323098000511 pantothenate kinase; Provisional; Region: PRK05439 323098000512 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 323098000513 ATP-binding site [chemical binding]; other site 323098000514 CoA-binding site [chemical binding]; other site 323098000515 Mg2+-binding site [ion binding]; other site 323098000516 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 323098000517 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 323098000518 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 323098000519 substrate binding site [chemical binding]; other site 323098000520 glutamase interaction surface [polypeptide binding]; other site 323098000521 Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase [Amino acid transport and metabolism]; Region: HisA; COG0106 323098000522 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 323098000523 catalytic residues [active] 323098000524 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 323098000525 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 323098000526 putative active site [active] 323098000527 oxyanion strand; other site 323098000528 catalytic triad [active] 323098000529 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 323098000530 imidazoleglycerol-phosphate dehydratase; Validated; Region: hisB; PRK00951 323098000531 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 323098000532 putative active site pocket [active] 323098000533 4-fold oligomerization interface [polypeptide binding]; other site 323098000534 metal binding residues [ion binding]; metal-binding site 323098000535 3-fold/trimer interface [polypeptide binding]; other site 323098000536 Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the...; Region: protease_HslV; cd01913 323098000537 active site 323098000538 HslU subunit interaction site [polypeptide binding]; other site 323098000539 Acetyltransferase (GNAT) domain; Region: Acetyltransf_8; pfam13523 323098000540 Siderophore biosynthesis protein domain; Region: AlcB; smart01006 323098000541 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 323098000542 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 323098000543 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 323098000544 Walker A motif; other site 323098000545 ATP binding site [chemical binding]; other site 323098000546 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098000547 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 323098000548 polyhydroxyalkanoate depolymerase, intracellular; Region: PHB_depoly_PhaZ; TIGR01849 323098000549 PHB de-polymerase C-terminus; Region: PHB_depo_C; cl14907 323098000550 Protein of unknown function DUF45; Region: DUF45; cl00636 323098000551 Transglycosylase; Region: Transgly; cl07896 323098000552 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 323098000553 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 323098000554 PII uridylyl-transferase; Provisional; Region: PRK05092 323098000555 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 323098000556 metal binding triad; other site 323098000557 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 323098000558 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 323098000559 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 323098000560 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 323098000561 Disulfide bond chaperones of the HSP33 family [Posttranslational modification, protein turnover, chaperones]; Region: COG1281 323098000562 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 323098000563 dimerization interface [polypeptide binding]; other site 323098000564 domain crossover interface; other site 323098000565 redox-dependent activation switch; other site 323098000566 Protein of unknown function (DUF525); Region: DUF525; cl01119 323098000567 OpgC protein; Region: OpgC_C; cl00792 323098000568 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; cl01053 323098000569 active site 323098000570 oxyanion hole [active] 323098000571 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; cl01053 323098000572 active site 323098000573 catalytic triad [active] 323098000574 oxyanion hole [active] 323098000575 O-succinylhomoserine sulfhydrylase; Reviewed; Region: PRK07504 323098000576 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 323098000577 homodimer interface [polypeptide binding]; other site 323098000578 substrate-cofactor binding pocket; other site 323098000579 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098000580 catalytic residue [active] 323098000581 2'-deoxycytidine 5'-triphosphate deaminase; Provisional; Region: PRK07559 323098000582 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cl00493 323098000583 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 323098000584 trimer interface [polypeptide binding]; other site 323098000585 active site 323098000586 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cl00493 323098000587 CrcB-like protein; Region: CRCB; cl09114 323098000588 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 323098000589 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 323098000590 Cu(I) binding site [ion binding]; other site 323098000591 Glycosyltransferases, probably involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG1215 323098000592 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 323098000593 Transposase zinc-ribbon domain; Region: Zn_Tnp_IS1595; pfam12760 323098000594 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; cl01481 323098000595 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 323098000596 active site 323098000597 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 323098000598 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 323098000599 substrate binding pocket [chemical binding]; other site 323098000600 membrane-bound complex binding site; other site 323098000601 hinge residues; other site 323098000602 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 323098000603 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 323098000604 active site 323098000605 nucleotide binding site [chemical binding]; other site 323098000606 HIGH motif; other site 323098000607 KMSKS motif; other site 323098000608 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 323098000609 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 323098000610 active site 323098000611 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 323098000612 Catalytic site; other site 323098000613 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 323098000614 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 323098000615 tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]; Region: Sun; COG0144 323098000616 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 323098000617 S-adenosylmethionine binding site [chemical binding]; other site 323098000618 Heparinase II/III-like protein; Region: Hepar_II_III; cl15421 323098000619 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 323098000620 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 323098000621 purine monophosphate binding site [chemical binding]; other site 323098000622 dimer interface [polypeptide binding]; other site 323098000623 putative catalytic residues [active] 323098000624 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 323098000625 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 323098000626 Cytochrome c; Region: Cytochrom_C; cl11414 323098000627 Cytochrome c; Region: Cytochrom_C; cl11414 323098000628 Permeases of the major facilitator superfamily [General function prediction only]; Region: COG2270 323098000629 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 323098000630 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 323098000631 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 323098000632 MatE; Region: MatE; cl10513 323098000633 MatE; Region: MatE; cl10513 323098000634 2-dehydropantoate 2-reductase; Provisional; Region: PRK12921 323098000635 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098000636 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 323098000637 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 323098000638 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 323098000639 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 323098000640 N-terminal domain interface [polypeptide binding]; other site 323098000641 dimer interface [polypeptide binding]; other site 323098000642 substrate binding pocket (H-site) [chemical binding]; other site 323098000643 Bacitracin resistance protein BacA; Region: BacA; cl00858 323098000644 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 323098000645 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 323098000646 putative NAD(P) binding site [chemical binding]; other site 323098000647 active site 323098000648 Tetratricopeptide repeat; Region: TPR_12; pfam13424 323098000649 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 323098000650 binding surface 323098000651 TPR motif; other site 323098000652 Tetratricopeptide repeat; Region: TPR_12; pfam13424 323098000653 Tetratricopeptide repeat; Region: TPR_12; pfam13424 323098000654 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 323098000655 Uncharacterized subfamily of N-terminal LabA-like domains; Region: LabA_like_N_1; cd11297 323098000656 putative metal binding site [ion binding]; other site 323098000657 C-terminal domain of LabA_like proteins; Region: LabA_like_C; cd10146 323098000658 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 323098000659 putative active site [active] 323098000660 catalytic site [active] 323098000661 putative substrate binding site [chemical binding]; other site 323098000662 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 323098000663 OstA-like protein; Region: OstA; cl00844 323098000664 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 323098000665 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 323098000666 Walker A/P-loop; other site 323098000667 ATP binding site [chemical binding]; other site 323098000668 Q-loop/lid; other site 323098000669 ABC transporter signature motif; other site 323098000670 Walker B; other site 323098000671 D-loop; other site 323098000672 H-loop/switch region; other site 323098000673 RNA polymerase factor sigma-54; Provisional; Region: PRK12469 323098000674 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 323098000675 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 323098000676 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 323098000677 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 323098000678 30S subunit binding site; other site 323098000679 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 323098000680 active site 323098000681 phosphorylation site [posttranslational modification] 323098000682 Transposase domain (DUF772); Region: DUF772; cl15789 323098000683 Transposase domain (DUF772); Region: DUF772; cl15789 323098000684 Glutamate-cysteine ligase family 2(GCS2); Region: GCS2; cl00954 323098000685 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 323098000686 Sel1 repeat; Region: Sel1; cl02723 323098000687 Sel1 repeat; Region: Sel1; cl02723 323098000688 Sel1 repeat; Region: Sel1; cl02723 323098000689 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 323098000690 Putative transmembrane protein (Alph_Pro_TM); Region: Alph_Pro_TM; cl09826 323098000691 Pyrococcus furiosus PF1019 and related proteins, metallophosphatase domain; Region: MPP_PF1019; cd07391 323098000692 putative active site [active] 323098000693 putative metal binding site [ion binding]; other site 323098000694 DEXH box helicase, DNA ligase-associated; Region: DEXH_lig_assoc; TIGR04121 323098000695 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 323098000696 ATP binding site [chemical binding]; other site 323098000697 putative Mg++ binding site [ion binding]; other site 323098000698 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 323098000699 nucleotide binding region [chemical binding]; other site 323098000700 ATP-binding site [chemical binding]; other site 323098000701 DEAD/H associated; Region: DEAD_assoc; pfam08494 323098000702 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 323098000703 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 323098000704 Peptidase family M48; Region: Peptidase_M48; cl12018 323098000705 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 323098000706 putative ligand binding site [chemical binding]; other site 323098000707 coproporphyrinogen III oxidase; Provisional; Region: PRK09057 323098000708 HemN C-terminal domain; Region: HemN_C; pfam06969 323098000709 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 323098000710 active site 323098000711 dimerization interface [polypeptide binding]; other site 323098000712 ribonuclease PH; Reviewed; Region: rph; PRK00173 323098000713 Ribonuclease PH; Region: RNase_PH_bact; cd11362 323098000714 hexamer interface [polypeptide binding]; other site 323098000715 active site 323098000716 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 323098000717 HrcA protein C terminal domain; Region: HrcA; pfam01628 323098000718 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 323098000719 dimer interface [polypeptide binding]; other site 323098000720 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 323098000721 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 323098000722 chaperone protein DnaJ; Provisional; Region: PRK10767 323098000723 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 323098000724 HSP70 interaction site [polypeptide binding]; other site 323098000725 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 323098000726 substrate binding site [polypeptide binding]; other site 323098000727 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 323098000728 Zn binding sites [ion binding]; other site 323098000729 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 323098000730 dimer interface [polypeptide binding]; other site 323098000731 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 323098000732 S-adenosylmethionine binding site [chemical binding]; other site 323098000733 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 323098000734 dihydrodipicolinate reductase; Provisional; Region: PRK00048 323098000735 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098000736 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 323098000737 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 323098000738 catalytic core [active] 323098000739 Helix-turn-helix domain; Region: HTH_18; pfam12833 323098000740 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 323098000741 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 323098000742 DNA binding site [nucleotide binding] 323098000743 active site 323098000744 Integral membrane protein (DUF2244); Region: DUF2244; cl02302 323098000745 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 323098000746 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 323098000747 minor groove reading motif; other site 323098000748 helix-hairpin-helix signature motif; other site 323098000749 substrate binding pocket [chemical binding]; other site 323098000750 active site 323098000751 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 323098000752 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 323098000753 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 323098000754 RNA binding site [nucleotide binding]; other site 323098000755 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 323098000756 RNA binding site [nucleotide binding]; other site 323098000757 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 323098000758 RNA binding site [nucleotide binding]; other site 323098000759 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 323098000760 RNA binding site [nucleotide binding]; other site 323098000761 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 323098000762 RNA binding site [nucleotide binding]; other site 323098000763 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 323098000764 RNA binding site [nucleotide binding]; other site 323098000765 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098000766 cytidylate kinase; Provisional; Region: cmk; PRK00023 323098000767 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 323098000768 CMP-binding site; other site 323098000769 The sites determining sugar specificity; other site 323098000770 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 323098000771 3-phosphoshikimate 1-carboxyvinyltransferase; Region: aroA; TIGR01356 323098000772 hinge; other site 323098000773 active site 323098000774 TIGR02300 family protein; Region: FYDLN_acid 323098000775 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation...; Region: ACD_IbpA-B_like; cd06470 323098000776 putative dimer interface [polypeptide binding]; other site 323098000777 Protein of unknown function (DUF1150); Region: DUF1150; cl11577 323098000778 Dehydratase family; Region: ILVD_EDD; cl00340 323098000779 Transposase domain (DUF772); Region: DUF772; cl15789 323098000780 Transposase domain (DUF772); Region: DUF772; cl15789 323098000781 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 323098000782 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 323098000783 active site 323098000784 HIGH motif; other site 323098000785 dimer interface [polypeptide binding]; other site 323098000786 KMSKS motif; other site 323098000787 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 323098000788 Adenosine kinase (AK) catalyzes the phosphorylation of ribofuranosyl-containing nucleoside analogues at the 5'-hydroxyl using ATP or GTP as the phosphate donor.The physiological function of AK is associated with the regulation of extracellular adenosine...; Region: adenosine_kinase; cd01168 323098000789 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 323098000790 substrate binding site [chemical binding]; other site 323098000791 ATP binding site [chemical binding]; other site 323098000792 Pirin-related protein [General function prediction only]; Region: COG1741 323098000793 Cupin domain; Region: Cupin_2; cl09118 323098000794 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 323098000795 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 323098000796 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 323098000797 Invasion associated locus B (IalB) protein; Region: IalB; cl02207 323098000798 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00051 323098000799 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 323098000800 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 323098000801 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 323098000802 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 323098000803 Subunit I/III interface [polypeptide binding]; other site 323098000804 D-pathway; other site 323098000805 Subunit I/VIIc interface [polypeptide binding]; other site 323098000806 Subunit I/IV interface [polypeptide binding]; other site 323098000807 Subunit I/II interface [polypeptide binding]; other site 323098000808 Low-spin heme (heme a) binding site [chemical binding]; other site 323098000809 Subunit I/VIIa interface [polypeptide binding]; other site 323098000810 Subunit I/VIa interface [polypeptide binding]; other site 323098000811 Dimer interface; other site 323098000812 Putative water exit pathway; other site 323098000813 Binuclear center (heme a3/CuB) [ion binding]; other site 323098000814 K-pathway; other site 323098000815 Subunit I/Vb interface [polypeptide binding]; other site 323098000816 Putative proton exit pathway; other site 323098000817 Subunit I/VIb interface; other site 323098000818 Subunit I/VIc interface [polypeptide binding]; other site 323098000819 Electron transfer pathway; other site 323098000820 Subunit I/VIIIb interface [polypeptide binding]; other site 323098000821 Subunit I/VIIb interface [polypeptide binding]; other site 323098000822 UbiA prenyltransferase family; Region: UbiA; cl00337 323098000823 Cytochrome c oxidase assembly protein CtaG/Cox11; Region: CtaG_Cox11; cl01240 323098000824 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 323098000825 Subunit III/VIIa interface [polypeptide binding]; other site 323098000826 Phospholipid binding site [chemical binding]; other site 323098000827 Subunit I/III interface [polypeptide binding]; other site 323098000828 Subunit III/VIb interface [polypeptide binding]; other site 323098000829 Subunit III/VIa interface; other site 323098000830 Subunit III/Vb interface [polypeptide binding]; other site 323098000831 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 323098000832 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants, cyanobacteria; Region: Thr-synth_2; cd01560 323098000833 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098000834 catalytic residue [active] 323098000835 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 323098000836 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 323098000837 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 323098000838 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 323098000839 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 323098000840 Integrase core domain; Region: rve; cl01316 323098000841 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098000842 Winged helix-turn helix; Region: HTH_29; pfam13551 323098000843 Helix-turn-helix domains; Region: HTH; cl00088 323098000844 Helix-turn-helix domains; Region: HTH; cl00088 323098000845 F0F1 ATP synthase subunit B; Provisional; Region: PRK14475 323098000846 Plant ATP synthase F0; Region: YMF19; cl07975 323098000847 Plant ATP synthase F0; Region: YMF19; cl07975 323098000848 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 323098000849 ATP synthase subunit C; Region: ATP-synt_C; cl00466 323098000850 ATP synthase A chain; Region: ATP-synt_A; cl00413 323098000851 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; cl09754 323098000852 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 323098000853 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 323098000854 active site 323098000855 phosphorylation site [posttranslational modification] 323098000856 intermolecular recognition site; other site 323098000857 dimerization interface [polypeptide binding]; other site 323098000858 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 323098000859 DNA binding residues [nucleotide binding] 323098000860 dimerization interface [polypeptide binding]; other site 323098000861 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 323098000862 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 323098000863 substrate-cofactor binding pocket; other site 323098000864 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098000865 catalytic residue [active] 323098000866 biotin synthase; Region: bioB; TIGR00433 323098000867 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 323098000868 FeS/SAM binding site; other site 323098000869 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 323098000870 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 323098000871 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 323098000872 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 323098000873 hinge; other site 323098000874 active site 323098000875 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 323098000876 histidinol dehydrogenase; Region: hisD; TIGR00069 323098000877 NAD binding site [chemical binding]; other site 323098000878 dimerization interface [polypeptide binding]; other site 323098000879 product binding site; other site 323098000880 substrate binding site [chemical binding]; other site 323098000881 zinc binding site [ion binding]; other site 323098000882 catalytic residues [active] 323098000883 Uncharacterized protein family (UPF0262); Region: UPF0262; cl11489 323098000884 Low molecular weight phosphatase family; Region: LMWPc; cd00115 323098000885 active site 323098000886 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 323098000887 ERCC4-like helicases [DNA replication, recombination, and repair]; Region: MPH1; COG1111 323098000888 ATP binding site [chemical binding]; other site 323098000889 putative Mg++ binding site [ion binding]; other site 323098000890 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 323098000891 nucleotide binding region [chemical binding]; other site 323098000892 ATP-binding site [chemical binding]; other site 323098000893 Helix-turn-helix domains; Region: HTH; cl00088 323098000894 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 323098000895 dimerization interface [polypeptide binding]; other site 323098000896 substrate binding pocket [chemical binding]; other site 323098000897 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; cl00284 323098000898 ParB-like nuclease domain; Region: ParBc; cl02129 323098000899 PRTRC system ParB family protein; Region: PRTRC_parB; TIGR03734 323098000900 Helix-turn-helix domains; Region: HTH; cl00088 323098000901 putative transposase OrfB; Reviewed; Region: PHA02517 323098000902 Helix-turn-helix domains; Region: HTH; cl00088 323098000903 Integrase core domain; Region: rve; cl01316 323098000904 Integrase core domain; Region: rve_3; cl15866 323098000905 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 323098000906 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 323098000907 TIR domain; Region: TIR_2; cl15770 323098000908 HNH endonuclease; Region: HNH_5; pfam14279 323098000909 Domain of unknown function (DUF4365); Region: DUF4365; pfam14280 323098000910 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; cl00973 323098000911 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 323098000912 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 323098000913 Ligand Binding Site [chemical binding]; other site 323098000914 Domain of unknown function (DUF955); Region: DUF955; cl01076 323098000915 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]; Region: COG2405 323098000916 AAA domain; Region: AAA_13; pfam13166 323098000917 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098000918 ABC transporter signature motif; other site 323098000919 Walker B; other site 323098000920 D-loop; other site 323098000921 H-loop/switch region; other site 323098000922 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 323098000923 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 323098000924 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 323098000925 HsdM N-terminal domain; Region: HsdM_N; pfam12161 323098000926 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 323098000927 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098000928 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: HsdR; COG4096 323098000929 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 323098000930 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 323098000931 ATP binding site [chemical binding]; other site 323098000932 putative Mg++ binding site [ion binding]; other site 323098000933 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 323098000934 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 323098000935 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 323098000936 DNA binding site [nucleotide binding] 323098000937 Int/Topo IB signature motif; other site 323098000938 active site 323098000939 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 323098000940 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 323098000941 Domain of unknown function (DUF329); Region: DUF329; cl01144 323098000942 Maf-like protein; Region: Maf; pfam02545 323098000943 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 323098000944 active site 323098000945 dimer interface [polypeptide binding]; other site 323098000946 acetyl-CoA acetyltransferase; Provisional; Region: PRK07108 323098000947 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 323098000948 dimer interface [polypeptide binding]; other site 323098000949 active site 323098000950 glycerol kinase; Provisional; Region: glpK; PRK00047 323098000951 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 323098000952 N- and C-terminal domain interface [polypeptide binding]; other site 323098000953 active site 323098000954 MgATP binding site [chemical binding]; other site 323098000955 catalytic site [active] 323098000956 metal binding site [ion binding]; metal-binding site 323098000957 glycerol binding site [chemical binding]; other site 323098000958 homotetramer interface [polypeptide binding]; other site 323098000959 homodimer interface [polypeptide binding]; other site 323098000960 FBP binding site [chemical binding]; other site 323098000961 protein IIAGlc interface [polypeptide binding]; other site 323098000962 PAS domain; Region: PAS_9; pfam13426 323098000963 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 323098000964 putative active site [active] 323098000965 heme pocket [chemical binding]; other site 323098000966 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 323098000967 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 323098000968 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 323098000969 substrate binding pocket [chemical binding]; other site 323098000970 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 323098000971 B12 binding site [chemical binding]; other site 323098000972 cobalt ligand [ion binding]; other site 323098000973 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 323098000974 Methylenetetrahydrofolate reductase; Region: MTHFR; pfam02219 323098000975 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; cd00537 323098000976 FAD binding site [chemical binding]; other site 323098000977 prephenate dehydratase; Provisional; Region: PRK11899 323098000978 Prephenate dehydratase; Region: PDT; pfam00800 323098000979 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 323098000980 putative L-Phe binding site [chemical binding]; other site 323098000981 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 323098000982 Ligand binding site; other site 323098000983 oligomer interface; other site 323098000984 Cytochrome c; Region: Cytochrom_C; cl11414 323098000985 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 323098000986 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 323098000987 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 323098000988 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 323098000989 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 323098000990 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 323098000991 dimer interface [polypeptide binding]; other site 323098000992 conserved gate region; other site 323098000993 putative PBP binding loops; other site 323098000994 ABC-ATPase subunit interface; other site 323098000995 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 323098000996 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 323098000997 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 323098000998 dimer interface [polypeptide binding]; other site 323098000999 conserved gate region; other site 323098001000 ABC-ATPase subunit interface; other site 323098001001 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 323098001002 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 323098001003 Walker A/P-loop; other site 323098001004 ATP binding site [chemical binding]; other site 323098001005 Q-loop/lid; other site 323098001006 ABC transporter signature motif; other site 323098001007 Walker B; other site 323098001008 D-loop; other site 323098001009 H-loop/switch region; other site 323098001010 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 323098001011 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 323098001012 Walker A/P-loop; other site 323098001013 ATP binding site [chemical binding]; other site 323098001014 Q-loop/lid; other site 323098001015 ABC transporter signature motif; other site 323098001016 Walker B; other site 323098001017 D-loop; other site 323098001018 H-loop/switch region; other site 323098001019 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 323098001020 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 323098001021 NlpC/P60 family; Region: NLPC_P60; cl11438 323098001022 Leucyl aminopeptidase [Amino acid transport and metabolism]; Region: PepB; COG0260 323098001023 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 323098001024 interface (dimer of trimers) [polypeptide binding]; other site 323098001025 Substrate-binding/catalytic site; other site 323098001026 Zn-binding sites [ion binding]; other site 323098001027 Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]; Region: TadD; COG5010 323098001028 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 323098001029 binding surface 323098001030 TPR motif; other site 323098001031 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 323098001032 TPR motif; other site 323098001033 binding surface 323098001034 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 323098001035 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 323098001036 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 323098001037 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 323098001038 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 323098001039 ATP binding site [chemical binding]; other site 323098001040 Walker A motif; other site 323098001041 hexamer interface [polypeptide binding]; other site 323098001042 Walker B motif; other site 323098001043 Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]; Region: CpaE; COG4963 323098001044 This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains...; Region: CpaE_like; cd03111 323098001045 Type IV pili component [Cell motility and secretion]; Region: COG5461; cl02279 323098001046 Pilus biogenesis CpaD protein (pilus_cpaD); Region: Pilus_CpaD; pfam09476 323098001047 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 323098001048 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 323098001049 BON domain; Region: BON; cl02771 323098001050 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 323098001051 SAF domain; Region: SAF; cl00555 323098001052 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 323098001053 Flp/Fap pilin component; Region: Flp_Fap; cl01585 323098001054 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 323098001055 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 323098001056 TadE-like protein; Region: TadE; cl10688 323098001057 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 323098001058 TadE-like protein; Region: TadE; cl10688 323098001059 Winged helix-turn helix; Region: HTH_29; pfam13551 323098001060 Integrase core domain; Region: rve; cl01316 323098001061 Integrase core domain; Region: rve_3; cl15866 323098001062 Transposase domain (DUF772); Region: DUF772; cl15789 323098001063 Transposase domain (DUF772); Region: DUF772; cl15789 323098001064 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 323098001065 DNA-binding site [nucleotide binding]; DNA binding site 323098001066 RNA-binding motif; other site 323098001067 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 323098001068 rRNA binding site [nucleotide binding]; other site 323098001069 predicted 30S ribosome binding site; other site 323098001070 ATP-dependent RNA helicase RhlB; Provisional; Region: PRK04837 323098001071 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 323098001072 ATP binding site [chemical binding]; other site 323098001073 Mg++ binding site [ion binding]; other site 323098001074 motif III; other site 323098001075 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 323098001076 nucleotide binding region [chemical binding]; other site 323098001077 ATP-binding site [chemical binding]; other site 323098001078 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 323098001079 active site 323098001080 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 323098001081 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 323098001082 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 323098001083 P loop; other site 323098001084 GTP binding site [chemical binding]; other site 323098001085 Intracellular septation protein A; Region: IspA; cl01098 323098001086 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 323098001087 catalytic residues [active] 323098001088 central insert; other site 323098001089 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 323098001090 CcmB protein; Region: CcmB; cl01016 323098001091 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13539 323098001092 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098001093 Walker A/P-loop; other site 323098001094 ATP binding site [chemical binding]; other site 323098001095 Q-loop/lid; other site 323098001096 ABC transporter signature motif; other site 323098001097 Walker B; other site 323098001098 D-loop; other site 323098001099 H-loop/switch region; other site 323098001100 aconitate hydratase; Validated; Region: PRK09277 323098001101 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 323098001102 substrate binding site [chemical binding]; other site 323098001103 ligand binding site [chemical binding]; other site 323098001104 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 323098001105 substrate binding site [chemical binding]; other site 323098001106 Protein of unknown function (DUF1223); Region: DUF1223; cl10501 323098001107 Protein of unknown function (DUF2794); Region: DUF2794; pfam10984 323098001108 This family is most closely related to the GT1 family of glycosyltransferases. aviGT4 in Streptomyces viridochromogenes has been shown to be involved in biosynthesis of oligosaccharide antibiotic avilamycin A. Inactivation of aviGT4 resulted in a mutant...; Region: GT1_AviGT4_like; cd03802 323098001109 Glycosyltransferase Family 4; Region: Glyco_transf_4; pfam13439 323098001110 putative ADP-binding pocket [chemical binding]; other site 323098001111 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 323098001112 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 323098001113 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098001114 Walker A/P-loop; other site 323098001115 ATP binding site [chemical binding]; other site 323098001116 Q-loop/lid; other site 323098001117 ABC transporter signature motif; other site 323098001118 Walker B; other site 323098001119 D-loop; other site 323098001120 H-loop/switch region; other site 323098001121 Glycogen debranching enzyme [Carbohydrate transport and metabolism]; Region: GDB1; COG3408 323098001122 Bacterial alpha-L-rhamnosidase; Region: Bac_rhamnosid; cl01801 323098001123 Bacterial alpha-L-rhamnosidase; Region: Bac_rhamnosid; cl01801 323098001124 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 323098001125 Carbohydrate-selective porin, OprB family; Region: OprB; pfam04966 323098001126 Carbohydrate-selective porin [Cell envelope biogenesis, outer membrane]; Region: OprB; COG3659 323098001127 Creatinine amidohydrolase; Region: Creatininase; cl00618 323098001128 NMT1/THI5 like; Region: NMT1; pfam09084 323098001129 NMT1-like family; Region: NMT1_2; cl15260 323098001130 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 323098001131 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 323098001132 Walker A/P-loop; other site 323098001133 ATP binding site [chemical binding]; other site 323098001134 Q-loop/lid; other site 323098001135 ABC transporter signature motif; other site 323098001136 Walker B; other site 323098001137 D-loop; other site 323098001138 H-loop/switch region; other site 323098001139 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 323098001140 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 323098001141 hypothetical protein; Reviewed; Region: PRK00024 323098001142 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 323098001143 MPN+ (JAMM) motif; other site 323098001144 Zinc-binding site [ion binding]; other site 323098001145 methionine aminopeptidase; Provisional; Region: PRK12318 323098001146 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 323098001147 active site 323098001148 potassium/proton antiporter; Reviewed; Region: PRK05326 323098001149 Transporter associated domain; Region: CorC_HlyC; cl08393 323098001150 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 323098001151 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098001152 Walker A/P-loop; other site 323098001153 ATP binding site [chemical binding]; other site 323098001154 Q-loop/lid; other site 323098001155 ABC transporter signature motif; other site 323098001156 Walker B; other site 323098001157 D-loop; other site 323098001158 H-loop/switch region; other site 323098001159 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 323098001160 dimer interface [polypeptide binding]; other site 323098001161 conserved gate region; other site 323098001162 putative PBP binding loops; other site 323098001163 ABC-ATPase subunit interface; other site 323098001164 ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: ModA; COG0725 323098001165 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 323098001166 Penicillin-insensitive murein endopeptidase; Region: Peptidase_M74; cl01538 323098001167 GTP-binding protein LepA; Provisional; Region: PRK05433 323098001168 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 323098001169 G1 box; other site 323098001170 putative GEF interaction site [polypeptide binding]; other site 323098001171 GTP/Mg2+ binding site [chemical binding]; other site 323098001172 Switch I region; other site 323098001173 G2 box; other site 323098001174 G3 box; other site 323098001175 Switch II region; other site 323098001176 G4 box; other site 323098001177 G5 box; other site 323098001178 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 323098001179 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 323098001180 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 323098001181 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 323098001182 regulatory protein interface [polypeptide binding]; other site 323098001183 active site 323098001184 regulatory phosphorylation site [posttranslational modification]; other site 323098001185 PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIA_man; cd00006 323098001186 active pocket/dimerization site; other site 323098001187 active site 323098001188 phosphorylation site [posttranslational modification] 323098001189 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 323098001190 Hpr binding site; other site 323098001191 active site 323098001192 homohexamer subunit interaction site [polypeptide binding]; other site 323098001193 Sensor N-terminal transmembrane domain; Region: Sensor_TM1; pfam13755 323098001194 Stimulus-sensing domain; Region: Stimulus_sens_1; pfam13756 323098001195 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 323098001196 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 323098001197 dimer interface [polypeptide binding]; other site 323098001198 phosphorylation site [posttranslational modification] 323098001199 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 323098001200 ATP binding site [chemical binding]; other site 323098001201 Mg2+ binding site [ion binding]; other site 323098001202 G-X-G motif; other site 323098001203 proteobacterial dedicated sortase system response regulator; Region: marine_sort_RR; TIGR03787 323098001204 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 323098001205 active site 323098001206 phosphorylation site [posttranslational modification] 323098001207 intermolecular recognition site; other site 323098001208 dimerization interface [polypeptide binding]; other site 323098001209 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 323098001210 DNA binding site [nucleotide binding] 323098001211 Putative heme iron utilization protein [Inorganic ion transport and metabolism]; Region: HugZ; COG0748 323098001212 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 323098001213 Protein of unknown function (DUF2470); Region: DUF2470; pfam10615 323098001214 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 323098001215 active site 323098001216 substrate-binding site [chemical binding]; other site 323098001217 metal-binding site [ion binding] 323098001218 ATP binding site [chemical binding]; other site 323098001219 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 323098001220 Arginase family; Region: Arginase; cl00306 323098001221 ATP-dependent DNA ligase; Reviewed; Region: ligD; PRK05972 323098001222 DNA polymerase Ligase (LigD); Region: LigD_N; cl11819 323098001223 Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; Region: Adenylation_DNA_ligase_LigD_LigC; cd07906 323098001224 active site 323098001225 DNA binding site [nucleotide binding] 323098001226 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD is a DNA-binding module that is part of the catalytic core unit; Region: OBF_DNA_ligase_LigD; cd07971 323098001227 DNA binding site [nucleotide binding] 323098001228 PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for...; Region: PaeLigD_Pol_like; cd04862 323098001229 nucleotide binding site [chemical binding]; other site 323098001230 Ku protein, prokaryotic; Region: Ku_bact; TIGR02772 323098001231 Ku-core domain, Ku-like subfamily; composed of prokaryotic homologs of the eukaryotic DNA binding protein Ku. The alignment includes the core domain shared by the prokaryotic YkoV-like proteins and the eukaryotic Ku70 and Ku80. The prokaryotic Ku...; Region: KU_like; cd00789 323098001232 putative DNA binding site [nucleotide binding]; other site 323098001233 putative homodimer interface [polypeptide binding]; other site 323098001234 LysE type translocator; Region: LysE; cl00565 323098001235 5'-3' exonuclease; Region: 53EXOc; smart00475 323098001236 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 323098001237 active site 323098001238 metal binding site 1 [ion binding]; metal-binding site 323098001239 putative 5' ssDNA interaction site; other site 323098001240 metal binding site 3; metal-binding site 323098001241 metal binding site 2 [ion binding]; metal-binding site 323098001242 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 323098001243 putative DNA binding site [nucleotide binding]; other site 323098001244 putative metal binding site [ion binding]; other site 323098001245 DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]; Region: PolA; COG0749 323098001246 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 323098001247 active site 323098001248 catalytic site [active] 323098001249 substrate binding site [chemical binding]; other site 323098001250 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 323098001251 active site 323098001252 DNA binding site [nucleotide binding] 323098001253 catalytic site [active] 323098001254 OpgC protein; Region: OpgC_C; cl00792 323098001255 Acyltransferase family; Region: Acyl_transf_3; pfam01757 323098001256 ATP-dependent helicase HrpB; Region: DEAH_box_HrpB; TIGR01970 323098001257 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 323098001258 ATP binding site [chemical binding]; other site 323098001259 putative Mg++ binding site [ion binding]; other site 323098001260 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 323098001261 nucleotide binding region [chemical binding]; other site 323098001262 ATP-binding site [chemical binding]; other site 323098001263 Helicase associated domain (HA2); Region: HA2; cl04503 323098001264 ATP-dependent helicase C-terminal; Region: HrpB_C; pfam08482 323098001265 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 323098001266 catalytic motif [active] 323098001267 Catalytic residue [active] 323098001268 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 323098001269 The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a...; Region: PMM_PGM; cd03089 323098001270 active site 323098001271 substrate binding site [chemical binding]; other site 323098001272 metal binding site [ion binding]; metal-binding site 323098001273 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 323098001274 Helix-turn-helix domains; Region: HTH; cl00088 323098001275 Integrase core domain; Region: rve; cl01316 323098001276 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098001277 Helix-turn-helix domains; Region: HTH; cl00088 323098001278 Winged helix-turn helix; Region: HTH_29; pfam13551 323098001279 Helix-turn-helix domains; Region: HTH; cl00088 323098001280 Transposase domain (DUF772); Region: DUF772; cl15789 323098001281 Winged helix-turn helix; Region: HTH_29; pfam13551 323098001282 Integrase core domain; Region: rve; cl01316 323098001283 Integrase core domain; Region: rve_3; cl15866 323098001284 recombination protein RecR; Reviewed; Region: recR; PRK00076 323098001285 RecR protein; Region: RecR; pfam02132 323098001286 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 323098001287 tetramer interface [polypeptide binding]; other site 323098001288 putative active site [active] 323098001289 putative metal-binding site [ion binding]; other site 323098001290 YbaB/EbfC DNA-binding family; Region: YbaB_DNA_bd; cl00494 323098001291 DNA polymerase III subunits gamma and tau; Validated; Region: PRK09111 323098001292 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 323098001293 Walker A motif; other site 323098001294 ATP binding site [chemical binding]; other site 323098001295 Walker B motif; other site 323098001296 arginine finger; other site 323098001297 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 323098001298 DNA polymerase III gamma and tau subunits C terminal; Region: DUF3646; pfam12362 323098001299 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 323098001300 Cupin superfamily (DUF985); Region: Cupin_5; cl01418 323098001301 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 323098001302 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 323098001303 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098001304 Domain of unknown function (DUF4167); Region: DUF4167; pfam13763 323098001305 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 323098001306 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 323098001307 S-adenosylmethionine binding site [chemical binding]; other site 323098001308 peptide chain release factor 1; Validated; Region: prfA; PRK00591 323098001309 RF-1 domain; Region: RF-1; cl02875 323098001310 RF-1 domain; Region: RF-1; cl02875 323098001311 Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms]; Region: PtsP; COG3605 323098001312 GAF domain; Region: GAF; cl15785 323098001313 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 323098001314 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 323098001315 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 323098001316 aspartate kinase; Reviewed; Region: PRK06635 323098001317 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 323098001318 putative nucleotide binding site [chemical binding]; other site 323098001319 putative catalytic residues [active] 323098001320 putative Mg ion binding site [ion binding]; other site 323098001321 putative aspartate binding site [chemical binding]; other site 323098001322 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 323098001323 putative allosteric regulatory site; other site 323098001324 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 323098001325 putative allosteric regulatory residue; other site 323098001326 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 323098001327 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 323098001328 S-adenosylmethionine binding site [chemical binding]; other site 323098001329 Zinc ribbon domain; Region: CxxC_CxxC_SSSS; cl00993 323098001330 Zinc ribbon domain; Region: CxxC_CxxC_SSSS; cl00993 323098001331 Predicted amidohydrolase [General function prediction only]; Region: COG0388 323098001332 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 323098001333 putative active site [active] 323098001334 catalytic triad [active] 323098001335 dimer interface [polypeptide binding]; other site 323098001336 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 323098001337 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 323098001338 active site 323098001339 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098001340 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 323098001341 active site 323098001342 8-oxo-dGMP binding site [chemical binding]; other site 323098001343 nudix motif; other site 323098001344 metal binding site [ion binding]; metal-binding site 323098001345 Ornithine acetyltransferase (OAT) family; also referred to as ArgJ. OAT catalyzes the first and fifth steps in arginine biosynthesis, coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group in...; Region: OAT; cd02152 323098001346 heterotetramer interface [polypeptide binding]; other site 323098001347 active site pocket [active] 323098001348 cleavage site 323098001349 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 323098001350 PPIC-type PPIASE domain; Region: Rotamase; cl08278 323098001351 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 323098001352 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 323098001353 preprotein translocase subunit SecA; Reviewed; Region: secA; PRK12901 323098001354 SEC-C motif; Region: SEC-C; pfam02810 323098001355 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3034 323098001356 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 323098001357 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 323098001358 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 323098001359 DNA binding site [nucleotide binding] 323098001360 Int/Topo IB signature motif; other site 323098001361 active site 323098001362 shikimate kinase; Provisional; Region: PRK13946 323098001363 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 323098001364 ADP binding site [chemical binding]; other site 323098001365 magnesium binding site [ion binding]; other site 323098001366 putative shikimate binding site; other site 323098001367 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 323098001368 active site 323098001369 dimer interface [polypeptide binding]; other site 323098001370 metal binding site [ion binding]; metal-binding site 323098001371 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 323098001372 Domain of unknown function DUF21; Region: DUF21; pfam01595 323098001373 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 323098001374 Transporter associated domain; Region: CorC_HlyC; cl08393 323098001375 PilZ domain; Region: PilZ; cl01260 323098001376 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; cl15419 323098001377 BolA-like protein; Region: BolA; cl00386 323098001378 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 323098001379 HSP70 interaction site [polypeptide binding]; other site 323098001380 Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn); Region: PHA_gran_rgn; cl09865 323098001381 Cobaltochelatase CobS subunit N terminal; Region: CobS_N; pfam12556 323098001382 cobaltochelatase, CobS subunit; Region: PD_CobS; TIGR01650 323098001383 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098001384 Cobalamin biosynthesis protein CobT; Region: CobT; pfam06213 323098001385 cobaltochelatase, CobT subunit; Region: CobT; TIGR01651 323098001386 norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial...; Region: vWA_norD_type; cd01454 323098001387 metal ion-dependent adhesion site (MIDAS); other site 323098001388 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4246 323098001389 Esterase-like activity of phytase; Region: Phytase-like; pfam13449 323098001390 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 323098001391 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 323098001392 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098001393 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 323098001394 nucleotide binding region [chemical binding]; other site 323098001395 ATP-binding site [chemical binding]; other site 323098001396 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 323098001397 RNA binding surface [nucleotide binding]; other site 323098001398 Ferredoxin [Energy production and conversion]; Region: COG1146 323098001399 4Fe-4S binding domain; Region: Fer4; cl02805 323098001400 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 323098001401 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 323098001402 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 323098001403 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 323098001404 FtsX-like permease family; Region: FtsX; cl15850 323098001405 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 323098001406 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 323098001407 Walker A/P-loop; other site 323098001408 ATP binding site [chemical binding]; other site 323098001409 Q-loop/lid; other site 323098001410 ABC transporter signature motif; other site 323098001411 Walker B; other site 323098001412 D-loop; other site 323098001413 H-loop/switch region; other site 323098001414 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 323098001415 active site 323098001416 oxyanion hole [active] 323098001417 switch loop; other site 323098001418 catalytic triad [active] 323098001419 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 323098001420 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 323098001421 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 323098001422 Predicted ATPase [General function prediction only]; Region: COG1485 323098001423 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098001424 malate dehydrogenase; Reviewed; Region: PRK06223 323098001425 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 323098001426 NAD(P) binding site [chemical binding]; other site 323098001427 dimer interface [polypeptide binding]; other site 323098001428 tetramer (dimer of dimers) interface [polypeptide binding]; other site 323098001429 substrate binding site [chemical binding]; other site 323098001430 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 323098001431 ATP-grasp domain; Region: ATP-grasp_4; cl03087 323098001432 CoA-ligase; Region: Ligase_CoA; cl02894 323098001433 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 323098001434 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098001435 CoA-ligase; Region: Ligase_CoA; cl02894 323098001436 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 323098001437 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 323098001438 TPP-binding site [chemical binding]; other site 323098001439 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 323098001440 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 323098001441 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 323098001442 E3 interaction surface; other site 323098001443 lipoyl attachment site [posttranslational modification]; other site 323098001444 e3 binding domain; Region: E3_binding; pfam02817 323098001445 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 323098001446 dihydrolipoamide dehydrogenase; Validated; Region: PRK06292 323098001447 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098001448 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 323098001449 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 323098001450 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 323098001451 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 323098001452 DNA binding site [nucleotide binding] 323098001453 Int/Topo IB signature motif; other site 323098001454 active site 323098001455 primosome assembly protein PriA; Validated; Region: PRK05580 323098001456 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 323098001457 ATP binding site [chemical binding]; other site 323098001458 putative Mg++ binding site [ion binding]; other site 323098001459 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098001460 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 323098001461 Plant ATP synthase F0; Region: YMF19; cl07975 323098001462 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 323098001463 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 323098001464 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 323098001465 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 323098001466 beta subunit interaction interface [polypeptide binding]; other site 323098001467 Walker A motif; other site 323098001468 ATP binding site [chemical binding]; other site 323098001469 Walker B motif; other site 323098001470 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 323098001471 ATP synthase; Region: ATP-synt; cl00365 323098001472 F0F1 ATP synthase subunit gamma; Provisional; Region: PRK13422 323098001473 OsmC-like protein; Region: OsmC; cl00767 323098001474 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 323098001475 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 323098001476 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 323098001477 alpha subunit interaction interface [polypeptide binding]; other site 323098001478 Walker A motif; other site 323098001479 ATP binding site [chemical binding]; other site 323098001480 Walker B motif; other site 323098001481 inhibitor binding site; inhibition site 323098001482 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 323098001483 F0F1 ATP synthase subunit epsilon; Provisional; Region: atpC; PRK13448 323098001484 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 323098001485 Transposase domain (DUF772); Region: DUF772; cl15789 323098001486 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 323098001487 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 323098001488 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 323098001489 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 323098001490 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 323098001491 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 323098001492 GTPase CgtA; Reviewed; Region: obgE; PRK12299 323098001493 GTP1/OBG; Region: GTP1_OBG; pfam01018 323098001494 Obg GTPase; Region: Obg; cd01898 323098001495 G1 box; other site 323098001496 GTP/Mg2+ binding site [chemical binding]; other site 323098001497 Switch I region; other site 323098001498 G2 box; other site 323098001499 G3 box; other site 323098001500 Switch II region; other site 323098001501 G4 box; other site 323098001502 G5 box; other site 323098001503 gamma-glutamyl kinase; Provisional; Region: PRK05429 323098001504 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 323098001505 nucleotide binding site [chemical binding]; other site 323098001506 homotetrameric interface [polypeptide binding]; other site 323098001507 putative phosphate binding site [ion binding]; other site 323098001508 putative allosteric binding site; other site 323098001509 PUA domain; Region: PUA; cl00607 323098001510 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 323098001511 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 323098001512 putative catalytic cysteine [active] 323098001513 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 323098001514 active site 323098001515 (T/H)XGH motif; other site 323098001516 Oligomerisation domain; Region: Oligomerisation; cl00519 323098001517 Uncharacterized conserved protein [Function unknown]; Region: COG1576; cl00679 323098001518 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; pfam02590 323098001519 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 323098001520 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 323098001521 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 323098001522 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 323098001523 protein binding site [polypeptide binding]; other site 323098001524 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 323098001525 Catalytic dyad [active] 323098001526 Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria; Region: CE4_DAC2; cd10936 323098001527 NodB motif; other site 323098001528 putative active site [active] 323098001529 Zn binding site [ion binding]; other site 323098001530 putative catalytic site [active] 323098001531 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 323098001532 putative active site [active] 323098001533 Ap4A binding site [chemical binding]; other site 323098001534 nudix motif; other site 323098001535 putative metal binding site [ion binding]; other site 323098001536 Putative Zn-dependent protease [General function prediction only]; Region: COG4784 323098001537 Peptidase family M48; Region: Peptidase_M48; cl12018 323098001538 Staphylococcal nuclease homologues; Region: SNc; smart00318 323098001539 Transglycosylase associated protein; Region: Transgly_assoc; cl00978 323098001540 Bacterial protein of unknown function (DUF937); Region: DUF937; cl01528 323098001541 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 323098001542 NMT1-like family; Region: NMT1_2; cl15260 323098001543 NMT1/THI5 like; Region: NMT1; pfam09084 323098001544 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 323098001545 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 323098001546 Walker A/P-loop; other site 323098001547 ATP binding site [chemical binding]; other site 323098001548 Q-loop/lid; other site 323098001549 ABC transporter signature motif; other site 323098001550 Walker B; other site 323098001551 D-loop; other site 323098001552 H-loop/switch region; other site 323098001553 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 323098001554 active site 323098001555 Uncharacterized conserved protein [Function unknown]; Region: COG2128 323098001556 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 323098001557 putative exonuclease, DNA ligase-associated; Region: Xnuc_lig_assoc; TIGR04122 323098001558 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 323098001559 ATP-dependent DNA ligase; Validated; Region: PRK09247 323098001560 Adenylation domain of putative bacterial ATP-dependent DNA ligases; Region: Adenylation_DNA_ligase_Bac1; cd07897 323098001561 active site 323098001562 DNA binding site [nucleotide binding] 323098001563 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit; Region: OBF_DNA_ligase_Arch_LigB; cd07972 323098001564 DNA binding site [nucleotide binding] 323098001565 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 323098001566 quinone interaction residues [chemical binding]; other site 323098001567 Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Region: PyrD; COG0167 323098001568 active site 323098001569 catalytic residues [active] 323098001570 FMN binding site [chemical binding]; other site 323098001571 substrate binding site [chemical binding]; other site 323098001572 Protein of unknown function (DUF952); Region: DUF952; cl01393 323098001573 Predicted transcriptional regulator [Transcription]; Region: COG2932 323098001574 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 323098001575 Catalytic site [active] 323098001576 acetyl-CoA synthetase; Provisional; Region: PRK00174 323098001577 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 323098001578 AMP-binding enzyme; Region: AMP-binding; cl15778 323098001579 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 323098001580 EVE domain; Region: EVE; cl00728 323098001581 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 323098001582 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098001583 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 323098001584 UGMP family protein; Validated; Region: PRK09604 323098001585 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 323098001586 Porphobilinogen deaminase [Coenzyme metabolism]; Region: HemC; COG0181 323098001587 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; cl03189 323098001588 domain interfaces; other site 323098001589 active site 323098001590 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 323098001591 active site 323098001592 Uroporphyrinogen-III synthase HemD; Region: HEM4; pfam02602 323098001593 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4223 323098001594 Uncharacterized membrane-bound protein [Function unknown]; Region: COG3898 323098001595 tellurium resistance terB-like protein, subgroup 2; Region: terB_like_2; cd07313 323098001596 putative metal binding site [ion binding]; other site 323098001597 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 323098001598 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098001599 NAD(P) binding site [chemical binding]; other site 323098001600 active site 323098001601 YGGT family; Region: YGGT; cl00508 323098001602 Uncharacterized ACR, YggU family COG1872; Region: DUF167; cl00811 323098001603 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14188 323098001604 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 323098001605 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 323098001606 homodimer interface [polypeptide binding]; other site 323098001607 NADP binding site [chemical binding]; other site 323098001608 substrate binding site [chemical binding]; other site 323098001609 Winged helix-turn helix; Region: HTH_29; pfam13551 323098001610 Integrase core domain; Region: rve; cl01316 323098001611 Integrase core domain; Region: rve_3; cl15866 323098001612 Winged helix-turn helix; Region: HTH_29; pfam13551 323098001613 Helix-turn-helix domains; Region: HTH; cl00088 323098001614 Helix-turn-helix domains; Region: HTH; cl00088 323098001615 Integrase core domain; Region: rve; cl01316 323098001616 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098001617 Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers; Region: pyrophosphatase; cd00412 323098001618 dimer interface [polypeptide binding]; other site 323098001619 substrate binding site [chemical binding]; other site 323098001620 metal binding sites [ion binding]; metal-binding site 323098001621 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 323098001622 short chain dehydrogenase; Provisional; Region: PRK12744 323098001623 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098001624 NAD(P) binding site [chemical binding]; other site 323098001625 active site 323098001626 transcriptional regulator; Provisional; Region: PRK10632 323098001627 Helix-turn-helix domains; Region: HTH; cl00088 323098001628 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_3; cd08472 323098001629 putative effector binding pocket; other site 323098001630 putative dimerization interface [polypeptide binding]; other site 323098001631 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098001632 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098001633 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 323098001634 MutS domain I; Region: MutS_I; pfam01624 323098001635 MutS domain II; Region: MutS_II; pfam05188 323098001636 MutS family domain IV; Region: MutS_IV; pfam05190 323098001637 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 323098001638 Walker A/P-loop; other site 323098001639 ATP binding site [chemical binding]; other site 323098001640 Q-loop/lid; other site 323098001641 ABC transporter signature motif; other site 323098001642 Walker B; other site 323098001643 D-loop; other site 323098001644 H-loop/switch region; other site 323098001645 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 323098001646 S-adenosylmethionine binding site [chemical binding]; other site 323098001647 acetoin dehydrogenase E2 subunit dihydrolipoyllysine-residue acetyltransferase; Provisional; Region: PRK14875 323098001648 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 323098001649 metal binding site 2 [ion binding]; metal-binding site 323098001650 putative DNA binding helix; other site 323098001651 metal binding site 1 [ion binding]; metal-binding site 323098001652 dimer interface [polypeptide binding]; other site 323098001653 structural Zn2+ binding site [ion binding]; other site 323098001654 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 323098001655 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 323098001656 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 323098001657 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 323098001658 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 323098001659 substrate binding pocket [chemical binding]; other site 323098001660 chain length determination region; other site 323098001661 substrate-Mg2+ binding site; other site 323098001662 catalytic residues [active] 323098001663 aspartate-rich region 1; other site 323098001664 active site lid residues [active] 323098001665 aspartate-rich region 2; other site 323098001666 Transglycosylase; Region: Transgly; cl07896 323098001667 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 323098001668 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 323098001669 metal binding site [ion binding]; metal-binding site 323098001670 active site 323098001671 I-site; other site 323098001672 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 323098001673 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 323098001674 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 323098001675 Putative catalytic NodB homology domain of Mesorhizobium loti Mlr8448 protein and its bacterial homologs; Region: CE4_Mlr8448_like_5s; cd10968 323098001676 putative active site [active] 323098001677 putative metal binding site [ion binding]; other site 323098001678 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 323098001679 ligand binding site [chemical binding]; other site 323098001680 Uncharacterized protein family (UPF0104); Region: UPF0104; cl04219 323098001681 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 323098001682 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 323098001683 dimer interface [polypeptide binding]; other site 323098001684 phosphorylation site [posttranslational modification] 323098001685 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 323098001686 ATP binding site [chemical binding]; other site 323098001687 Mg2+ binding site [ion binding]; other site 323098001688 G-X-G motif; other site 323098001689 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 323098001690 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 323098001691 dimer interface [polypeptide binding]; other site 323098001692 conserved gate region; other site 323098001693 putative PBP binding loops; other site 323098001694 ABC-ATPase subunit interface; other site 323098001695 phosphate transporter permease subunit PtsA; Provisional; Region: pstA; PRK11268 323098001696 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 323098001697 dimer interface [polypeptide binding]; other site 323098001698 conserved gate region; other site 323098001699 putative PBP binding loops; other site 323098001700 ABC-ATPase subunit interface; other site 323098001701 phosphate transporter ATP-binding protein; Provisional; Region: pstB; PRK10744 323098001702 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 323098001703 Walker A/P-loop; other site 323098001704 ATP binding site [chemical binding]; other site 323098001705 Q-loop/lid; other site 323098001706 ABC transporter signature motif; other site 323098001707 Walker B; other site 323098001708 D-loop; other site 323098001709 H-loop/switch region; other site 323098001710 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 323098001711 PhoU domain; Region: PhoU; pfam01895 323098001712 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098001713 PhoU domain; Region: PhoU; pfam01895 323098001714 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 323098001715 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 323098001716 active site 323098001717 phosphorylation site [posttranslational modification] 323098001718 intermolecular recognition site; other site 323098001719 dimerization interface [polypeptide binding]; other site 323098001720 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 323098001721 DNA binding site [nucleotide binding] 323098001722 GcrA cell cycle regulator; Region: GcrA; cl11564 323098001723 acetylornithine transaminase protein; Provisional; Region: argD; PRK01278 323098001724 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 323098001725 inhibitor-cofactor binding pocket; inhibition site 323098001726 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098001727 catalytic residue [active] 323098001728 ornithine carbamoyltransferase; Provisional; Region: PRK00779 323098001729 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 323098001730 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098001731 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 323098001732 Protein of unknown function (DUF1134); Region: DUF1134; cl02235 323098001733 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in cysteine...; Region: CysQ; cd01638 323098001734 active site 323098001735 Uncharacterized protein conserved in bacteria (DUF2328); Region: DUF2328; pfam10090 323098001736 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 323098001737 putative binding surface; other site 323098001738 active site 323098001739 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 323098001740 Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]; Region: COG2972 323098001741 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 323098001742 ATP binding site [chemical binding]; other site 323098001743 G-X-G motif; other site 323098001744 CheA regulatory domain; CheA is a histidine protein kinase present in bacteria and archea. Activated by the chemotaxis receptor a histidine phosphoryl group from CheA is passed directly to an aspartate in the response regulator CheY. This signalling...; Region: CheA_reg; cd00731 323098001745 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 323098001746 Response regulator receiver domain; Region: Response_reg; pfam00072 323098001747 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 323098001748 active site 323098001749 phosphorylation site [posttranslational modification] 323098001750 intermolecular recognition site; other site 323098001751 dimerization interface [polypeptide binding]; other site 323098001752 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 323098001753 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 323098001754 Response regulator receiver domain; Region: Response_reg; pfam00072 323098001755 active site 323098001756 phosphorylation site [posttranslational modification] 323098001757 intermolecular recognition site; other site 323098001758 dimerization interface [polypeptide binding]; other site 323098001759 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 323098001760 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 323098001761 active site 323098001762 phosphorylation site [posttranslational modification] 323098001763 intermolecular recognition site; other site 323098001764 dimerization interface [polypeptide binding]; other site 323098001765 CheB methylesterase; Region: CheB_methylest; pfam01339 323098001766 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 323098001767 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 323098001768 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098001769 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 323098001770 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 323098001771 active site 323098001772 phosphorylation site [posttranslational modification] 323098001773 intermolecular recognition site; other site 323098001774 dimerization interface [polypeptide binding]; other site 323098001775 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 323098001776 DNA binding site [nucleotide binding] 323098001777 flagellum-specific ATP synthase; Validated; Region: fliI; PRK08927 323098001778 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 323098001779 Walker A motif/ATP binding site; other site 323098001780 Walker B motif; other site 323098001781 flagellar export protein FliJ; Region: flagell_FliJ; TIGR02473 323098001782 flagellar biosynthesis protein FlhA; Validated; Region: flhA; cl07980 323098001783 FHIPEP family; Region: FHIPEP; pfam00771 323098001784 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 323098001785 PAS domain; Region: PAS_9; pfam13426 323098001786 putative active site [active] 323098001787 heme pocket [chemical binding]; other site 323098001788 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 323098001789 dimer interface [polypeptide binding]; other site 323098001790 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 323098001791 putative CheW interface [polypeptide binding]; other site 323098001792 Helix-turn-helix domains; Region: HTH; cl00088 323098001793 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 323098001794 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 323098001795 P-loop; other site 323098001796 Magnesium ion binding site [ion binding]; other site 323098001797 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 323098001798 Hemolysin-type calcium-binding repeat (2 copies); Region: HemolysinCabind; pfam00353 323098001799 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 323098001800 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098001801 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098001802 Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the 'double-glycine' leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage...; Region: Peptidase_C39_like; cl00296 323098001803 putative active site [active] 323098001804 ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]; Region: SunT; COG2274 323098001805 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 323098001806 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098001807 Walker A/P-loop; other site 323098001808 ATP binding site [chemical binding]; other site 323098001809 Q-loop/lid; other site 323098001810 ABC transporter signature motif; other site 323098001811 Walker B; other site 323098001812 D-loop; other site 323098001813 H-loop/switch region; other site 323098001814 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 323098001815 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 323098001816 ABC transporter; Region: ABC_tran_2; pfam12848 323098001817 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 323098001818 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 323098001819 Sel1 repeat; Region: Sel1; cl02723 323098001820 Sel1 repeat; Region: Sel1; cl02723 323098001821 Sel1 repeat; Region: Sel1; cl02723 323098001822 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 323098001823 Sel1 repeat; Region: Sel1; cl02723 323098001824 Sel1 repeat; Region: Sel1; cl02723 323098001825 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 323098001826 Sel1 repeat; Region: Sel1; cl02723 323098001827 Sel1 repeat; Region: Sel1; cl02723 323098001828 Sel1 repeat; Region: Sel1; cl02723 323098001829 Sel1 repeat; Region: Sel1; cl02723 323098001830 Sel1 repeat; Region: Sel1; cl02723 323098001831 Rhamnan synthesis protein F; Region: RgpF; cl01529 323098001832 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 323098001833 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 323098001834 active site 323098001835 Rhamnan synthesis protein F; Region: RgpF; cl01529 323098001836 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 323098001837 TPR motif; other site 323098001838 Tetratricopeptide repeat; Region: TPR_16; pfam13432 323098001839 binding surface 323098001840 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 323098001841 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 323098001842 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098001843 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 323098001844 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098001845 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 323098001846 dTDP-glucose 4,6 dehydratase; Provisional; Region: PRK10084 323098001847 NAD binding site [chemical binding]; other site 323098001848 substrate binding site [chemical binding]; other site 323098001849 homodimer interface [polypeptide binding]; other site 323098001850 active site 323098001851 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 323098001852 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 323098001853 substrate binding site; other site 323098001854 tetramer interface; other site 323098001855 Cupin domain; Region: Cupin_2; cl09118 323098001856 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 323098001857 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 323098001858 NADP binding site [chemical binding]; other site 323098001859 active site 323098001860 putative substrate binding site [chemical binding]; other site 323098001861 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 323098001862 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 323098001863 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 323098001864 Probable Catalytic site; other site 323098001865 metal-binding site 323098001866 TPR repeat; Region: TPR_11; pfam13414 323098001867 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 323098001868 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 323098001869 Probable Catalytic site; other site 323098001870 metal-binding site 323098001871 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 323098001872 This family is most closely related to the GT1 family of glycosyltransferases. ExpC in Rhizobium meliloti has been shown to be involved in the biosynthesis of galactoglucan (exopolysaccharide II); Region: GT1_ExpC_like; cd03818 323098001873 putative ADP-binding pocket [chemical binding]; other site 323098001874 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 323098001875 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 323098001876 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 323098001877 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 323098001878 G1 box; other site 323098001879 putative GEF interaction site [polypeptide binding]; other site 323098001880 GTP/Mg2+ binding site [chemical binding]; other site 323098001881 Switch I region; other site 323098001882 G2 box; other site 323098001883 G3 box; other site 323098001884 Switch II region; other site 323098001885 G4 box; other site 323098001886 G5 box; other site 323098001887 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 323098001888 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 323098001889 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 323098001890 Helix-turn-helix domains; Region: HTH; cl00088 323098001891 Response regulator receiver domain; Region: Response_reg; pfam00072 323098001892 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 323098001893 active site 323098001894 phosphorylation site [posttranslational modification] 323098001895 intermolecular recognition site; other site 323098001896 dimerization interface [polypeptide binding]; other site 323098001897 NnrS protein; Region: NnrS; cl01258 323098001898 Peptidase propeptide and YPEB domain; Region: PepSY; cl15815 323098001899 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 323098001900 Histidine kinase; Region: HisKA_2; cl06527 323098001901 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 323098001902 ligand binding site [chemical binding]; other site 323098001903 flexible hinge region; other site 323098001904 putative indolepyruvate oxidoreductase subunit B; Reviewed; Region: PRK08312 323098001905 Helix-turn-helix domains; Region: HTH; cl00088 323098001906 Putative glycerate kinase [Carbohydrate transport and metabolism]; Region: GckA; COG2379 323098001907 Domain of unknown function (DUF4147); Region: DUF4147; pfam13660 323098001908 MOFRL family; Region: MOFRL; pfam05161 323098001909 Peptidase family M23; Region: Peptidase_M23; pfam01551 323098001910 AIFL (apoptosis-inducing factor like) family, N-terminal Rieske domain; members of this family show similarity to human AIFL, containing an N-terminal Rieske domain and a C-terminal pyridine nucleotide-disulfide oxidoreductase domain (Pyr_redox). The...; Region: Rieske_AIFL_N; cd03478 323098001911 [2Fe-2S] cluster binding site [ion binding]; other site 323098001912 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 323098001913 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 323098001914 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 323098001915 active site 323098001916 DNA binding site [nucleotide binding] 323098001917 Domain of unknown function (DUF4175); Region: DUF4175; pfam13779 323098001918 Response regulator receiver domain; Region: Response_reg; pfam00072 323098001919 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 323098001920 active site 323098001921 phosphorylation site [posttranslational modification] 323098001922 intermolecular recognition site; other site 323098001923 dimerization interface [polypeptide binding]; other site 323098001924 zinc-ribbon domain; Region: zinc_ribbon_5; cl11777 323098001925 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 323098001926 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 323098001927 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098001928 Walker A/P-loop; other site 323098001929 ATP binding site [chemical binding]; other site 323098001930 Q-loop/lid; other site 323098001931 ABC transporter signature motif; other site 323098001932 Walker B; other site 323098001933 D-loop; other site 323098001934 H-loop/switch region; other site 323098001935 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 323098001936 FtsX-like permease family; Region: FtsX; cl15850 323098001937 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 323098001938 putative active site [active] 323098001939 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 323098001940 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 323098001941 putative acyl-acceptor binding pocket; other site 323098001942 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cd06661 323098001943 putative active site pocket [active] 323098001944 dimerization interface [polypeptide binding]; other site 323098001945 putative catalytic residue [active] 323098001946 Uncharacterized protein conserved in bacteria (DUF2125); Region: DUF2125; pfam09898 323098001947 cyclohexadienyl dehydrogenase; Validated; Region: PRK07502 323098001948 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098001949 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 323098001950 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 323098001951 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098001952 homodimer interface [polypeptide binding]; other site 323098001953 catalytic residue [active] 323098001954 hypothetical protein; Provisional; Region: PRK06034 323098001955 Chorismate mutase type II; Region: CM_2; cl00693 323098001956 Homoserine acetyltransferase [Amino acid transport and metabolism]; Region: MET2; COG2021 323098001957 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 323098001958 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 323098001959 S-adenosylmethionine binding site [chemical binding]; other site 323098001960 NlpC/P60 family; Region: NLPC_P60; cl11438 323098001961 Uncharacterized Fe-S protein [General function prediction only]; Region: COG3217 323098001962 MOSC N-terminal beta barrel domain; Region: MOSC_N; pfam03476 323098001963 MOSC domain; Region: MOSC; pfam03473 323098001964 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 323098001965 Clp amino terminal domain; Region: Clp_N; pfam02861 323098001966 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 323098001967 Walker A motif; other site 323098001968 ATP binding site [chemical binding]; other site 323098001969 Walker B motif; other site 323098001970 arginine finger; other site 323098001971 TATA element modulatory factor 1 TATA binding; Region: TMF_TATA_bd; pfam12325 323098001972 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 323098001973 Walker A motif; other site 323098001974 ATP binding site [chemical binding]; other site 323098001975 Walker B motif; other site 323098001976 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 323098001977 sulfite reductase [NADPH] flavoprotein, alpha-component; Region: cysJ; TIGR01931 323098001978 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 323098001979 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 323098001980 FAD binding pocket [chemical binding]; other site 323098001981 FAD binding motif [chemical binding]; other site 323098001982 catalytic residues [active] 323098001983 NAD binding pocket [chemical binding]; other site 323098001984 phosphate binding motif [ion binding]; other site 323098001985 beta-alpha-beta structure motif; other site 323098001986 sulfite reductase subunit beta; Provisional; Region: PRK13504 323098001987 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 323098001988 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 323098001989 O-succinylhomoserine (thiol)-lyase; Region: O_succ_thio_ly; TIGR02080 323098001990 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 323098001991 homodimer interface [polypeptide binding]; other site 323098001992 substrate-cofactor binding pocket; other site 323098001993 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098001994 catalytic residue [active] 323098001995 BA14K-like protein; Region: BA14K; pfam07886 323098001996 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 323098001997 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098001998 Walker A motif; other site 323098001999 ATP binding site [chemical binding]; other site 323098002000 Family description; Region: UvrD_C_2; cl15862 323098002001 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 323098002002 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 323098002003 Walker A motif; other site 323098002004 ATP binding site [chemical binding]; other site 323098002005 Walker B motif; other site 323098002006 arginine finger; other site 323098002007 Helix-turn-helix domains; Region: HTH; cl00088 323098002008 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 323098002009 flagellar assembly protein H; Validated; Region: fliH; PRK06032 323098002010 Flagellar assembly protein FliH; Region: FliH; pfam02108 323098002011 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 323098002012 MgtE intracellular N domain; Region: MgtE_N; cl15244 323098002013 FliG C-terminal domain; Region: FliG_C; pfam01706 323098002014 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 323098002015 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 323098002016 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 323098002017 Protein of unknown function (DUF1153); Region: DUF1153; pfam06627 323098002018 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 323098002019 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 323098002020 FlgD Ig-like domain; Region: FlgD_ig; cl15790 323098002021 Flagellar hook-length control protein FliK; Region: Flg_hook; cl15269 323098002022 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 323098002023 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 323098002024 Ligand Binding Site [chemical binding]; other site 323098002025 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 323098002026 S-adenosylmethionine binding site [chemical binding]; other site 323098002027 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 323098002028 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 323098002029 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098002030 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09311 323098002031 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 323098002032 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 323098002033 dimerization interface [polypeptide binding]; other site 323098002034 active site 323098002035 Glutaryl-CoA dehydrogenase; Region: GCD; cd01151 323098002036 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 323098002037 FAD binding site [chemical binding]; other site 323098002038 substrate binding pocket [chemical binding]; other site 323098002039 catalytic base [active] 323098002040 ATP-grasp domain; Region: ATP-grasp_4; cl03087 323098002041 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098002042 cell division ATP-binding protein FtsE; Region: FtsE; TIGR02673 323098002043 Walker A/P-loop; other site 323098002044 ATP binding site [chemical binding]; other site 323098002045 Q-loop/lid; other site 323098002046 ABC transporter signature motif; other site 323098002047 Walker B; other site 323098002048 D-loop; other site 323098002049 H-loop/switch region; other site 323098002050 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 323098002051 Protein of unknown function (DUF1499); Region: DUF1499; cl01841 323098002052 LysR family transcriptional regulator; Provisional; Region: PRK14997 323098002053 Helix-turn-helix domains; Region: HTH; cl00088 323098002054 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_4; cd08473 323098002055 putative effector binding pocket; other site 323098002056 putative dimerization interface [polypeptide binding]; other site 323098002057 Pirin-related protein [General function prediction only]; Region: COG1741 323098002058 Cupin domain; Region: Cupin_2; cl09118 323098002059 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 323098002060 putative acyl-CoA synthetase; Provisional; Region: PRK06018 323098002061 AMP-binding enzyme; Region: AMP-binding; cl15778 323098002062 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 323098002063 Extensin-like protein C-terminus; Region: Extensin-like_C; pfam06904 323098002064 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 323098002065 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 323098002066 classical (c) SDRs; Region: SDR_c; cd05233 323098002067 NAD(P) binding site [chemical binding]; other site 323098002068 active site 323098002069 pyridoxamine 5'-phosphate oxidase; Provisional; Region: PRK05679 323098002070 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 323098002071 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 323098002072 curved DNA-binding protein CbpA; Provisional; Region: PRK10266 323098002073 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 323098002074 HSP70 interaction site [polypeptide binding]; other site 323098002075 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 323098002076 substrate binding site [polypeptide binding]; other site 323098002077 dimer interface [polypeptide binding]; other site 323098002078 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 323098002079 LuxR family transcriptional regulatory, chaperone HchA-associated; Region: reg_near_HchA; TIGR03541 323098002080 Autoinducer binding domain; Region: Autoind_bind; pfam03472 323098002081 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 323098002082 DNA binding residues [nucleotide binding] 323098002083 dimerization interface [polypeptide binding]; other site 323098002084 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 323098002085 catalytic core [active] 323098002086 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 323098002087 Tetramer interface [polypeptide binding]; other site 323098002088 active site 323098002089 FMN-binding site [chemical binding]; other site 323098002090 ATP-dependent Clp protease adaptor protein ClpS; Region: ClpS; cl00933 323098002091 TRAM domain; Region: TRAM; cl01282 323098002092 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 323098002093 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; cl15754 323098002094 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 323098002095 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 323098002096 RNA binding surface [nucleotide binding]; other site 323098002097 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; cl15754 323098002098 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 323098002099 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 323098002100 TPP-binding site; other site 323098002101 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 323098002102 PYR/PP interface [polypeptide binding]; other site 323098002103 dimer interface [polypeptide binding]; other site 323098002104 TPP binding site [chemical binding]; other site 323098002105 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 323098002106 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 323098002107 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 323098002108 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 323098002109 enoyl-CoA hydratase; Provisional; Region: PRK06688 323098002110 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 323098002111 substrate binding site [chemical binding]; other site 323098002112 oxyanion hole (OAH) forming residues; other site 323098002113 trimer interface [polypeptide binding]; other site 323098002114 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 323098002115 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 323098002116 active site 323098002117 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 323098002118 Helix-turn-helix domains; Region: HTH; cl00088 323098002119 Helix-turn-helix domains; Region: HTH; cl00088 323098002120 Winged helix-turn helix; Region: HTH_29; pfam13551 323098002121 Helix-turn-helix domains; Region: HTH; cl00088 323098002122 Integrase core domain; Region: rve; cl01316 323098002123 Integrase core domain; Region: rve_3; cl15866 323098002124 Capsule polysaccharide biosynthesis protein; Region: Capsule_synth; pfam05159 323098002125 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 323098002126 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 323098002127 inhibitor-cofactor binding pocket; inhibition site 323098002128 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098002129 catalytic residue [active] 323098002130 UDP-N-acetylglucosamine 4,6-dehydratase; Region: PseB; TIGR03589 323098002131 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 323098002132 NAD(P) binding site [chemical binding]; other site 323098002133 homodimer interface [polypeptide binding]; other site 323098002134 substrate binding site [chemical binding]; other site 323098002135 active site 323098002136 SpsF is a glycosyltrnasferase implicated in the synthesis of the spore coat; Region: GT2_SpsF; cd02518 323098002137 ligand binding site; other site 323098002138 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098002139 pseudaminic acid synthase; Region: PseI; TIGR03586 323098002140 NeuB family; Region: NeuB; cl00496 323098002141 SAF domain; Region: SAF; cl00555 323098002142 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 323098002143 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 323098002144 motif II; other site 323098002145 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 323098002146 S-adenosylmethionine binding site [chemical binding]; other site 323098002147 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 323098002148 MOSC domain; Region: MOSC; pfam03473 323098002149 3-alpha domain; Region: 3-alpha; pfam03475 323098002150 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 323098002151 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 323098002152 Domain of unknown function (DUF3471); Region: DUF3471; pfam11954 323098002153 Integrase core domain; Region: rve; cl01316 323098002154 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098002155 Winged helix-turn helix; Region: HTH_29; pfam13551 323098002156 Helix-turn-helix domains; Region: HTH; cl00088 323098002157 Helix-turn-helix domains; Region: HTH; cl00088 323098002158 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 323098002159 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 323098002160 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 323098002161 FecR protein; Region: FecR; pfam04773 323098002162 Secretin and TonB N terminus short domain; Region: STN; cl06624 323098002163 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 323098002164 N-terminal plug; other site 323098002165 ligand-binding site [chemical binding]; other site 323098002166 Helix-turn-helix domains; Region: HTH; cl00088 323098002167 Helix-turn-helix domains; Region: HTH; cl00088 323098002168 Winged helix-turn helix; Region: HTH_29; pfam13551 323098002169 Helix-turn-helix domains; Region: HTH; cl00088 323098002170 Integrase core domain; Region: rve; cl01316 323098002171 Integrase core domain; Region: rve_3; cl15866 323098002172 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 323098002173 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 323098002174 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 323098002175 non-specific DNA binding site [nucleotide binding]; other site 323098002176 salt bridge; other site 323098002177 sequence-specific DNA binding site [nucleotide binding]; other site 323098002178 Cupin domain; Region: Cupin_2; cl09118 323098002179 Porin subfamily; Region: Porin_2; pfam02530 323098002180 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 323098002181 TM-ABC transporter signature motif; other site 323098002182 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 323098002183 TM-ABC transporter signature motif; other site 323098002184 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 323098002185 Type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene; Region: PBP1_alkylbenzenes_like; cd06360 323098002186 putative ligand binding site [chemical binding]; other site 323098002187 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 323098002188 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 323098002189 Walker A/P-loop; other site 323098002190 ATP binding site [chemical binding]; other site 323098002191 Q-loop/lid; other site 323098002192 ABC transporter signature motif; other site 323098002193 Walker B; other site 323098002194 D-loop; other site 323098002195 H-loop/switch region; other site 323098002196 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 323098002197 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 323098002198 Walker A/P-loop; other site 323098002199 ATP binding site [chemical binding]; other site 323098002200 Q-loop/lid; other site 323098002201 ABC transporter signature motif; other site 323098002202 Walker B; other site 323098002203 D-loop; other site 323098002204 H-loop/switch region; other site 323098002205 Cytochrome c; Region: Cytochrom_C; cl11414 323098002206 Cytochrome c; Region: Cytochrom_C; cl11414 323098002207 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 323098002208 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 323098002209 Walker A/P-loop; other site 323098002210 ATP binding site [chemical binding]; other site 323098002211 Q-loop/lid; other site 323098002212 ABC transporter signature motif; other site 323098002213 Walker B; other site 323098002214 D-loop; other site 323098002215 H-loop/switch region; other site 323098002216 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 323098002217 dimer interface [polypeptide binding]; other site 323098002218 conserved gate region; other site 323098002219 putative PBP binding loops; other site 323098002220 ABC-ATPase subunit interface; other site 323098002221 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 323098002222 NMT1-like family; Region: NMT1_2; cl15260 323098002223 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 323098002224 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 323098002225 ligand binding site [chemical binding]; other site 323098002226 flexible hinge region; other site 323098002227 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 323098002228 putative switch regulator; other site 323098002229 non-specific DNA interactions [nucleotide binding]; other site 323098002230 DNA binding site [nucleotide binding] 323098002231 sequence specific DNA binding site [nucleotide binding]; other site 323098002232 putative cAMP binding site [chemical binding]; other site 323098002233 FOG: HEAT repeat [Energy production and conversion]; Region: COG1413 323098002234 PBS lyase HEAT-like repeat; Region: HEAT_PBS; cl15388 323098002235 Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin; Region: ARM; cl02500 323098002236 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 323098002237 Ferredoxin [Energy production and conversion]; Region: COG1146 323098002238 putative oxidoreductase; Provisional; Region: PRK08275 323098002239 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098002240 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 323098002241 Protein of unknown function (DUF971); Region: DUF971; cl01414 323098002242 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 323098002243 substrate binding pocket [chemical binding]; other site 323098002244 membrane-bound complex binding site; other site 323098002245 NMT1-like family; Region: NMT1_2; cl15260 323098002246 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 323098002247 alkanesulfonate monooxygenase; Provisional; Region: PRK00719 323098002248 active site 323098002249 dimer interface [polypeptide binding]; other site 323098002250 non-prolyl cis peptide bond; other site 323098002251 insertion regions; other site 323098002252 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 323098002253 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 323098002254 dimer interface [polypeptide binding]; other site 323098002255 conserved gate region; other site 323098002256 putative PBP binding loops; other site 323098002257 ABC-ATPase subunit interface; other site 323098002258 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098002259 Walker A/P-loop; other site 323098002260 ATP binding site [chemical binding]; other site 323098002261 ABC transporter; Region: ABC_tran; pfam00005 323098002262 Q-loop/lid; other site 323098002263 ABC transporter signature motif; other site 323098002264 Walker B; other site 323098002265 D-loop; other site 323098002266 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098002267 H-loop/switch region; other site 323098002268 Flavin Reductases; Region: FlaRed; cl00801 323098002269 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 323098002270 dimer interface [polypeptide binding]; other site 323098002271 pyrroloquinoline quinone biosynthesis protein PqqE; Provisional; Region: PRK05301 323098002272 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 323098002273 FeS/SAM binding site; other site 323098002274 Domain of unknown function (DUF4008); Region: DUF4008; cl14869 323098002275 Coenzyme PQQ synthesis protein D (PqqD); Region: PqqD; cl05126 323098002276 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 323098002277 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 323098002278 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 323098002279 Cytochrome c; Region: Cytochrom_C; cl11414 323098002280 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 323098002281 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_2; cd03814 323098002282 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 323098002283 Protein of unknown function (DUF962); Region: DUF962; cl01879 323098002284 Glutamate-1-semialdehyde aminotransferase [Coenzyme metabolism]; Region: HemL; COG0001 323098002285 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 323098002286 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 323098002287 catalytic residue [active] 323098002288 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 323098002289 catecholate siderophore receptor Fiu; Provisional; Region: PRK09840 323098002290 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 323098002291 N-terminal plug; other site 323098002292 ligand-binding site [chemical binding]; other site 323098002293 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 323098002294 Prolyl 4-hydroxylase alpha subunit homologues; Region: P4Hc; smart00702 323098002295 Family of homologous FMN-dependent alpha-hydroxyacid oxidizing enzymes. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate...; Region: alpha_hydroxyacid_oxid_FMN; cd02809 323098002296 FMN-dependent dehydrogenase; Region: FMN_dh; pfam01070 323098002297 active site 323098002298 substrate binding site [chemical binding]; other site 323098002299 FMN binding site [chemical binding]; other site 323098002300 putative catalytic residues [active] 323098002301 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 323098002302 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 323098002303 Gram-negative bacterial tonB protein; Region: TonB; cl10048 323098002304 Invasion associated locus B (IalB) protein; Region: IalB; cl02207 323098002305 Integrase core domain; Region: rve; cl01316 323098002306 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098002307 Winged helix-turn helix; Region: HTH_29; pfam13551 323098002308 Helix-turn-helix domains; Region: HTH; cl00088 323098002309 Helix-turn-helix domains; Region: HTH; cl00088 323098002310 Domain of unknown function DUF59; Region: DUF59; cl00941 323098002311 Cytochrome c; Region: Cytochrom_C; cl11414 323098002312 diaminopimelate decarboxylase; Region: lysA; TIGR01048 323098002313 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 323098002314 active site 323098002315 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 323098002316 substrate binding site [chemical binding]; other site 323098002317 catalytic residues [active] 323098002318 dimer interface [polypeptide binding]; other site 323098002319 argininosuccinate lyase; Provisional; Region: PRK00855 323098002320 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 323098002321 active sites [active] 323098002322 tetramer interface [polypeptide binding]; other site 323098002323 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 323098002324 catalytic residues [active] 323098002325 G8 domain; Region: G8; pfam10162 323098002326 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 323098002327 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 323098002328 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 323098002329 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 323098002330 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 323098002331 Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain...; Region: Rieske_NirD_small_Bacillus; cd03530 323098002332 [2Fe-2S] cluster binding site [ion binding]; other site 323098002333 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 323098002334 glutathionine S-transferase; Provisional; Region: PRK10542 323098002335 C-terminal domain interface [polypeptide binding]; other site 323098002336 GSH binding site (G-site) [chemical binding]; other site 323098002337 dimer interface [polypeptide binding]; other site 323098002338 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 323098002339 dimer interface [polypeptide binding]; other site 323098002340 substrate binding pocket (H-site) [chemical binding]; other site 323098002341 N-terminal domain interface [polypeptide binding]; other site 323098002342 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 323098002343 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 323098002344 FecR protein; Region: FecR; pfam04773 323098002345 Secretin and TonB N terminus short domain; Region: STN; cl06624 323098002346 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 323098002347 N-terminal plug; other site 323098002348 ligand-binding site [chemical binding]; other site 323098002349 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; cl00284 323098002350 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098002351 Walker A motif; other site 323098002352 ATP binding site [chemical binding]; other site 323098002353 Walker B motif; other site 323098002354 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 323098002355 Phage derived protein Gp49-like (DUF891); Region: Gp49; cl01470 323098002356 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 323098002357 Integrase core domain; Region: rve_3; cl15866 323098002358 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 323098002359 catalytic residues [active] 323098002360 catalytic nucleophile [active] 323098002361 Recombinase; Region: Recombinase; pfam07508 323098002362 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 323098002363 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 323098002364 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 323098002365 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 323098002366 catalytic residues [active] 323098002367 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 323098002368 apolar tunnel; other site 323098002369 heme binding site [chemical binding]; other site 323098002370 dimerization interface [polypeptide binding]; other site 323098002371 Helix-turn-helix domains; Region: HTH; cl00088 323098002372 Predicted transcriptional regulator [Transcription]; Region: COG1959 323098002373 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 323098002374 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 323098002375 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 323098002376 protein binding site [polypeptide binding]; other site 323098002377 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; cd00085 323098002378 active site 323098002379 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 323098002380 endonuclease III; Region: ENDO3c; smart00478 323098002381 minor groove reading motif; other site 323098002382 helix-hairpin-helix signature motif; other site 323098002383 substrate binding pocket [chemical binding]; other site 323098002384 active site 323098002385 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 323098002386 active site 323098002387 HIGH motif; other site 323098002388 nucleotide binding site [chemical binding]; other site 323098002389 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 323098002390 active site 323098002391 KMSKS motif; other site 323098002392 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 323098002393 dimer interface [polypeptide binding]; other site 323098002394 phosphorylation site [posttranslational modification] 323098002395 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 323098002396 ATP binding site [chemical binding]; other site 323098002397 Mg2+ binding site [ion binding]; other site 323098002398 G-X-G motif; other site 323098002399 Response regulator receiver domain; Region: Response_reg; pfam00072 323098002400 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 323098002401 active site 323098002402 phosphorylation site [posttranslational modification] 323098002403 intermolecular recognition site; other site 323098002404 dimerization interface [polypeptide binding]; other site 323098002405 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 323098002406 Hypoxia induced protein conserved region; Region: HIG_1_N; pfam04588 323098002407 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; cl00920 323098002408 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_beta; cd01714 323098002409 Ligand binding site [chemical binding]; other site 323098002410 Electron transfer flavoprotein domain; Region: ETF; pfam01012 323098002411 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 323098002412 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_alpha; cd01715 323098002413 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 323098002414 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK07530 323098002415 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098002416 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 323098002417 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 323098002418 The function of this protein family is unkown. The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage...; Region: CobW_like; cd03112 323098002419 P-loop, Walker A motif; other site 323098002420 Base recognition motif; other site 323098002421 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 323098002422 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098002423 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 323098002424 homodimer interaction site [polypeptide binding]; other site 323098002425 cofactor binding site; other site 323098002426 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00051 323098002427 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 323098002428 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 323098002429 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 323098002430 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 323098002431 Subunit I/III interface [polypeptide binding]; other site 323098002432 D-pathway; other site 323098002433 Subunit I/VIIc interface [polypeptide binding]; other site 323098002434 Subunit I/IV interface [polypeptide binding]; other site 323098002435 Subunit I/II interface [polypeptide binding]; other site 323098002436 Low-spin heme (heme a) binding site [chemical binding]; other site 323098002437 Subunit I/VIIa interface [polypeptide binding]; other site 323098002438 Subunit I/VIa interface [polypeptide binding]; other site 323098002439 Dimer interface; other site 323098002440 Putative water exit pathway; other site 323098002441 Binuclear center (heme a3/CuB) [ion binding]; other site 323098002442 K-pathway; other site 323098002443 Subunit I/Vb interface [polypeptide binding]; other site 323098002444 Putative proton exit pathway; other site 323098002445 Subunit I/VIb interface; other site 323098002446 Subunit I/VIc interface [polypeptide binding]; other site 323098002447 Electron transfer pathway; other site 323098002448 Subunit I/VIIIb interface [polypeptide binding]; other site 323098002449 Subunit I/VIIb interface [polypeptide binding]; other site 323098002450 UbiA prenyltransferase family; Region: UbiA; cl00337 323098002451 Cytochrome c oxidase assembly protein CtaG/Cox11; Region: CtaG_Cox11; cl01240 323098002452 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 323098002453 Subunit III/VIIa interface [polypeptide binding]; other site 323098002454 Phospholipid binding site [chemical binding]; other site 323098002455 Subunit I/III interface [polypeptide binding]; other site 323098002456 Subunit III/VIb interface [polypeptide binding]; other site 323098002457 Subunit III/VIa interface; other site 323098002458 Subunit III/Vb interface [polypeptide binding]; other site 323098002459 Protein of unknown function (DUF983); Region: DUF983; cl02211 323098002460 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 323098002461 Heme-copper oxidase subunit III. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane. The...; Region: Heme_Cu_Oxidase_III_like; cl00211 323098002462 Subunit I/III interface [polypeptide binding]; other site 323098002463 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 323098002464 Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons...; Region: Ubiquinol_Oxidase_I; cd01662 323098002465 D-pathway; other site 323098002466 Putative ubiquinol binding site [chemical binding]; other site 323098002467 Low-spin heme (heme b) binding site [chemical binding]; other site 323098002468 Putative water exit pathway; other site 323098002469 Binuclear center (heme o3/CuB) [ion binding]; other site 323098002470 K-pathway; other site 323098002471 Putative proton exit pathway; other site 323098002472 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl15769 323098002473 Cytochrome c; Region: Cytochrom_C; cl11414 323098002474 Cytochrome c; Region: Cytochrom_C; cl11414 323098002475 Nitrate reductase alpha subunit [Energy production and conversion]; Region: NarG; COG5013 323098002476 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to...; Region: MopB_Nitrate-R-NarG-like; cd02750 323098002477 [4Fe-4S] binding site [ion binding]; other site 323098002478 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 323098002479 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 323098002480 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 323098002481 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 323098002482 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to...; Region: MopB_CT_Nitrate-R-NarG-like; cd02776 323098002483 molybdopterin cofactor binding site; other site 323098002484 Nitrate reductase beta subunit [Energy production and conversion]; Region: NarY; COG1140 323098002485 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 323098002486 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; cl00959 323098002487 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 323098002488 putative substrate translocation pore; other site 323098002489 The Tellurite-resistance/Dicarboxylate Transporter (TDT) family; Region: TDT_like_1; cd09319 323098002490 gating phenylalanine in ion channel; other site 323098002491 Integrase core domain; Region: rve; cl01316 323098002492 Integrase core domain; Region: rve_3; cl15866 323098002493 Helix-turn-helix domains; Region: HTH; cl00088 323098002494 NlpC/P60 family; Region: NLPC_P60; cl11438 323098002495 Protein of unknown function (DUF2793); Region: DUF2793; pfam10983 323098002496 GTA TIM-barrel-like domain; Region: GTA_TIM; pfam13547 323098002497 Putative phage tail protein; Region: Phage-tail_3; pfam13550 323098002498 NlpC/P60 family; Region: NLPC_P60; cl11438 323098002499 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 323098002500 phage conserved hypothetical protein BR0599; Region: phg_TIGR02218 323098002501 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 323098002502 Conserved hypothetical protein 2217 (DUF2460); Region: DUF2460; cl02268 323098002503 Prophage tail length tape measure protein; Region: TMP_2; pfam06791 323098002504 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 323098002505 Uncharacterized conserved protein (DUF2190); Region: DUF2190; cl02289 323098002506 Caudovirus prohead protease; Region: Peptidase_U35; cl01521 323098002507 Phage portal protein, lambda family; Region: Phage_portal_2; pfam05136 323098002508 Caudovirales tail fibre assembly protein; Region: Caudo_TAP; cl05448 323098002509 Phage terminase large subunit (GpA); Region: Terminase_GpA; pfam05876 323098002510 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 323098002511 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 323098002512 S-adenosylmethionine binding site [chemical binding]; other site 323098002513 ParB-like nuclease domain; Region: ParBc; cl02129 323098002514 AAA domain; Region: AAA_25; pfam13481 323098002515 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098002516 Walker A motif; other site 323098002517 ATP binding site [chemical binding]; other site 323098002518 Walker B motif; other site 323098002519 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 323098002520 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 323098002521 Domain of unknown function (DUF955); Region: DUF955; cl01076 323098002522 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 323098002523 non-specific DNA binding site [nucleotide binding]; other site 323098002524 salt bridge; other site 323098002525 sequence-specific DNA binding site [nucleotide binding]; other site 323098002526 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 323098002527 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 323098002528 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 323098002529 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 323098002530 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 323098002531 Int/Topo IB signature motif; other site 323098002532 active site 323098002533 DNA binding site [nucleotide binding] 323098002534 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 323098002535 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 323098002536 Magnesium ion binding site [ion binding]; other site 323098002537 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 323098002538 catalytic residues [active] 323098002539 Recombinase; Region: Recombinase; pfam07508 323098002540 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 323098002541 Protein of unknown function (DUF1778); Region: DUF1778; cl01845 323098002542 Integrase core domain; Region: rve; cl01316 323098002543 Integrase core domain; Region: rve_3; cl15866 323098002544 Protein of unknown function (DUF736); Region: DUF736; cl02303 323098002545 Transposase domain (DUF772); Region: DUF772; cl15789 323098002546 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 323098002547 non-specific DNA binding site [nucleotide binding]; other site 323098002548 salt bridge; other site 323098002549 sequence-specific DNA binding site [nucleotide binding]; other site 323098002550 Uncharacterized conserved protein (DUF2285); Region: DUF2285; cl02246 323098002551 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 323098002552 Replication initiator protein A; Region: RPA; cl02339 323098002553 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098002554 Protein of unknown function (DUF2840); Region: DUF2840; pfam11000 323098002555 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the...; Region: Peptidase_S24_S26; cl10465 323098002556 Signal peptidase, peptidase S26; Region: Peptidase_S26; pfam10502 323098002557 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 323098002558 N-acetyl-D-glucosamine binding site [chemical binding]; other site 323098002559 catalytic residue [active] 323098002560 Integrase core domain; Region: rve; cl01316 323098002561 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098002562 Winged helix-turn helix; Region: HTH_29; pfam13551 323098002563 Helix-turn-helix domains; Region: HTH; cl00088 323098002564 Helix-turn-helix domains; Region: HTH; cl00088 323098002565 Transposase; Region: DEDD_Tnp_IS110; pfam01548 323098002566 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 323098002567 Relaxase/Mobilisation nuclease domain; Region: Relaxase; cl01584 323098002568 Protein of unknown function (DUF3363); Region: DUF3363; pfam11843 323098002569 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 323098002570 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 323098002571 oligomeric interface; other site 323098002572 putative active site [active] 323098002573 homodimer interface [polypeptide binding]; other site 323098002574 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 323098002575 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 323098002576 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 323098002577 Protein of unknown function (DUF2274); Region: DUF2274; cl02406 323098002578 Phage protein Gp37/Gp68; Region: Gp37_Gp68; cl15384 323098002579 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098002580 Walker A/P-loop; other site 323098002581 ATP binding site [chemical binding]; other site 323098002582 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 323098002583 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 323098002584 Helix-turn-helix domains; Region: HTH; cl00088 323098002585 Winged helix-turn helix; Region: HTH_29; pfam13551 323098002586 Helix-turn-helix domains; Region: HTH; cl00088 323098002587 Integrase core domain; Region: rve; cl01316 323098002588 Integrase core domain; Region: rve_3; cl15866 323098002589 Helix-turn-helix domains; Region: HTH; cl00088 323098002590 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 323098002591 Helix-turn-helix domains; Region: HTH; cl00088 323098002592 Helix-turn-helix domains; Region: HTH; cl00088 323098002593 putative transposase OrfB; Reviewed; Region: PHA02517 323098002594 Helix-turn-helix domains; Region: HTH; cl00088 323098002595 Integrase core domain; Region: rve; cl01316 323098002596 Integrase core domain; Region: rve_3; cl15866 323098002597 Helix-turn-helix domains; Region: HTH; cl00088 323098002598 Helix-turn-helix domains; Region: HTH; cl00088 323098002599 Winged helix-turn helix; Region: HTH_29; pfam13551 323098002600 Helix-turn-helix domains; Region: HTH; cl00088 323098002601 Integrase core domain; Region: rve; cl01316 323098002602 Integrase core domain; Region: rve_3; cl15866 323098002603 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 323098002604 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 323098002605 Family of unknown function (DUF490); Region: DUF490; pfam04357 323098002606 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 323098002607 Surface antigen; Region: Bac_surface_Ag; cl03097 323098002608 Choloylglycine hydrolase (CGH) is a bile salt-modifying enzyme that hydrolyzes non-peptide carbon-nitrogen bonds in choloylglycine and choloyltaurine, both of which are present in bile. CGH is present in a number of probiotic microbial organisms that...; Region: Ntn_CGH; cd01902 323098002609 Linear amide C-N hydrolases, choloylglycine hydrolase family; Region: CBAH; pfam02275 323098002610 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 323098002611 Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic...; Region: PRX_like1; cd02969 323098002612 putative catalytic residue [active] 323098002613 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; cl00284 323098002614 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 323098002615 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 323098002616 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 323098002617 DNA-binding site [nucleotide binding]; DNA binding site 323098002618 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 323098002619 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 323098002620 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098002621 homodimer interface [polypeptide binding]; other site 323098002622 catalytic residue [active] 323098002623 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II); Region: Aldolase_II; cl00214 323098002624 intersubunit interface [polypeptide binding]; other site 323098002625 active site 323098002626 Zn2+ binding site [ion binding]; other site 323098002627 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 323098002628 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 323098002629 inhibitor site; inhibition site 323098002630 active site 323098002631 dimer interface [polypeptide binding]; other site 323098002632 catalytic residue [active] 323098002633 Clostridium P-47 protein; Region: Clostridium_P47; pfam06597 323098002634 Clostridium P-47 protein; Region: Clostridium_P47; pfam06597 323098002635 Clostridium P-47 protein; Region: Clostridium_P47; pfam06597 323098002636 Clostridium P-47 protein; Region: Clostridium_P47; pfam06597 323098002637 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 323098002638 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 323098002639 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 323098002640 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 323098002641 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 323098002642 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 323098002643 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 323098002644 dimerization interface [polypeptide binding]; other site 323098002645 putative DNA binding site [nucleotide binding]; other site 323098002646 putative Zn2+ binding site [ion binding]; other site 323098002647 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_2; cd08895 323098002648 putative hydrophobic ligand binding site [chemical binding]; other site 323098002649 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 323098002650 extracytoplasmic-function sigma-70 factor; Validated; Region: PRK07037 323098002651 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 323098002652 DNA binding residues [nucleotide binding] 323098002653 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 323098002654 FecR protein; Region: FecR; pfam04773 323098002655 Secretin and TonB N terminus short domain; Region: STN; cl06624 323098002656 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 323098002657 ATP-grasp domain; Region: ATP-grasp_4; cl03087 323098002658 hopanoid-associated sugar epimerase; Region: HpnA; TIGR03466 323098002659 uncharacterized subgroup of aldehyde reductase and flavonoid reductase related proteins, extended (e) SDRs; Region: AR_FR_like_1_SDR_e; cd05228 323098002660 putative NADP binding site [chemical binding]; other site 323098002661 putative substrate binding site [chemical binding]; other site 323098002662 active site 323098002663 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 323098002664 Bacteriocin-protection, YdeI or OmpD-Associated; Region: OmdA; pfam13376 323098002665 Domain of unknown function (DUF4104); Region: DUF4104; pfam13372 323098002666 heavy metal efflux pump (cobalt-zinc-cadmium); Region: 2A0601; TIGR00914 323098002667 Cupin domain; Region: Cupin_2; cl09118 323098002668 AAA domain; Region: AAA_27; pfam13514 323098002669 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 323098002670 active site 323098002671 metal binding site [ion binding]; metal-binding site 323098002672 DNA binding site [nucleotide binding] 323098002673 Protein of unknown function (DUF4011); Region: DUF4011; pfam13195 323098002674 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098002675 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098002676 Family description; Region: UvrD_C_2; cl15862 323098002677 Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and...; Region: Restriction_endonuclease_like; cl00277 323098002678 putative active site [active] 323098002679 Protein of unknown function (DUF3320); Region: DUF3320; pfam11784 323098002680 Transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this domain superfamily was previously known as DUF156; Region: CsoR-like_DUF156; cd10148 323098002681 putative homotetramer interface [polypeptide binding]; other site 323098002682 putative homodimer interface [polypeptide binding]; other site 323098002683 putative allosteric switch controlling residues; other site 323098002684 putative metal binding site [ion binding]; other site 323098002685 putative homodimer-homodimer interface [polypeptide binding]; other site 323098002686 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 323098002687 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 323098002688 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 323098002689 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 323098002690 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; cl01951 323098002691 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 323098002692 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 323098002693 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 323098002694 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 323098002695 ABC component of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of...; Region: ABC_Metallic_Cations; cd03235 323098002696 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 323098002697 ABC-ATPase subunit interface; other site 323098002698 dimer interface [polypeptide binding]; other site 323098002699 putative PBP binding regions; other site 323098002700 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 323098002701 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 323098002702 intersubunit interface [polypeptide binding]; other site 323098002703 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 323098002704 The function of this protein family is unkown. The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage...; Region: CobW_like; cd03112 323098002705 P-loop, Walker A motif; other site 323098002706 Base recognition motif; other site 323098002707 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 323098002708 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from...; Region: WD40; cl02567 323098002709 structural tetrad; other site 323098002710 Homospermidine synthase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG5310 323098002711 Saccharopine dehydrogenase; Region: Saccharop_dh; pfam03435 323098002712 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 323098002713 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 323098002714 Predicted acetyltransferase [General function prediction only]; Region: COG3153 323098002715 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 323098002716 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase; Region: PLPDE_III_ODC; cd00622 323098002717 dimer interface [polypeptide binding]; other site 323098002718 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 323098002719 active site 323098002720 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 323098002721 catalytic residues [active] 323098002722 substrate binding site [chemical binding]; other site 323098002723 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 323098002724 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 323098002725 active site 323098002726 Zn binding site [ion binding]; other site 323098002727 MAPEG family; Region: MAPEG; cl09190 323098002728 ferrochelatase; Reviewed; Region: hemH; PRK00035 323098002729 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 323098002730 C-terminal domain interface [polypeptide binding]; other site 323098002731 active site 323098002732 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 323098002733 active site 323098002734 N-terminal domain interface [polypeptide binding]; other site 323098002735 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 323098002736 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 323098002737 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 323098002738 KpsF/GutQ family protein; Region: kpsF; TIGR00393 323098002739 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 323098002740 putative active site [active] 323098002741 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 323098002742 Uncharacterized protein conserved in bacteria (DUF2320); Region: DUF2320; cl12051 323098002743 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098002744 Helix-turn-helix domains; Region: HTH; cl00088 323098002745 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 323098002746 Protein of unknown function (DUF3772); Region: DUF3772; pfam12607 323098002747 Mechanosensitive ion channel; Region: MS_channel; pfam00924 323098002748 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 323098002749 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 323098002750 active site 323098002751 Flavin Reductases; Region: FlaRed; cl00801 323098002752 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 323098002753 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 323098002754 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 323098002755 N-terminal plug; other site 323098002756 ligand-binding site [chemical binding]; other site 323098002757 di-heme enzyme, MXAN_0977 family; Region: MXAN_0977_Heme2; TIGR04039 323098002758 Uncharacterized conserved protein [Function unknown]; Region: COG0397; cl00428 323098002759 Uncharacterized ACR, YdiU/UPF0061 family; Region: UPF0061; pfam02696 323098002760 maltooligosyl trehalose synthase; Provisional; Region: PRK14511 323098002761 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 323098002762 Alpha amylase catalytic domain found in maltooligosyl trehalose synthase (MTSase); Region: AmyAc_MTSase; cd11336 323098002763 active site 323098002764 catalytic site [active] 323098002765 AAK_UMPK-MosAB: This CD includes the alpha and beta subunits of the Mo storage protein (MosA and MosB) which are related to uridine monophosphate kinase (UMPK) enzymes that catalyze the phosphorylation of UMP by ATP, yielding UDP, and playing a key role...; Region: AAK_UMPK-MosAB; cd04255 323098002766 putative nucleotide binding site [chemical binding]; other site 323098002767 putative substrate binding site [chemical binding]; other site 323098002768 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 323098002769 nucleotide binding site [chemical binding]; other site 323098002770 substrate binding site [chemical binding]; other site 323098002771 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 323098002772 Glutamine amidotransferase class-I; Region: GATase; pfam00117 323098002773 glutamine binding [chemical binding]; other site 323098002774 catalytic triad [active] 323098002775 Anthranilate/para-aminobenzoate synthases component I [Amino acid transport and metabolism / Coenzyme metabolism]; Region: TrpE; COG0147 323098002776 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 323098002777 chorismate binding enzyme; Region: Chorismate_bind; cl10555 323098002778 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 323098002779 Ligand Binding Site [chemical binding]; other site 323098002780 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cl11442 323098002781 Integrase core domain; Region: rve; cl01316 323098002782 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098002783 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-II-III; cl00656 323098002784 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 323098002785 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl09944 323098002786 active site 323098002787 phosphorylation site [posttranslational modification] 323098002788 intermolecular recognition site; other site 323098002789 dimerization interface [polypeptide binding]; other site 323098002790 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 323098002791 DNA binding residues [nucleotide binding] 323098002792 dimerization interface [polypeptide binding]; other site 323098002793 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 323098002794 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 323098002795 This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain. They export...; Region: ABCC_Protease_Secretion; cd03246 323098002796 Walker A/P-loop; other site 323098002797 ATP binding site [chemical binding]; other site 323098002798 Q-loop/lid; other site 323098002799 ABC transporter signature motif; other site 323098002800 Walker B; other site 323098002801 D-loop; other site 323098002802 H-loop/switch region; other site 323098002803 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 323098002804 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 323098002805 Merozoite surface protein 1 (MSP1) C-terminus; Region: MSP1_C; pfam07462 323098002806 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 323098002807 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 323098002808 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 323098002809 binding surface 323098002810 TPR motif; other site 323098002811 TPR repeat; Region: TPR_11; pfam13414 323098002812 Nitrate reductase beta subunit [Energy production and conversion]; Region: NarY; COG1140 323098002813 Common central domain of tyrosinase; Region: Tyrosinase; pfam00264 323098002814 Polyphenol oxidase middle domain; Region: PPO1_DWL; pfam12142 323098002815 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 323098002816 Transposase domain (DUF772); Region: DUF772; cl15789 323098002817 Transposase domain (DUF772); Region: DUF772; cl15789 323098002818 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 323098002819 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 323098002820 GTP binding site; other site 323098002821 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; cd00291 323098002822 CPxP motif; other site 323098002823 Integrase core domain; Region: rve; cl01316 323098002824 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098002825 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 323098002826 substrate binding site [chemical binding]; other site 323098002827 active site 323098002828 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 323098002829 Pirin-related protein [General function prediction only]; Region: COG1741 323098002830 Cupin domain; Region: Cupin_2; cl09118 323098002831 Helix-turn-helix domains; Region: HTH; cl00088 323098002832 transcriptional regulator; Provisional; Region: PRK10632 323098002833 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 323098002834 putative effector binding pocket; other site 323098002835 dimerization interface [polypeptide binding]; other site 323098002836 Cysteine rich repeat; Region: Cys_rich_FGFR; pfam00839 323098002837 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 323098002838 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 323098002839 active site 323098002840 phosphorylation site [posttranslational modification] 323098002841 intermolecular recognition site; other site 323098002842 dimerization interface [polypeptide binding]; other site 323098002843 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 323098002844 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 323098002845 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 323098002846 binding surface 323098002847 Tetratricopeptide repeat; Region: TPR_16; pfam13432 323098002848 TPR motif; other site 323098002849 pyruvate kinase; Provisional; Region: PRK06247 323098002850 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 323098002851 domain interfaces; other site 323098002852 active site 323098002853 Protein of unknown function (DUF1036); Region: DUF1036; cl02296 323098002854 Protein of unknown function (DUF1244); Region: DUF1244; cl01385 323098002855 Uncharacterized protein conserved in bacteria (DUF2312); Region: DUF2312; cl11480 323098002856 Peptidase M15; Region: Peptidase_M15_3; cl01194 323098002857 DNA polymerase III subunits gamma and tau; Validated; Region: PRK07994 323098002858 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 323098002859 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 323098002860 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 323098002861 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 323098002862 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 323098002863 active site 323098002864 phosphorylation site [posttranslational modification] 323098002865 intermolecular recognition site; other site 323098002866 dimerization interface [polypeptide binding]; other site 323098002867 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 323098002868 Walker A motif; other site 323098002869 ATP binding site [chemical binding]; other site 323098002870 Walker B motif; other site 323098002871 arginine finger; other site 323098002872 Helix-turn-helix domains; Region: HTH; cl00088 323098002873 oligoendopeptidase, pepF/M3 family; Region: M3_fam_3; TIGR02290 323098002874 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_5; cd09610 323098002875 active site 323098002876 Zn binding site [ion binding]; other site 323098002877 Bacterial aa3 type cytochrome c oxidase subunit IV; Region: COX4_pro_2; pfam07835 323098002878 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 323098002879 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; cl15379 323098002880 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098002881 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098002882 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 323098002883 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 323098002884 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; cl00566 323098002885 Protein of unknown function (DUF3606); Region: DUF3606; pfam12244 323098002886 Protein of unknown function (DUF3606); Region: DUF3606; pfam12244 323098002887 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 323098002888 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; cd00333 323098002889 amphipathic channel; other site 323098002890 Asn-Pro-Ala signature motifs; other site 323098002891 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 323098002892 ATP-grasp domain; Region: ATP-grasp_4; cl03087 323098002893 AIR carboxylase; Region: AIRC; cl00310 323098002894 Protein of unknown function (DUF465); Region: DUF465; cl01070 323098002895 Protein of unknown function (DUF465); Region: DUF465; cl01070 323098002896 Predicted dehydrogenase [General function prediction only]; Region: COG0579 323098002897 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 323098002898 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098002899 Walker A/P-loop; other site 323098002900 ATP binding site [chemical binding]; other site 323098002901 Q-loop/lid; other site 323098002902 ABC transporter signature motif; other site 323098002903 Walker B; other site 323098002904 D-loop; other site 323098002905 H-loop/switch region; other site 323098002906 TOBE domain; Region: TOBE_2; cl01440 323098002907 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 323098002908 dimer interface [polypeptide binding]; other site 323098002909 conserved gate region; other site 323098002910 putative PBP binding loops; other site 323098002911 ABC-ATPase subunit interface; other site 323098002912 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 323098002913 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 323098002914 dimer interface [polypeptide binding]; other site 323098002915 conserved gate region; other site 323098002916 putative PBP binding loops; other site 323098002917 ABC-ATPase subunit interface; other site 323098002918 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 323098002919 Type II secretion system (T2SS), protein N; Region: T2SN; pfam01203 323098002920 AsmA-like C-terminal region; Region: AsmA_2; cl15864 323098002921 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 323098002922 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 323098002923 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 323098002924 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 323098002925 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 323098002926 putative active site [active] 323098002927 heme pocket [chemical binding]; other site 323098002928 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 323098002929 dimer interface [polypeptide binding]; other site 323098002930 phosphorylation site [posttranslational modification] 323098002931 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 323098002932 ATP binding site [chemical binding]; other site 323098002933 Mg2+ binding site [ion binding]; other site 323098002934 G-X-G motif; other site 323098002935 Phasin protein; Region: Phasin_2; cl11491 323098002936 Phasin protein; Region: Phasin_2; cl11491 323098002937 Transposase domain (DUF772); Region: DUF772; cl15789 323098002938 Integrase core domain; Region: rve; cl01316 323098002939 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098002940 Helix-turn-helix domains; Region: HTH; cl00088 323098002941 Helix-turn-helix domains; Region: HTH; cl00088 323098002942 Winged helix-turn helix; Region: HTH_29; pfam13551 323098002943 Helix-turn-helix domains; Region: HTH; cl00088 323098002944 Integrase core domain; Region: rve; cl01316 323098002945 Integrase core domain; Region: rve_3; cl15866 323098002946 FOG: CBS domain [General function prediction only]; Region: COG0517 323098002947 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the BON (bacterial OsmY and nodulation domain) domain. BON is a putative phospholipid-binding domain found in a family of osmotic shock protection...; Region: CBS_pair_BON_assoc; cd04586 323098002948 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 323098002949 BON domain; Region: BON; cl02771 323098002950 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 323098002951 Ligand Binding Site [chemical binding]; other site 323098002952 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 323098002953 glucokinase, proteobacterial type; Region: glk; TIGR00749 323098002954 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 323098002955 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 323098002956 Response regulator receiver domain; Region: Response_reg; pfam00072 323098002957 active site 323098002958 phosphorylation site [posttranslational modification] 323098002959 intermolecular recognition site; other site 323098002960 dimerization interface [polypeptide binding]; other site 323098002961 response regulator FixJ; Provisional; Region: fixJ; PRK09390 323098002962 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 323098002963 active site 323098002964 phosphorylation site [posttranslational modification] 323098002965 intermolecular recognition site; other site 323098002966 dimerization interface [polypeptide binding]; other site 323098002967 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 323098002968 DNA binding residues [nucleotide binding] 323098002969 dimerization interface [polypeptide binding]; other site 323098002970 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 323098002971 PAS fold; Region: PAS_3; pfam08447 323098002972 putative active site [active] 323098002973 heme pocket [chemical binding]; other site 323098002974 PAS domain S-box; Region: sensory_box; TIGR00229 323098002975 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 323098002976 putative active site [active] 323098002977 heme pocket [chemical binding]; other site 323098002978 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 323098002979 dimer interface [polypeptide binding]; other site 323098002980 phosphorylation site [posttranslational modification] 323098002981 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 323098002982 ATP binding site [chemical binding]; other site 323098002983 Mg2+ binding site [ion binding]; other site 323098002984 G-X-G motif; other site 323098002985 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2187 323098002986 FOG: CBS domain [General function prediction only]; Region: COG0517 323098002987 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 323098002988 Protein of unknown function (DUF330); Region: DUF330; cl01135 323098002989 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 323098002990 Ligand Binding Site [chemical binding]; other site 323098002991 transcriptional regulator FixK; Provisional; Region: fixK; PRK09391 323098002992 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 323098002993 ligand binding site [chemical binding]; other site 323098002994 flexible hinge region; other site 323098002995 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 323098002996 putative switch regulator; other site 323098002997 non-specific DNA interactions [nucleotide binding]; other site 323098002998 DNA binding site [nucleotide binding] 323098002999 sequence specific DNA binding site [nucleotide binding]; other site 323098003000 putative cAMP binding site [chemical binding]; other site 323098003001 CsbD-like; Region: CsbD; cl15799 323098003002 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 323098003003 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 323098003004 amidase catalytic site [active] 323098003005 Zn binding residues [ion binding]; other site 323098003006 substrate binding site [chemical binding]; other site 323098003007 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 323098003008 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 323098003009 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098003010 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 323098003011 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 323098003012 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 323098003013 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 323098003014 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 323098003015 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 323098003016 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 323098003017 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 323098003018 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanine ligase; Provisional; Region: PRK14093 323098003019 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 323098003020 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 323098003021 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 323098003022 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 323098003023 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 323098003024 Mg++ binding site [ion binding]; other site 323098003025 putative catalytic motif [active] 323098003026 putative substrate binding site [chemical binding]; other site 323098003027 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01390 323098003028 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098003029 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 323098003030 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 323098003031 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 323098003032 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 323098003033 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 323098003034 active site 323098003035 homodimer interface [polypeptide binding]; other site 323098003036 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 323098003037 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 323098003038 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 323098003039 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 323098003040 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 323098003041 GIY-YIG motif/motif A; other site 323098003042 putative active site [active] 323098003043 putative metal binding site [ion binding]; other site 323098003044 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 323098003045 FAD binding domain; Region: FAD_binding_4; pfam01565 323098003046 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 323098003047 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 323098003048 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 323098003049 ATP-grasp domain; Region: ATP-grasp_4; cl03087 323098003050 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 323098003051 Cell division protein FtsQ; Region: FtsQ; pfam03799 323098003052 Cell division ATPase FtsA [Cell division and chromosome partitioning]; Region: ftsA; COG0849 323098003053 Cell division protein FtsA; Region: FtsA; cl11496 323098003054 Cell division protein FtsA; Region: FtsA; cl11496 323098003055 cell division protein FtsZ; Validated; Region: PRK09330 323098003056 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 323098003057 nucleotide binding site [chemical binding]; other site 323098003058 SulA interaction site; other site 323098003059 cell division protein FtsZ, alphaProteobacterial C-terminal extension; Region: FtsZ_alphas_C; TIGR03483 323098003060 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 323098003061 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 323098003062 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 323098003063 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 323098003064 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 323098003065 Walker A/P-loop; other site 323098003066 ATP binding site [chemical binding]; other site 323098003067 Q-loop/lid; other site 323098003068 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 323098003069 ABC transporter signature motif; other site 323098003070 Walker B; other site 323098003071 D-loop; other site 323098003072 H-loop/switch region; other site 323098003073 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 323098003074 NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction...; Region: LIGANc; cd00114 323098003075 nucleotide binding pocket [chemical binding]; other site 323098003076 K-X-D-G motif; other site 323098003077 catalytic site [active] 323098003078 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 323098003079 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 323098003080 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 323098003081 Dimer interface [polypeptide binding]; other site 323098003082 BRCT sequence motif; other site 323098003083 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 323098003084 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 323098003085 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 323098003086 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 323098003087 Walker A/P-loop; other site 323098003088 ATP binding site [chemical binding]; other site 323098003089 Q-loop/lid; other site 323098003090 ABC transporter signature motif; other site 323098003091 Walker B; other site 323098003092 D-loop; other site 323098003093 H-loop/switch region; other site 323098003094 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 323098003095 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 323098003096 NAD binding site [chemical binding]; other site 323098003097 homodimer interface [polypeptide binding]; other site 323098003098 active site 323098003099 substrate binding site [chemical binding]; other site 323098003100 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 323098003101 Glycosyltransferase family 9 (heptosyltransferase); Region: Glyco_transf_9; pfam01075 323098003102 putative active site [active] 323098003103 histidinol-phosphate phosphatase family domain; Region: Histidinol-ppas; TIGR01656 323098003104 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 323098003105 active site 323098003106 motif I; other site 323098003107 motif II; other site 323098003108 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 323098003109 dimer interface [polypeptide binding]; other site 323098003110 active site 323098003111 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 323098003112 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 323098003113 putative active site [active] 323098003114 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 323098003115 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 323098003116 NADP binding site [chemical binding]; other site 323098003117 homopentamer interface [polypeptide binding]; other site 323098003118 substrate binding site [chemical binding]; other site 323098003119 active site 323098003120 ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaE; COG2870 323098003121 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 323098003122 putative ribose interaction site [chemical binding]; other site 323098003123 putative ADP binding site [chemical binding]; other site 323098003124 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 323098003125 active site 323098003126 nucleotide binding site [chemical binding]; other site 323098003127 HIGH motif; other site 323098003128 KMSKS motif; other site 323098003129 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 323098003130 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 323098003131 NAD(P) binding site [chemical binding]; other site 323098003132 homodimer interface [polypeptide binding]; other site 323098003133 substrate binding site [chemical binding]; other site 323098003134 active site 323098003135 Uncharacterized protein family (UPF0104); Region: UPF0104; cl04219 323098003136 Uncharacterized protein family (UPF0104); Region: UPF0104; cl04219 323098003137 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 323098003138 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 323098003139 putative NAD(P) binding site [chemical binding]; other site 323098003140 active site 323098003141 putative substrate binding site [chemical binding]; other site 323098003142 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 323098003143 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 323098003144 Substrate binding site; other site 323098003145 Cupin domain; Region: Cupin_2; cl09118 323098003146 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 323098003147 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098003148 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 323098003149 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 323098003150 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 323098003151 inhibitor-cofactor binding pocket; inhibition site 323098003152 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098003153 catalytic residue [active] 323098003154 integral membrane protein MviN; Region: mviN; TIGR01695 323098003155 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 323098003156 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 323098003157 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 323098003158 CHRD domain; Region: CHRD; cl06473 323098003159 Helix-turn-helix domains; Region: HTH; cl00088 323098003160 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 323098003161 dimer interface [polypeptide binding]; other site 323098003162 substrate binding site [chemical binding]; other site 323098003163 ATP binding site [chemical binding]; other site 323098003164 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 323098003165 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 323098003166 putative active site [active] 323098003167 putative metal binding site [ion binding]; other site 323098003168 L-Ala-D/L-Glu epimerase catalyzes the epimerization of L-Ala-D/L-Glu and other dipeptides. The genomic context and the substrate specificity of characterized members of this family from E.coli and B.subtilis indicates a possible role in the metabolism of...; Region: L-Ala-DL-Glu_epimerase; cd03319 323098003169 L-Ala-D/L-Glu epimerase; Provisional; Region: PRK15129 323098003170 active site 323098003171 Equine herpesvirus glycoprotein gp2; Region: Herpes_gp2; pfam05955 323098003172 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 323098003173 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 323098003174 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098003175 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 323098003176 SEST_like. A family of secreted SGNH-hydrolases similar to Streptomyces scabies esterase (SEST), a causal agent of the potato scab disease, which hydrolyzes a specific ester bond in suberin, a plant lipid. The tertiary fold of this enzyme is...; Region: SEST_like; cd01823 323098003177 oxyanion hole [active] 323098003178 Predicted integral membrane protein [Function unknown]; Region: COG0392 323098003179 Uncharacterized protein family (UPF0104); Region: UPF0104; cl04219 323098003180 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 323098003181 catalytic core [active] 323098003182 Transposase domain (DUF772); Region: DUF772; cl15789 323098003183 Transposase domain (DUF772); Region: DUF772; cl15789 323098003184 Winged helix-turn helix; Region: HTH_29; pfam13551 323098003185 Integrase core domain; Region: rve; cl01316 323098003186 Integrase core domain; Region: rve_3; cl15866 323098003187 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 323098003188 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098003189 fagellar hook-basal body proteins; Region: FlgEFG_subfam; TIGR03506 323098003190 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 323098003191 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 323098003192 flagellar basal body rod protein FlgG; Reviewed; Region: flgG; PRK12692 323098003193 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 323098003194 flagellar hook-associated protein FlgK; Region: flgK_ends; TIGR02492 323098003195 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK07521 323098003196 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 323098003197 flagellar hook-associated protein 3; Region: flagell_flgL; TIGR02550 323098003198 flagellar hook-associated protein FlgL; Validated; Region: flgL; PRK06008 323098003199 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 323098003200 Glutamate decarboxylase and related PLP-dependent proteins [Amino acid transport and metabolism]; Region: GadB; COG0076 323098003201 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 323098003202 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 323098003203 catalytic residue [active] 323098003204 Flagellar protein FlbT; Region: FlbT; cl11455 323098003205 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 323098003206 flagellin; Reviewed; Region: PRK12688 323098003207 flagellin; Reviewed; Region: PRK12688 323098003208 flagellin; Provisional; Region: PRK14708 323098003209 flagellin; Reviewed; Region: PRK12688 323098003210 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 323098003211 Flagellar protein FlaF; Region: FlaF; cl11454 323098003212 FlgN protein; Region: FlgN; cl09176 323098003213 Rod binding protein; Region: Rod-binding; cl01626 323098003214 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 323098003215 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 323098003216 Class II flagellar assembly regulator; Region: FliX; cl11677 323098003217 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 323098003218 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 323098003219 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 323098003220 putative dimer interface [polypeptide binding]; other site 323098003221 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 323098003222 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation...; Region: ACD_IbpA-B_like; cd06470 323098003223 putative dimer interface [polypeptide binding]; other site 323098003224 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 323098003225 ligand binding site [chemical binding]; other site 323098003226 flexible hinge region; other site 323098003227 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 323098003228 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 323098003229 active site 323098003230 nucleophile elbow; other site 323098003231 Flagellar L-ring protein; Region: FlgH; cl00905 323098003232 flagellar basal body P-ring biosynthesis protein FlgA; Reviewed; Region: flgA; PRK12786 323098003233 SAF domain; Region: SAF; cl00555 323098003234 flagellar basal body rod protein FlgG; Reviewed; Region: flgG; PRK12691 323098003235 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 323098003236 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 323098003237 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12689 323098003238 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 323098003239 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 323098003240 flagellar motor switch protein FliM; Reviewed; Region: fliM; PRK12795 323098003241 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 323098003242 Afadin- and alpha -actinin-Binding; Region: ADIP; pfam11559 323098003243 MgtE intracellular N domain; Region: MgtE_N; cl15244 323098003244 Domain of unknown function (DUF4104); Region: DUF4104; pfam13372 323098003245 FliP family; Region: FliP; cl00593 323098003246 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK06004 323098003247 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 323098003248 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 323098003249 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 323098003250 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 323098003251 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 323098003252 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 323098003253 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 323098003254 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 323098003255 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 323098003256 PAS domain; Region: PAS_9; pfam13426 323098003257 putative active site [active] 323098003258 heme pocket [chemical binding]; other site 323098003259 PAS fold; Region: PAS_4; pfam08448 323098003260 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 323098003261 dimer interface [polypeptide binding]; other site 323098003262 phosphorylation site [posttranslational modification] 323098003263 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 323098003264 ATP binding site [chemical binding]; other site 323098003265 Mg2+ binding site [ion binding]; other site 323098003266 G-X-G motif; other site 323098003267 Response regulator receiver domain; Region: Response_reg; pfam00072 323098003268 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 323098003269 active site 323098003270 phosphorylation site [posttranslational modification] 323098003271 intermolecular recognition site; other site 323098003272 dimerization interface [polypeptide binding]; other site 323098003273 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; cl15419 323098003274 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 323098003275 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 323098003276 DNA binding site [nucleotide binding] 323098003277 Int/Topo IB signature motif; other site 323098003278 active site 323098003279 catalytic residues [active] 323098003280 phenylalanyl-tRNA synthetase subunit alpha; Provisional; Region: pheS; PRK04172 323098003281 Helix-turn-helix domains; Region: HTH; cl00088 323098003282 putative transposase OrfB; Reviewed; Region: PHA02517 323098003283 Helix-turn-helix domains; Region: HTH; cl00088 323098003284 Integrase core domain; Region: rve; cl01316 323098003285 Integrase core domain; Region: rve_3; cl15866 323098003286 Helix-turn-helix domains; Region: HTH; cl00088 323098003287 Low affinity iron permease; Region: Iron_permease; cl12096 323098003288 Protein of unknown function (DUF1254); Region: DUF1254; cl02257 323098003289 Protein of unknown function (DUF1214); Region: DUF1214; cl08447 323098003290 Transglycosylase; Region: Transgly; cl07896 323098003291 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 323098003292 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 323098003293 Flagellin N-methylase; Region: FliB; cl00497 323098003294 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 323098003295 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 323098003296 putative substrate translocation pore; other site 323098003297 Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: AlaS; COG0013 323098003298 Transposase zinc-ribbon domain; Region: Zn_Tnp_IS1595; pfam12760 323098003299 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 323098003300 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; cl01481 323098003301 Integrase core domain; Region: rve; cl01316 323098003302 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098003303 Winged helix-turn helix; Region: HTH_29; pfam13551 323098003304 Helix-turn-helix domains; Region: HTH; cl00088 323098003305 Helix-turn-helix domains; Region: HTH; cl00088 323098003306 Uncharacterized conserved protein [Function unknown]; Region: COG5323 323098003307 Phage-related protein [Function unknown]; Region: COG4695; cl01923 323098003308 Phage portal protein; Region: Phage_portal; pfam04860 323098003309 Caudovirus prohead protease; Region: Peptidase_U35; cl01521 323098003310 phage major capsid protein, HK97 family; Region: major_cap_HK97; TIGR01554 323098003311 Phage capsid family; Region: Phage_capsid; pfam05065 323098003312 Domain of unknown function (DUF2019); Region: DUF2019; pfam09450 323098003313 Domain of unknown function (DUF2019); Region: DUF2019; pfam09450 323098003314 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 323098003315 active site 323098003316 substrate binding sites [chemical binding]; other site 323098003317 phage conserved hypothetical protein, phiE125 gp8 family; Region: phage_chp_gp8; TIGR02215 323098003318 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins; Region: gp6; cd08054 323098003319 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins; Region: gp6; cd08054 323098003320 oligomerization interface [polypeptide binding]; other site 323098003321 Protein of unknown function (DUF3168); Region: DUF3168; pfam11367 323098003322 Phage major tail protein 2; Region: Phage_tail_2; cl11463 323098003323 Protein of unknown function (DUF3356); Region: DUF3356; pfam11836 323098003324 Conserved hypothetical phage protein (DUF2376); Region: DUF2376; cl09774 323098003325 Phage-related minor tail protein [Function unknown]; Region: COG5281 323098003326 Conserved hypothetical protein 2217 (DUF2460); Region: DUF2460; cl02268 323098003327 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 323098003328 phage conserved hypothetical protein BR0599; Region: phg_TIGR02218 323098003329 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 323098003330 NlpC/P60 family; Region: NLPC_P60; cl11438 323098003331 GTA TIM-barrel-like domain; Region: GTA_TIM; pfam13547 323098003332 Putative phage tail protein; Region: Phage-tail_3; pfam13550 323098003333 Protein of unknown function (DUF2793); Region: DUF2793; pfam10983 323098003334 D-ala-D-ala dipeptidase; Region: Peptidase_M15; cl00813 323098003335 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 323098003336 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 323098003337 active site 323098003338 phosphorylation site [posttranslational modification] 323098003339 intermolecular recognition site; other site 323098003340 dimerization interface [polypeptide binding]; other site 323098003341 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 323098003342 DNA binding site [nucleotide binding] 323098003343 sensor protein PhoQ; Provisional; Region: PRK10815 323098003344 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 323098003345 ATP binding site [chemical binding]; other site 323098003346 Mg2+ binding site [ion binding]; other site 323098003347 G-X-G motif; other site 323098003348 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 323098003349 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 323098003350 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 323098003351 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 323098003352 binding surface 323098003353 TPR motif; other site 323098003354 CcmE; Region: CcmE; cl00994 323098003355 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 323098003356 Cytochrome C biogenesis protein; Region: CcmH; cl01179 323098003357 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 323098003358 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 323098003359 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 323098003360 protein binding site [polypeptide binding]; other site 323098003361 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 323098003362 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 323098003363 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 323098003364 active site 323098003365 phosphorylation site [posttranslational modification] 323098003366 intermolecular recognition site; other site 323098003367 dimerization interface [polypeptide binding]; other site 323098003368 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 323098003369 DNA binding site [nucleotide binding] 323098003370 Bacterial aa3 type cytochrome c oxidase subunit IV; Region: COX4_pro_2; pfam07835 323098003371 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 323098003372 dimerization interface [polypeptide binding]; other site 323098003373 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 323098003374 dimer interface [polypeptide binding]; other site 323098003375 phosphorylation site [posttranslational modification] 323098003376 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 323098003377 ATP binding site [chemical binding]; other site 323098003378 Mg2+ binding site [ion binding]; other site 323098003379 G-X-G motif; other site 323098003380 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional; Region: PRK14108 323098003381 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 323098003382 metal binding triad; other site 323098003383 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 323098003384 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 323098003385 metal binding triad; other site 323098003386 PAS fold; Region: PAS_3; pfam08447 323098003387 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 323098003388 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 323098003389 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 323098003390 dimer interface [polypeptide binding]; other site 323098003391 phosphorylation site [posttranslational modification] 323098003392 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 323098003393 ATP binding site [chemical binding]; other site 323098003394 Mg2+ binding site [ion binding]; other site 323098003395 G-X-G motif; other site 323098003396 Cation efflux family; Region: Cation_efflux; cl00316 323098003397 Cation efflux family; Region: Cation_efflux; cl00316 323098003398 Cation efflux family; Region: Cation_efflux; cl00316 323098003399 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 323098003400 IHF dimer interface [polypeptide binding]; other site 323098003401 IHF - DNA interface [nucleotide binding]; other site 323098003402 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 323098003403 homodimer interface [polypeptide binding]; other site 323098003404 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 323098003405 active site pocket [active] 323098003406 N-terminal Early set domain associated with the catalytic domain of Maltooligosyl trehalose trehalohydrolase (also called Glycosyltrehalose trehalohydrolase) and similar proteins; Region: E_set_MTHase_like_N; cd02853 323098003407 malto-oligosyltrehalose trehalohydrolase; Region: trehalose_TreZ; TIGR02402 323098003408 Alpha amylase catalytic domain found in Glycosyltrehalose trehalohydrolase (also called Maltooligosyl trehalose Trehalohydrolase); Region: AmyAc_GTHase; cd11325 323098003409 catalytic site [active] 323098003410 active site 323098003411 Domain of unknown function (DUF3459); Region: DUF3459; pfam11941 323098003412 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 323098003413 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 323098003414 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 323098003415 active site 323098003416 catalytic site [active] 323098003417 glycogen branching enzyme; Provisional; Region: PRK05402 323098003418 Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; Region: E_set; cl09101 323098003419 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 323098003420 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 323098003421 active site 323098003422 catalytic site [active] 323098003423 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; cl02706 323098003424 trehalose synthase; Region: treS_nterm; TIGR02456 323098003425 Alpha amylase catalytic domain found in Trehalose synthetase; Region: AmyAc_TreS; cd11334 323098003426 active site 323098003427 catalytic site [active] 323098003428 Uncharacterized protein, probably involved in trehalose biosynthesis [Carbohydrate transport and metabolism]; Region: Ble; cl01286 323098003429 Domain of unknown function (DUF3416); Region: DUF3416; pfam11896 323098003430 Alpha amylase catalytic domain found in GlgE-like proteins; Region: AmyAc_GlgE_like; cd11344 323098003431 active site 323098003432 homodimer interface [polypeptide binding]; other site 323098003433 catalytic site [active] 323098003434 acceptor binding site [chemical binding]; other site 323098003435 4-alpha-glucanotransferase; Provisional; Region: malQ; PRK11052 323098003436 4-alpha-glucanotransferase; Region: Glyco_hydro_77; cl00711 323098003437 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 323098003438 catalytic motif [active] 323098003439 Catalytic residue [active] 323098003440 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 323098003441 dimer interface [polypeptide binding]; other site 323098003442 phosphorylation site [posttranslational modification] 323098003443 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 323098003444 ATP binding site [chemical binding]; other site 323098003445 Mg2+ binding site [ion binding]; other site 323098003446 G-X-G motif; other site 323098003447 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098003448 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 323098003449 NAD(P) binding pocket [chemical binding]; other site 323098003450 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_9; cd07245 323098003451 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 323098003452 dimer interface [polypeptide binding]; other site 323098003453 putative metal binding site [ion binding]; other site 323098003454 Domain of unknown function DUF59; Region: DUF59; cl00941 323098003455 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 323098003456 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098003457 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 323098003458 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 323098003459 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 323098003460 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 323098003461 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 323098003462 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 323098003463 FeS/SAM binding site; other site 323098003464 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 323098003465 phosphoglycolate phosphatase; Provisional; Region: PRK13222 323098003466 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 323098003467 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 323098003468 motif II; other site 323098003469 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 323098003470 tetramer (dimer of dimers) interface [polypeptide binding]; other site 323098003471 active site 323098003472 dimer interface [polypeptide binding]; other site 323098003473 Uncharacterized protein conserved in bacteria (DUF2059); Region: DUF2059; cl01243 323098003474 glutathione reductase; Validated; Region: PRK06116 323098003475 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 323098003476 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 323098003477 Class-II DAHP synthetase family; Region: DAHP_synth_2; cl03230 323098003478 NAD synthetase; Provisional; Region: PRK13981 323098003479 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 323098003480 multimer interface [polypeptide binding]; other site 323098003481 active site 323098003482 catalytic triad [active] 323098003483 protein interface 1 [polypeptide binding]; other site 323098003484 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 323098003485 homodimer interface [polypeptide binding]; other site 323098003486 NAD binding pocket [chemical binding]; other site 323098003487 ATP binding pocket [chemical binding]; other site 323098003488 Mg binding site [ion binding]; other site 323098003489 active-site loop [active] 323098003490 Protein of unknown function (DUF2865); Region: DUF2865; pfam11064 323098003491 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 323098003492 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 323098003493 active site 323098003494 HIGH motif; other site 323098003495 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 323098003496 KMSKS motif; other site 323098003497 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 323098003498 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 323098003499 putative active site [active] 323098003500 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 323098003501 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 323098003502 Coenzyme A binding pocket [chemical binding]; other site 323098003503 putative alpha-isopropylmalate/homocitrate synthase family transferase; Provisional; Region: PRK12344 323098003504 Desulfobacterium autotrophicum LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA3; cd07941 323098003505 active site 323098003506 catalytic residues [active] 323098003507 metal binding site [ion binding]; metal-binding site 323098003508 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 323098003509 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 323098003510 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 323098003511 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 323098003512 ATM1 is an ABC transporter that is expressed in the mitochondria. Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to...; Region: ABCC_ATM1_transporter; cd03253 323098003513 Walker A/P-loop; other site 323098003514 ATP binding site [chemical binding]; other site 323098003515 Q-loop/lid; other site 323098003516 ABC transporter signature motif; other site 323098003517 Walker B; other site 323098003518 D-loop; other site 323098003519 H-loop/switch region; other site 323098003520 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 323098003521 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 323098003522 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 323098003523 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 323098003524 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 323098003525 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 323098003526 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 323098003527 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 323098003528 ligand binding site [chemical binding]; other site 323098003529 K+ potassium transporter; Region: K_trans; cl15781 323098003530 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 323098003531 active site residue [active] 323098003532 hypothetical protein; Provisional; Region: PRK08912 323098003533 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 323098003534 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098003535 homodimer interface [polypeptide binding]; other site 323098003536 catalytic residue [active] 323098003537 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 323098003538 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 323098003539 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 323098003540 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 323098003541 putative acyl-acceptor binding pocket; other site 323098003542 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK06501 323098003543 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 323098003544 dimer interface [polypeptide binding]; other site 323098003545 active site 323098003546 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK06519 323098003547 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 323098003548 active site 323098003549 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 323098003550 Phosphopantetheine attachment site; Region: PP-binding; cl09936 323098003551 Domain of unknown function DUF87; Region: DUF87; pfam01935 323098003552 AAA-like domain; Region: AAA_10; pfam12846 323098003553 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 323098003554 catalytic residues [active] 323098003555 catalytic nucleophile [active] 323098003556 Recombinase; Region: Recombinase; pfam07508 323098003557 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 323098003558 putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/unknown domain fusion protein; Provisional; Region: PRK14495 323098003559 Predicted restriction endonuclease [Defense mechanisms]; Region: COG3440 323098003560 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 323098003561 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 323098003562 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 323098003563 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 323098003564 HsdM N-terminal domain; Region: HsdM_N; pfam12161 323098003565 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 323098003566 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098003567 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: HsdR; COG4096 323098003568 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 323098003569 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 323098003570 ATP binding site [chemical binding]; other site 323098003571 putative Mg++ binding site [ion binding]; other site 323098003572 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098003573 DNA primase (bacterial type) [DNA replication, recombination, and repair]; Region: DnaG; COG0358 323098003574 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 323098003575 active site 323098003576 metal binding site [ion binding]; metal-binding site 323098003577 interdomain interaction site; other site 323098003578 Domain of unknown function (DUF955); Region: DUF955; cl01076 323098003579 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 323098003580 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 323098003581 multidrug efflux system subunit MdtA; Provisional; Region: PRK11556 323098003582 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 323098003583 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 323098003584 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 323098003585 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 323098003586 Gram-negative bacterial tonB protein; Region: TonB; cl10048 323098003587 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_1; cd06158 323098003588 active site 323098003589 putative substrate binding region [chemical binding]; other site 323098003590 JmjC domain, hydroxylase; Region: JmjC; cl15814 323098003591 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 323098003592 Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide...; Region: CASc; cl00042 323098003593 active site 323098003594 substrate pocket [chemical binding]; other site 323098003595 proteolytic cleavage site; other site 323098003596 dimer interface [polypeptide binding]; other site 323098003597 Transposase zinc-ribbon domain; Region: Zn_Tnp_IS1595; pfam12760 323098003598 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; cl01481 323098003599 recombinase A; Provisional; Region: recA; PRK09354 323098003600 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 323098003601 hexamer interface [polypeptide binding]; other site 323098003602 Walker A motif; other site 323098003603 ATP binding site [chemical binding]; other site 323098003604 Walker B motif; other site 323098003605 Transposase domain (DUF772); Region: DUF772; cl15789 323098003606 Transposase domain (DUF772); Region: DUF772; cl15789 323098003607 glycine dehydrogenase; Provisional; Region: PRK05367 323098003608 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 323098003609 tetramer interface [polypeptide binding]; other site 323098003610 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098003611 catalytic residue [active] 323098003612 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 323098003613 tetramer interface [polypeptide binding]; other site 323098003614 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098003615 catalytic residue [active] 323098003616 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 323098003617 lipoyl attachment site [posttranslational modification]; other site 323098003618 glycine cleavage system aminomethyltransferase T; Provisional; Region: gcvT; PRK13579 323098003619 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 323098003620 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 323098003621 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 323098003622 motif 1; other site 323098003623 active site 323098003624 motif 2; other site 323098003625 motif 3; other site 323098003626 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 323098003627 Transposase domain (DUF772); Region: DUF772; cl15789 323098003628 Transposase domain (DUF772); Region: DUF772; cl15789 323098003629 Integrase core domain; Region: rve; cl01316 323098003630 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098003631 Transposase domain (DUF772); Region: DUF772; cl15789 323098003632 Winged helix-turn helix; Region: HTH_29; pfam13551 323098003633 Integrase core domain; Region: rve; cl01316 323098003634 Integrase core domain; Region: rve_3; cl15866 323098003635 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 323098003636 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 323098003637 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 323098003638 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 323098003639 putative active site [active] 323098003640 Winged helix-turn helix; Region: HTH_29; pfam13551 323098003641 Integrase core domain; Region: rve; cl01316 323098003642 Integrase core domain; Region: rve_3; cl15866 323098003643 Transposase domain (DUF772); Region: DUF772; cl15789 323098003644 Helix-turn-helix domains; Region: HTH; cl00088 323098003645 Helix-turn-helix domains; Region: HTH; cl00088 323098003646 Winged helix-turn helix; Region: HTH_29; pfam13551 323098003647 Helix-turn-helix domains; Region: HTH; cl00088 323098003648 Integrase core domain; Region: rve; cl01316 323098003649 Integrase core domain; Region: rve_3; cl15866 323098003650 Macro domain, Poa1p_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose...; Region: Macro_Poa1p_like; cd02901 323098003651 ADP-ribose binding site [chemical binding]; other site 323098003652 cyanate hydratase; Validated; Region: PRK02866 323098003653 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 323098003654 oligomer interface [polypeptide binding]; other site 323098003655 active site 323098003656 Domain of unknown function (DUF1476); Region: DUF1476; cl11571 323098003657 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 323098003658 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 323098003659 ATP binding site [chemical binding]; other site 323098003660 active site 323098003661 substrate binding site [chemical binding]; other site 323098003662 Phosphoribosylformylglycinamidine (FGAM) synthase; Region: PurS; cl00789 323098003663 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 323098003664 putative active site [active] 323098003665 catalytic triad [active] 323098003666 phosphoribosylformylglycinamidine synthase II; Provisional; Region: PRK01213 323098003667 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 323098003668 dimerization interface [polypeptide binding]; other site 323098003669 ATP binding site [chemical binding]; other site 323098003670 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 323098003671 dimerization interface [polypeptide binding]; other site 323098003672 ATP binding site [chemical binding]; other site 323098003673 BolA-like protein; Region: BolA; cl00386 323098003674 probable methyltransferase; Region: TIGR03438 323098003675 Uncharacterized conserved protein (DUF2260); Region: DUF2260; pfam10017 323098003676 TIGR03440 family protein; Region: unchr_TIGR03440 323098003677 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; cl15394 323098003678 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 323098003679 putative GSH binding site [chemical binding]; other site 323098003680 catalytic residues [active] 323098003681 Peptidase propeptide and YPEB domain; Region: PepSY; cl15815 323098003682 Winged helix-turn helix; Region: HTH_29; pfam13551 323098003683 Helix-turn-helix domains; Region: HTH; cl00088 323098003684 Helix-turn-helix domains; Region: HTH; cl00088 323098003685 Integrase core domain; Region: rve; cl01316 323098003686 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098003687 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 323098003688 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 323098003689 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 323098003690 RNA binding surface [nucleotide binding]; other site 323098003691 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 323098003692 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5388 323098003693 PAS domain; Region: PAS_5; pfam07310 323098003694 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_10; cd04623 323098003695 FOG: CBS domain [General function prediction only]; Region: COG0517 323098003696 Transposase domain (DUF772); Region: DUF772; cl15789 323098003697 Transposase domain (DUF772); Region: DUF772; cl15789 323098003698 hypothetical protein; Provisional; Region: PRK10279 323098003699 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 323098003700 nucleophile elbow; other site 323098003701 Haemolytic domain; Region: Haemolytic; cl00506 323098003702 Caseinolytic protease (ClpP) is an ATP-dependent protease; Region: Clp_protease_like; cl15763 323098003703 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 323098003704 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 323098003705 trimerization site [polypeptide binding]; other site 323098003706 active site 323098003707 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 323098003708 GTP cyclohydrolase I; Provisional; Region: PLN03044 323098003709 active site 323098003710 Phosphoribosyl-AMP cyclohydrolase; Region: PRA-CH; cl00344 323098003711 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 323098003712 N-acetyl-D-glucosamine binding site [chemical binding]; other site 323098003713 catalytic residue [active] 323098003714 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; cl15419 323098003715 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 323098003716 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 323098003717 Response regulator receiver domain; Region: Response_reg; pfam00072 323098003718 active site 323098003719 phosphorylation site [posttranslational modification] 323098003720 intermolecular recognition site; other site 323098003721 dimerization interface [polypeptide binding]; other site 323098003722 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 323098003723 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 323098003724 Secretin and TonB N terminus short domain; Region: STN; cl06624 323098003725 ferrichrome receptor precursor protein; Provisional; Region: PRK14050 323098003726 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 323098003727 N-terminal plug; other site 323098003728 ligand-binding site [chemical binding]; other site 323098003729 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 323098003730 FecR protein; Region: FecR; pfam04773 323098003731 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 323098003732 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 323098003733 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 323098003734 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 323098003735 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 323098003736 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 323098003737 putative homodimer interface [polypeptide binding]; other site 323098003738 KOW motif; Region: KOW; cl00354 323098003739 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 323098003740 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 323098003741 23S rRNA interface [nucleotide binding]; other site 323098003742 L7/L12 interface [polypeptide binding]; other site 323098003743 putative thiostrepton binding site; other site 323098003744 L25 interface [polypeptide binding]; other site 323098003745 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 323098003746 mRNA/rRNA interface [nucleotide binding]; other site 323098003747 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 323098003748 23S rRNA interface [nucleotide binding]; other site 323098003749 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 323098003750 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 323098003751 L11 interface [polypeptide binding]; other site 323098003752 putative EF-Tu interaction site [polypeptide binding]; other site 323098003753 putative EF-G interaction site [polypeptide binding]; other site 323098003754 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 323098003755 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 323098003756 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 323098003757 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 323098003758 RPB11 interaction site [polypeptide binding]; other site 323098003759 RPB12 interaction site [polypeptide binding]; other site 323098003760 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 323098003761 RPB3 interaction site [polypeptide binding]; other site 323098003762 RPB1 interaction site [polypeptide binding]; other site 323098003763 RPB11 interaction site [polypeptide binding]; other site 323098003764 RPB10 interaction site [polypeptide binding]; other site 323098003765 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 323098003766 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 323098003767 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 323098003768 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 323098003769 DNA-directed RNA polymerase subunit beta'; Provisional; Region: rpoC2; PRK02597 323098003770 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 323098003771 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 323098003772 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 323098003773 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 323098003774 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 323098003775 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 323098003776 DNA binding site [nucleotide binding] 323098003777 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 323098003778 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiH; COG0654 323098003779 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098003780 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098003781 Protein involved in cellulose biosynthesis (CelD) [Cell envelope biogenesis, outer membrane]; Region: COG5653 323098003782 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 323098003783 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 323098003784 Helix-turn-helix domains; Region: HTH; cl00088 323098003785 Transposase domain (DUF772); Region: DUF772; cl15789 323098003786 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 323098003787 S17 interaction site [polypeptide binding]; other site 323098003788 S8 interaction site; other site 323098003789 16S rRNA interaction site [nucleotide binding]; other site 323098003790 streptomycin interaction site [chemical binding]; other site 323098003791 23S rRNA interaction site [nucleotide binding]; other site 323098003792 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 323098003793 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 323098003794 elongation factor G; Reviewed; Region: PRK00007 323098003795 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 323098003796 G1 box; other site 323098003797 putative GEF interaction site [polypeptide binding]; other site 323098003798 GTP/Mg2+ binding site [chemical binding]; other site 323098003799 Switch I region; other site 323098003800 G2 box; other site 323098003801 G3 box; other site 323098003802 Switch II region; other site 323098003803 G4 box; other site 323098003804 G5 box; other site 323098003805 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 323098003806 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 323098003807 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 323098003808 elongation factor Tu; Reviewed; Region: PRK00049 323098003809 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 323098003810 G1 box; other site 323098003811 GEF interaction site [polypeptide binding]; other site 323098003812 GTP/Mg2+ binding site [chemical binding]; other site 323098003813 Switch I region; other site 323098003814 G2 box; other site 323098003815 G3 box; other site 323098003816 Switch II region; other site 323098003817 G4 box; other site 323098003818 G5 box; other site 323098003819 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 323098003820 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 323098003821 Antibiotic Binding Site [chemical binding]; other site 323098003822 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 323098003823 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 323098003824 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 323098003825 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 323098003826 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 323098003827 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 323098003828 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 323098003829 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 323098003830 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 323098003831 putative translocon binding site; other site 323098003832 protein-rRNA interface [nucleotide binding]; other site 323098003833 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 323098003834 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 323098003835 G-X-X-G motif; other site 323098003836 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 323098003837 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 323098003838 23S rRNA interface [nucleotide binding]; other site 323098003839 5S rRNA interface [nucleotide binding]; other site 323098003840 putative antibiotic binding site [chemical binding]; other site 323098003841 L25 interface [polypeptide binding]; other site 323098003842 L27 interface [polypeptide binding]; other site 323098003843 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 323098003844 23S rRNA interface [nucleotide binding]; other site 323098003845 putative translocon interaction site; other site 323098003846 signal recognition particle (SRP54) interaction site; other site 323098003847 L23 interface [polypeptide binding]; other site 323098003848 trigger factor interaction site; other site 323098003849 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 323098003850 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 323098003851 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 323098003852 KOW motif; Region: KOW; cl00354 323098003853 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 323098003854 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 323098003855 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 323098003856 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 323098003857 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 323098003858 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 323098003859 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 323098003860 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 323098003861 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 323098003862 5S rRNA interface [nucleotide binding]; other site 323098003863 23S rRNA interface [nucleotide binding]; other site 323098003864 L5 interface [polypeptide binding]; other site 323098003865 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 323098003866 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 323098003867 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 323098003868 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 323098003869 23S rRNA binding site [nucleotide binding]; other site 323098003870 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 323098003871 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 323098003872 SecY translocase; Region: SecY; pfam00344 323098003873 adenylate kinase; Reviewed; Region: adk; PRK00279 323098003874 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 323098003875 AMP-binding site [chemical binding]; other site 323098003876 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 323098003877 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 323098003878 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 323098003879 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 323098003880 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 323098003881 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 323098003882 alphaNTD - beta interaction site [polypeptide binding]; other site 323098003883 alphaNTD homodimer interface [polypeptide binding]; other site 323098003884 alphaNTD - beta' interaction site [polypeptide binding]; other site 323098003885 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 323098003886 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 323098003887 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 323098003888 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 323098003889 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 323098003890 protein binding site [polypeptide binding]; other site 323098003891 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 323098003892 protein binding site [polypeptide binding]; other site 323098003893 recombination factor protein RarA; Reviewed; Region: PRK13342 323098003894 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 323098003895 Walker A motif; other site 323098003896 ATP binding site [chemical binding]; other site 323098003897 Walker B motif; other site 323098003898 arginine finger; other site 323098003899 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 323098003900 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 323098003901 binding surface 323098003902 TPR motif; other site 323098003903 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 323098003904 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 323098003905 RNA binding surface [nucleotide binding]; other site 323098003906 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 323098003907 active site 323098003908 Winged helix-turn helix; Region: HTH_29; pfam13551 323098003909 Helix-turn-helix domains; Region: HTH; cl00088 323098003910 Helix-turn-helix domains; Region: HTH; cl00088 323098003911 Integrase core domain; Region: rve; cl01316 323098003912 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098003913 Transposase domain (DUF772); Region: DUF772; cl15789 323098003914 ATP12 chaperone protein; Region: ATP12; cl02228 323098003915 Flagellar hook-length control protein FliK; Region: Flg_hook; cl15269 323098003916 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 323098003917 methylmalonyl-CoA decarboxylase alpha subunit; Region: mmdA; TIGR01117 323098003918 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 323098003919 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 323098003920 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 323098003921 Ubiquinol-cytochrome C chaperone; Region: Ubiq_cyt_C_chap; cl12045 323098003922 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 323098003923 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 323098003924 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 323098003925 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 323098003926 dimer interface [polypeptide binding]; other site 323098003927 active site 323098003928 CoA binding pocket [chemical binding]; other site 323098003929 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 323098003930 IHF dimer interface [polypeptide binding]; other site 323098003931 IHF - DNA interface [nucleotide binding]; other site 323098003932 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 323098003933 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 323098003934 DNA binding residues [nucleotide binding] 323098003935 Uncharacterized conserved protein [Function unknown]; Region: COG3268 323098003936 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098003937 O-Antigen ligase; Region: Wzy_C; cl04850 323098003938 Undecaprenyl-phosphate glucose phosphotransferase; Region: WcaJ_sugtrans; TIGR03023 323098003939 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098003940 Bacterial sugar transferase; Region: Bac_transf; cl00939 323098003941 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 323098003942 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 323098003943 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 323098003944 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 323098003945 SLBB domain; Region: SLBB; pfam10531 323098003946 exopolysaccharide transport protein family; Region: eps_transp_fam; TIGR01005 323098003947 Chain length determinant protein; Region: Wzz; cl15801 323098003948 Chain length determinant protein; Region: Wzz; cl15801 323098003949 Protein involved in cellulose biosynthesis (CelD) [Cell envelope biogenesis, outer membrane]; Region: COG5653 323098003950 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 323098003951 Protein of unknown function (DUF2842); Region: DUF2842; pfam11003 323098003952 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 323098003953 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 323098003954 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 323098003955 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 323098003956 putative substrate translocation pore; other site 323098003957 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK05994 323098003958 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 323098003959 homodimer interface [polypeptide binding]; other site 323098003960 substrate-cofactor binding pocket; other site 323098003961 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098003962 catalytic residue [active] 323098003963 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 323098003964 23S rRNA interface [nucleotide binding]; other site 323098003965 L3 interface [polypeptide binding]; other site 323098003966 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 323098003967 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 323098003968 N-acetyl-D-glucosamine binding site [chemical binding]; other site 323098003969 catalytic residue [active] 323098003970 Sporulation related domain; Region: SPOR; cl10051 323098003971 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 323098003972 homodimer interaction site [polypeptide binding]; other site 323098003973 cofactor binding site; other site 323098003974 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 323098003975 Protein of unknown function, DUF482; Region: DUF482; pfam04339 323098003976 Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases; Region: GDPD_like_3; cd08585 323098003977 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 323098003978 putative active site [active] 323098003979 catalytic site [active] 323098003980 putative metal binding site [ion binding]; other site 323098003981 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_1; cd02199 323098003982 homotrimer interaction site [polypeptide binding]; other site 323098003983 putative active site [active] 323098003984 Domain of unknown function (DUF1849); Region: DUF1849; pfam08904 323098003985 DNA polymerase IV; Provisional; Region: PRK02794 323098003986 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 323098003987 active site 323098003988 DNA binding site [nucleotide binding] 323098003989 Protein of unknown function (DUF3572); Region: DUF3572; pfam12096 323098003990 Response regulator receiver domain; Region: Response_reg; pfam00072 323098003991 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 323098003992 active site 323098003993 phosphorylation site [posttranslational modification] 323098003994 intermolecular recognition site; other site 323098003995 dimerization interface [polypeptide binding]; other site 323098003996 response regulator PleD; Reviewed; Region: pleD; PRK09581 323098003997 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 323098003998 active site 323098003999 phosphorylation site [posttranslational modification] 323098004000 intermolecular recognition site; other site 323098004001 dimerization interface [polypeptide binding]; other site 323098004002 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 323098004003 active site 323098004004 phosphorylation site [posttranslational modification] 323098004005 intermolecular recognition site; other site 323098004006 dimerization interface [polypeptide binding]; other site 323098004007 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 323098004008 metal binding site [ion binding]; metal-binding site 323098004009 active site 323098004010 I-site; other site 323098004011 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 323098004012 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 323098004013 Protein of unknown function (DUF2497); Region: DUF2497; cl11534 323098004014 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 323098004015 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 323098004016 HIGH motif; other site 323098004017 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 323098004018 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 323098004019 active site 323098004020 KMSKS motif; other site 323098004021 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 323098004022 tRNA binding surface [nucleotide binding]; other site 323098004023 anticodon binding site; other site 323098004024 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 323098004025 Cyanate permease [Inorganic ion transport and metabolism]; Region: CynX; COG2807 323098004026 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 323098004027 DNA binding site [nucleotide binding] 323098004028 active site 323098004029 lipoyl synthase; Provisional; Region: PRK05481 323098004030 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 323098004031 FeS/SAM binding site; other site 323098004032 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 323098004033 putative coenzyme Q binding site [chemical binding]; other site 323098004034 Competence-damaged protein; Region: CinA; cl00666 323098004035 bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional; Region: ispDF; PRK09382 323098004036 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 323098004037 substrate binding site; other site 323098004038 dimer interface; other site 323098004039 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 323098004040 homotrimer interaction site [polypeptide binding]; other site 323098004041 zinc binding site [ion binding]; other site 323098004042 CDP-binding sites; other site 323098004043 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 323098004044 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 323098004045 FMN binding site [chemical binding]; other site 323098004046 active site 323098004047 catalytic residues [active] 323098004048 substrate binding site [chemical binding]; other site 323098004049 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 323098004050 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 323098004051 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 323098004052 dimer interface [polypeptide binding]; other site 323098004053 phosphorylation site [posttranslational modification] 323098004054 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 323098004055 ATP binding site [chemical binding]; other site 323098004056 Mg2+ binding site [ion binding]; other site 323098004057 G-X-G motif; other site 323098004058 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 323098004059 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 323098004060 active site 323098004061 phosphorylation site [posttranslational modification] 323098004062 intermolecular recognition site; other site 323098004063 dimerization interface [polypeptide binding]; other site 323098004064 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 323098004065 Walker A motif; other site 323098004066 ATP binding site [chemical binding]; other site 323098004067 Walker B motif; other site 323098004068 Helix-turn-helix domains; Region: HTH; cl00088 323098004069 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 323098004070 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 323098004071 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 323098004072 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 323098004073 dimer interface [polypeptide binding]; other site 323098004074 phosphorylation site [posttranslational modification] 323098004075 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 323098004076 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 323098004077 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 323098004078 active site 323098004079 phosphorylation site [posttranslational modification] 323098004080 intermolecular recognition site; other site 323098004081 dimerization interface [polypeptide binding]; other site 323098004082 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 323098004083 Walker A motif; other site 323098004084 ATP binding site [chemical binding]; other site 323098004085 Walker B motif; other site 323098004086 arginine finger; other site 323098004087 Helix-turn-helix domains; Region: HTH; cl00088 323098004088 D-Alanine aminotransferase (D-AAT_like): D-amino acid aminotransferase catalyzes transamination between D-amino acids and their respective alpha-keto acids. It plays a major role in the synthesis of bacterial cell wall components like D-alanine and...; Region: D-AAT_like; cd01558 323098004089 homodimer interface [polypeptide binding]; other site 323098004090 substrate-cofactor binding pocket; other site 323098004091 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098004092 catalytic residue [active] 323098004093 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 323098004094 Sm1 motif; other site 323098004095 intra - hexamer interaction site; other site 323098004096 inter - hexamer interaction site [polypeptide binding]; other site 323098004097 nucleotide binding pocket [chemical binding]; other site 323098004098 Sm2 motif; other site 323098004099 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 323098004100 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 323098004101 HflX GTPase family; Region: HflX; cd01878 323098004102 G1 box; other site 323098004103 GTP/Mg2+ binding site [chemical binding]; other site 323098004104 Switch I region; other site 323098004105 G2 box; other site 323098004106 G3 box; other site 323098004107 Switch II region; other site 323098004108 G4 box; other site 323098004109 G5 box; other site 323098004110 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 323098004111 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 323098004112 tetramerization interface [polypeptide binding]; other site 323098004113 NAD(P) binding site [chemical binding]; other site 323098004114 catalytic residues [active] 323098004115 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 323098004116 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 323098004117 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 323098004118 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 323098004119 Ligand Binding Site [chemical binding]; other site 323098004120 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 323098004121 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 323098004122 lipoyl-biotinyl attachment site [posttranslational modification]; other site 323098004123 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 323098004124 heavy metal efflux pump (cobalt-zinc-cadmium); Region: 2A0601; TIGR00914 323098004125 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 323098004126 Uncharacterized BCR, YnfA/UPF0060 family; Region: UPF0060; cl00757 323098004127 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 323098004128 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 323098004129 active site 323098004130 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 323098004131 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 323098004132 active site 323098004133 HIGH motif; other site 323098004134 KMSKS motif; other site 323098004135 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 323098004136 tRNA binding surface [nucleotide binding]; other site 323098004137 anticodon binding site; other site 323098004138 DNA polymerase III subunit delta'; Validated; Region: PRK07471 323098004139 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098004140 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098004141 thymidylate kinase; Region: DTMP_kinase; TIGR00041 323098004142 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 323098004143 TMP-binding site; other site 323098004144 ATP-binding site [chemical binding]; other site 323098004145 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 323098004146 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 323098004147 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; cl06814 323098004148 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 323098004149 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 323098004150 PilZ domain; Region: PilZ; cl01260 323098004151 tape measure domain; Region: tape_meas_nterm; TIGR02675 323098004152 Lambda phage tail tape-measure protein (Tape_meas_lam_C); Region: Tape_meas_lam_C; pfam09718 323098004153 Phage Terminase; Region: Terminase_1; pfam03354 323098004154 Phage terminase, small subunit; Region: Terminase_4; cl01525 323098004155 Phage head-tail joining protein; Region: Phage_H_T_join; cl11461 323098004156 Protein of unknown function (DUF3168); Region: DUF3168; pfam11367 323098004157 Bacteriophage protein of unknown function (DUF646); Region: DUF646; cl12124 323098004158 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins; Region: gp6; cd08054 323098004159 oligomerization interface [polypeptide binding]; other site 323098004160 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 323098004161 phage major capsid protein, HK97 family; Region: major_cap_HK97; TIGR01554 323098004162 Phage capsid family; Region: Phage_capsid; pfam05065 323098004163 Caudovirus prohead protease; Region: Peptidase_U35; cl01521 323098004164 Phage-related protein [Function unknown]; Region: COG4695; cl01923 323098004165 Phage portal protein; Region: Phage_portal; pfam04860 323098004166 AAA domain; Region: AAA_25; pfam13481 323098004167 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098004168 Walker A motif; other site 323098004169 ATP binding site [chemical binding]; other site 323098004170 Walker B motif; other site 323098004171 phiLC3 phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial (mainly gram positive) and phage integrases, including those similar to Lactococcus...; Region: INT_phiLC3_C; cd01189 323098004172 Int/Topo IB signature motif; other site 323098004173 Helix-turn-helix domains; Region: HTH; cl00088 323098004174 Helix-turn-helix domains; Region: HTH; cl00088 323098004175 Winged helix-turn helix; Region: HTH_29; pfam13551 323098004176 Helix-turn-helix domains; Region: HTH; cl00088 323098004177 Integrase core domain; Region: rve; cl01316 323098004178 Integrase core domain; Region: rve_3; cl15866 323098004179 DNA primase (bacterial type) [DNA replication, recombination, and repair]; Region: DnaG; COG0358 323098004180 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 323098004181 active site 323098004182 metal binding site [ion binding]; metal-binding site 323098004183 interdomain interaction site; other site 323098004184 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098004185 Walker A motif; other site 323098004186 ATP binding site [chemical binding]; other site 323098004187 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 323098004188 active site 323098004189 Int/Topo IB signature motif; other site 323098004190 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; cl01951 323098004191 Cupin domain; Region: Cupin_2; cl09118 323098004192 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; cl00896 323098004193 Allophanate hydrolase subunit 1; Region: AHS1; pfam02682 323098004194 Allophanate hydrolase subunit 2; Region: AHS2; cl00865 323098004195 LamB/YcsF family; Region: LamB_YcsF; cl00664 323098004196 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 323098004197 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 323098004198 NADP binding site [chemical binding]; other site 323098004199 dimer interface [polypeptide binding]; other site 323098004200 Integral membrane protein TerC family; Region: TerC; cl10468 323098004201 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 323098004202 2-octaprenyl-6-methoxyphenyl hydroxylase; Provisional; Region: PRK07494 323098004203 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098004204 Hemimethylated DNA-binding protein YccV like; Region: YccV-like; cl01548 323098004205 Invasion associated locus B (IalB) protein; Region: IalB; cl02207 323098004206 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 323098004207 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 323098004208 AMP-binding enzyme; Region: AMP-binding; cl15778 323098004209 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 323098004210 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 323098004211 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 323098004212 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 323098004213 ATP binding site [chemical binding]; other site 323098004214 putative Mg++ binding site [ion binding]; other site 323098004215 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 323098004216 nucleotide binding region [chemical binding]; other site 323098004217 ATP-binding site [chemical binding]; other site 323098004218 TRCF domain; Region: TRCF; cl04088 323098004219 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 323098004220 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 323098004221 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 323098004222 generic binding surface II; other site 323098004223 ssDNA binding site; other site 323098004224 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 323098004225 ATP binding site [chemical binding]; other site 323098004226 putative Mg++ binding site [ion binding]; other site 323098004227 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 323098004228 nucleotide binding region [chemical binding]; other site 323098004229 ATP-binding site [chemical binding]; other site 323098004230 Protein of unknown function (DUF502); Region: DUF502; cl01107 323098004231 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 323098004232 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 323098004233 glutaminase active site [active] 323098004234 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 323098004235 dimer interface [polypeptide binding]; other site 323098004236 active site 323098004237 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 323098004238 dimer interface [polypeptide binding]; other site 323098004239 active site 323098004240 DTW domain; Region: DTW; cl01221 323098004241 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 323098004242 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 323098004243 multidrug efflux system subunit MdtA; Provisional; Region: PRK11556 323098004244 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 323098004245 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 323098004246 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 323098004247 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 323098004248 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 323098004249 dimer interface [polypeptide binding]; other site 323098004250 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098004251 catalytic residue [active] 323098004252 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 323098004253 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 323098004254 Walker A/P-loop; other site 323098004255 ATP binding site [chemical binding]; other site 323098004256 Q-loop/lid; other site 323098004257 ABC transporter signature motif; other site 323098004258 Walker B; other site 323098004259 D-loop; other site 323098004260 H-loop/switch region; other site 323098004261 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 323098004262 dimer interface [polypeptide binding]; other site 323098004263 conserved gate region; other site 323098004264 putative PBP binding loops; other site 323098004265 ABC-ATPase subunit interface; other site 323098004266 ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]; Region: BatB; COG4597 323098004267 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 323098004268 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 323098004269 dimer interface [polypeptide binding]; other site 323098004270 conserved gate region; other site 323098004271 putative PBP binding loops; other site 323098004272 ABC-ATPase subunit interface; other site 323098004273 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 323098004274 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 323098004275 substrate binding pocket [chemical binding]; other site 323098004276 membrane-bound complex binding site; other site 323098004277 hinge residues; other site 323098004278 cystathionine beta-lyase; Provisional; Region: PRK05967 323098004279 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 323098004280 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 323098004281 catalytic residue [active] 323098004282 Lipid A Biosynthesis N-terminal domain; Region: LAB_N; cl01627 323098004283 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 323098004284 Ligand binding site; other site 323098004285 Putative Catalytic site; other site 323098004286 DXD motif; other site 323098004287 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl15769 323098004288 penicillin-binding protein 1C; Region: PBP_1c; TIGR02073 323098004289 Transglycosylase; Region: Transgly; cl07896 323098004290 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 323098004291 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 323098004292 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 323098004293 MG2 domain; Region: A2M_N; pfam01835 323098004294 Alpha-2-macroglobulin family N-terminal region; Region: A2M_N_2; pfam07703 323098004295 Alpha-2-macroglobulin family; Region: A2M; pfam00207 323098004296 Proteins similar to alpha2-macroglobulin (alpha (2)-M). Alpha (2)-M is a major carrier protein in serum. It is a broadly specific proteinase inhibitor. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of...; Region: A2M_like; cd02891 323098004297 surface patch; other site 323098004298 thioester region; other site 323098004299 specificity defining residues; other site 323098004300 D-ala-D-ala dipeptidase; Region: Peptidase_M15; cl00813 323098004301 Helix-turn-helix domains; Region: HTH; cl00088 323098004302 putative transposase OrfB; Reviewed; Region: PHA02517 323098004303 Helix-turn-helix domains; Region: HTH; cl00088 323098004304 Integrase core domain; Region: rve; cl01316 323098004305 Integrase core domain; Region: rve_3; cl15866 323098004306 Predicted phage phi-C31 gp36 major capsid-like protein [General function prediction only]; Region: COG4653 323098004307 Phage capsid family; Region: Phage_capsid; pfam05065 323098004308 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 323098004309 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_1; cd07016 323098004310 oligomer interface [polypeptide binding]; other site 323098004311 active site residues [active] 323098004312 Phage-related protein [Function unknown]; Region: COG4695; cl01923 323098004313 Phage portal protein; Region: Phage_portal; pfam04860 323098004314 Phage terminase-like protein, large subunit [General function prediction only]; Region: COG4626 323098004315 Phage Terminase; Region: Terminase_1; pfam03354 323098004316 ParB-like nuclease domain; Region: ParBc; cl02129 323098004317 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098004318 Phage terminase, small subunit; Region: Terminase_4; cl01525 323098004319 Transcription antiterminator [Transcription]; Region: NusG; COG0250 323098004320 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; Region: NGN_SP_UpxY; cd09895 323098004321 KOW motif; Region: KOW; cl00354 323098004322 Helix-turn-helix domains; Region: HTH; cl00088 323098004323 ASC-1 homology domain, ASC-1-like subfamily. 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 an RNA-binding domain...; Region: ASCH_ASC-1_like; cd06554 323098004324 MT-A70; Region: MT-A70; cl01947 323098004325 HNH endonuclease; Region: HNH_3; pfam13392 323098004326 Uncharacterized protein conserved in bacteria (DUF2312); Region: DUF2312; cl11480 323098004327 Phage protein Gp37/Gp68; Region: Gp37_Gp68; cl15384 323098004328 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 323098004329 DNA binding site [nucleotide binding] 323098004330 Int/Topo IB signature motif; other site 323098004331 active site 323098004332 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 323098004333 dimer interface [polypeptide binding]; other site 323098004334 ssDNA binding site [nucleotide binding]; other site 323098004335 tetramer (dimer of dimers) interface [polypeptide binding]; other site 323098004336 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 323098004337 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 323098004338 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 323098004339 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 323098004340 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 323098004341 BA14K-like protein; Region: BA14K; pfam07886 323098004342 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07562 323098004343 Class II vitamin B12-dependent ribonucleotide reductase; Region: Ribonuc_red_2_N; pfam08471 323098004344 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 323098004345 Transcriptional regulator; Region: Transcrip_reg; cl00361 323098004346 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 323098004347 active site 323098004348 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 323098004349 TSCPD domain; Region: TSCPD; cl14834 323098004350 putative transposase OrfB; Reviewed; Region: PHA02517 323098004351 HTH-like domain; Region: HTH_21; pfam13276 323098004352 Integrase core domain; Region: rve; cl01316 323098004353 Integrase core domain; Region: rve_3; cl15866 323098004354 Helix-turn-helix domains; Region: HTH; cl00088 323098004355 Protein of unknown function (DUF2442); Region: DUF2442; pfam10387 323098004356 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 323098004357 putative S-transferase; Provisional; Region: PRK11752 323098004358 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 323098004359 C-terminal domain interface [polypeptide binding]; other site 323098004360 GSH binding site (G-site) [chemical binding]; other site 323098004361 dimer interface [polypeptide binding]; other site 323098004362 C-terminal, alpha helical domain of Escherichia coli Yghu Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YghU_like; cd10292 323098004363 dimer interface [polypeptide binding]; other site 323098004364 N-terminal domain interface [polypeptide binding]; other site 323098004365 active site 323098004366 short chain dehydrogenase; Provisional; Region: PRK12828 323098004367 dihydropteridine reductase (DHPR), classical (c) SDRs; Region: DHPR_SDR_c_like; cd05334 323098004368 NAD binding site [chemical binding]; other site 323098004369 homodimer interface [polypeptide binding]; other site 323098004370 active site 323098004371 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 323098004372 active site 1 [active] 323098004373 dimer interface [polypeptide binding]; other site 323098004374 active site 2 [active] 323098004375 Uncharacterized conserved protein (DUF2161); Region: DUF2161; cl02298 323098004376 hypothetical protein; Provisional; Region: PRK10756 323098004377 CreA protein; Region: CreA; pfam05981 323098004378 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 323098004379 hypothetical protein; Provisional; Region: PRK06132 323098004380 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 323098004381 NodB motif; other site 323098004382 active site 323098004383 catalytic site [active] 323098004384 metal binding site [ion binding]; metal-binding site 323098004385 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 323098004386 folate binding site [chemical binding]; other site 323098004387 NADP+ binding site [chemical binding]; other site 323098004388 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 323098004389 Malic enzyme, N-terminal domain; Region: malic; pfam00390 323098004390 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 323098004391 putative NAD(P) binding site [chemical binding]; other site 323098004392 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 323098004393 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 323098004394 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 323098004395 dimer interface [polypeptide binding]; other site 323098004396 anticodon binding site; other site 323098004397 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 323098004398 homodimer interface [polypeptide binding]; other site 323098004399 motif 1; other site 323098004400 active site 323098004401 motif 2; other site 323098004402 GAD domain; Region: GAD; pfam02938 323098004403 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 323098004404 active site 323098004405 motif 3; other site 323098004406 ribonuclease D; Region: rnd; TIGR01388 323098004407 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 323098004408 putative active site [active] 323098004409 catalytic site [active] 323098004410 putative substrate binding site [chemical binding]; other site 323098004411 HRDC domain; Region: HRDC; cl02578 323098004412 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 323098004413 Domain of unknown function DUF21; Region: DUF21; pfam01595 323098004414 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 323098004415 Transporter associated domain; Region: CorC_HlyC; cl08393 323098004416 Transposase domain (DUF772); Region: DUF772; cl15789 323098004417 Transposase domain (DUF772); Region: DUF772; cl15789 323098004418 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 323098004419 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 323098004420 polyphosphate kinase; Provisional; Region: PRK05443 323098004421 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 323098004422 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 323098004423 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 323098004424 putative domain interface [polypeptide binding]; other site 323098004425 putative active site [active] 323098004426 catalytic site [active] 323098004427 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 323098004428 putative domain interface [polypeptide binding]; other site 323098004429 putative active site [active] 323098004430 catalytic site [active] 323098004431 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098004432 DnaA regulatory inactivator Hda; Region: DnaA_homol_Hda; TIGR03420 323098004433 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 323098004434 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 323098004435 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 323098004436 dimerization interface [polypeptide binding]; other site 323098004437 putative ATP binding site [chemical binding]; other site 323098004438 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 323098004439 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 323098004440 active site 323098004441 substrate binding site [chemical binding]; other site 323098004442 cosubstrate binding site; other site 323098004443 catalytic site [active] 323098004444 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 323098004445 DNA-binding site [nucleotide binding]; DNA binding site 323098004446 RNA-binding motif; other site 323098004447 Integral membrane protein TerC family; Region: TerC; cl10468 323098004448 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 323098004449 active site 323098004450 multimer interface [polypeptide binding]; other site 323098004451 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 323098004452 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 323098004453 ATP-grasp domain; Region: ATP-grasp_4; cl03087 323098004454 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 323098004455 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 323098004456 carboxyltransferase (CT) interaction site; other site 323098004457 biotinylation site [posttranslational modification]; other site 323098004458 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 323098004459 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 323098004460 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 323098004461 ETC complex I subunit conserved region; Region: ETC_C1_NDUFA4; pfam04800 323098004462 Uncharacterized ACR, COG1430; Region: DUF192; cl00627 323098004463 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 323098004464 DNA-binding site [nucleotide binding]; DNA binding site 323098004465 RNA-binding motif; other site 323098004466 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 323098004467 DNA-binding site [nucleotide binding]; DNA binding site 323098004468 RNA-binding motif; other site 323098004469 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 323098004470 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 323098004471 dimer interface [polypeptide binding]; other site 323098004472 active site 323098004473 metal binding site [ion binding]; metal-binding site 323098004474 glutathione binding site [chemical binding]; other site 323098004475 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 323098004476 tape measure domain; Region: tape_meas_nterm; TIGR02675 323098004477 Lambda phage tail tape-measure protein (Tape_meas_lam_C); Region: Tape_meas_lam_C; pfam09718 323098004478 Phage Terminase; Region: Terminase_1; pfam03354 323098004479 Phage terminase, small subunit; Region: Terminase_4; cl01525 323098004480 Phage head-tail joining protein; Region: Phage_H_T_join; cl11461 323098004481 Protein of unknown function (DUF3168); Region: DUF3168; pfam11367 323098004482 Bacteriophage protein of unknown function (DUF646); Region: DUF646; cl12124 323098004483 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins; Region: gp6; cd08054 323098004484 oligomerization interface [polypeptide binding]; other site 323098004485 phage major capsid protein, HK97 family; Region: major_cap_HK97; TIGR01554 323098004486 Phage capsid family; Region: Phage_capsid; pfam05065 323098004487 Caudovirus prohead protease; Region: Peptidase_U35; cl01521 323098004488 Phage-related protein [Function unknown]; Region: COG4695; cl01923 323098004489 Phage portal protein; Region: Phage_portal; pfam04860 323098004490 Prim_Pol: Primase-polymerase (primpol) domain of the type found in bifunctional replicases from archaeal plasmids, including ORF904 protein of the crenarchaeal plasmid pRN1 from Sulfolobus islandicus (pRN1 primpol). These primpol domains belong to the...; Region: Prim_Pol; cd04859 323098004491 polymerase nucleotide-binding site; other site 323098004492 DNA-binding residues [nucleotide binding]; DNA binding site 323098004493 nucleotide binding site [chemical binding]; other site 323098004494 primase nucleotide-binding site [nucleotide binding]; other site 323098004495 Primase C terminal 2 (PriCT-2); Region: PriCT_2; pfam08707 323098004496 AAA domain; Region: AAA_25; pfam13481 323098004497 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 323098004498 Helix-turn-helix domains; Region: HTH; cl00088 323098004499 integrase/recombinase; Provisional; Region: PRK15417 323098004500 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 323098004501 DNA binding site [nucleotide binding] 323098004502 Int/Topo IB signature motif; other site 323098004503 active site 323098004504 catalytic residues [active] 323098004505 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 323098004506 active site 323098004507 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 323098004508 Lysine 2,3-aminomutase [Amino acid transport and metabolism]; Region: KamA; COG1509 323098004509 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 323098004510 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 323098004511 EF-P lysine aminoacylase GenX; Region: genX; TIGR00462 323098004512 motif 1; other site 323098004513 dimer interface [polypeptide binding]; other site 323098004514 active site 323098004515 motif 2; other site 323098004516 motif 3; other site 323098004517 elongation factor P; Validated; Region: PRK00529 323098004518 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 323098004519 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 323098004520 RNA binding site [nucleotide binding]; other site 323098004521 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 323098004522 RNA binding site [nucleotide binding]; other site 323098004523 lytic murein transglycosylase; Region: MltB_2; TIGR02283 323098004524 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 323098004525 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 323098004526 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 323098004527 DHH family; Region: DHH; pfam01368 323098004528 DHHA1 domain; Region: DHHA1; pfam02272 323098004529 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 323098004530 putative active site [active] 323098004531 homoserine dehydrogenase; Provisional; Region: PRK06349 323098004532 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098004533 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 323098004534 ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains; Region: ACT_HSDH-Hom; cd04881 323098004535 aminotransferase; Validated; Region: PRK09148 323098004536 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 323098004537 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098004538 homodimer interface [polypeptide binding]; other site 323098004539 catalytic residue [active] 323098004540 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 323098004541 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 323098004542 N-acetyl-gamma-glutamyl-phosphate reductase; Provisional; Region: PRK11863 323098004543 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098004544 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 323098004545 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 323098004546 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 323098004547 Mg2+ binding site [ion binding]; other site 323098004548 G-X-G motif; other site 323098004549 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 323098004550 anchoring element; other site 323098004551 dimer interface [polypeptide binding]; other site 323098004552 ATP binding site [chemical binding]; other site 323098004553 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 323098004554 active site 323098004555 metal binding site [ion binding]; metal-binding site 323098004556 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 323098004557 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_14; cd08355 323098004558 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 323098004559 hypothetical protein; Provisional; Region: PRK06185 323098004560 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098004561 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098004562 Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide...; Region: CASc; cl00042 323098004563 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 323098004564 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 323098004565 ATP binding site [chemical binding]; other site 323098004566 Mg++ binding site [ion binding]; other site 323098004567 motif III; other site 323098004568 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 323098004569 nucleotide binding region [chemical binding]; other site 323098004570 ATP-binding site [chemical binding]; other site 323098004571 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 323098004572 metal binding site [ion binding]; metal-binding site 323098004573 active site 323098004574 I-site; other site 323098004575 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 323098004576 Domain of unknown function DUF59; Region: DUF59; cl00941 323098004577 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 323098004578 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 323098004579 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 323098004580 catalytic residue [active] 323098004581 Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]; Region: SufB; COG0719 323098004582 Uncharacterized protein family (UPF0051); Region: UPF0051; cl03223 323098004583 FeS assembly ATPase SufC; Region: sufC; TIGR01978 323098004584 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 323098004585 Walker A/P-loop; other site 323098004586 ATP binding site [chemical binding]; other site 323098004587 Q-loop/lid; other site 323098004588 ABC transporter signature motif; other site 323098004589 Walker B; other site 323098004590 D-loop; other site 323098004591 H-loop/switch region; other site 323098004592 Uncharacterized protein family (UPF0051); Region: UPF0051; cl03223 323098004593 putative ABC transporter; Region: ycf24; CHL00085 323098004594 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 323098004595 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 323098004596 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 323098004597 catalytic residue [active] 323098004598 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 323098004599 Uncharacterized protein family (UPF0075); Region: UPF0075; cl04217 323098004600 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 323098004601 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 323098004602 active site 323098004603 HIGH motif; other site 323098004604 dimer interface [polypeptide binding]; other site 323098004605 KMSKS motif; other site 323098004606 Protein of unknown function; Region: DUF3971; pfam13116 323098004607 AsmA-like C-terminal region; Region: AsmA_2; cl15864 323098004608 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 323098004609 catalytic triad [active] 323098004610 Peptidase family M23; Region: Peptidase_M23; pfam01551 323098004611 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 323098004612 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 323098004613 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 323098004614 ABC transporter; Region: ABC_tran_2; pfam12848 323098004615 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 323098004616 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; cl01106 323098004617 multifunctional aminopeptidase A; Provisional; Region: PRK00913 323098004618 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 323098004619 interface (dimer of trimers) [polypeptide binding]; other site 323098004620 Substrate-binding/catalytic site; other site 323098004621 Zn-binding sites [ion binding]; other site 323098004622 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 323098004623 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 323098004624 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 323098004625 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 323098004626 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 323098004627 Organic solvent tolerance protein; Region: OstA_C; pfam04453 323098004628 SurA N-terminal domain; Region: SurA_N_3; cl07813 323098004629 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 323098004630 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 323098004631 S-adenosylmethionine binding site [chemical binding]; other site 323098004632 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 323098004633 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 323098004634 catalytic site [active] 323098004635 G-X2-G-X-G-K; other site 323098004636 hypothetical protein; Provisional; Region: PRK11820 323098004637 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 323098004638 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 323098004639 YceG-like family; Region: YceG; pfam02618 323098004640 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 323098004641 dimerization interface [polypeptide binding]; other site 323098004642 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 323098004643 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 323098004644 dimer interface [polypeptide binding]; other site 323098004645 active site 323098004646 Phosphopantetheine attachment site; Region: PP-binding; cl09936 323098004647 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098004648 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 323098004649 NAD(P) binding site [chemical binding]; other site 323098004650 active site 323098004651 DNA polymerase II large subunit; Provisional; Region: PRK14714 323098004652 Acyl transferase domain; Region: Acyl_transf_1; cl08282 323098004653 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 323098004654 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 323098004655 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 323098004656 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 323098004657 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 323098004658 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 323098004659 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 323098004660 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 323098004661 Walker A motif; other site 323098004662 ATP binding site [chemical binding]; other site 323098004663 Walker B motif; other site 323098004664 arginine finger; other site 323098004665 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 323098004666 Walker A motif; other site 323098004667 ATP binding site [chemical binding]; other site 323098004668 Walker B motif; other site 323098004669 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 323098004670 ATP-dependent Clp protease adaptor protein ClpS; Region: ClpS; cl00933 323098004671 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 323098004672 TadE-like protein; Region: TadE; cl10688 323098004673 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 323098004674 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 323098004675 metal ion-dependent adhesion site (MIDAS); other site 323098004676 Phasin protein; Region: Phasin_2; cl11491 323098004677 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 323098004678 Sporulation related domain; Region: SPOR; cl10051 323098004679 Dna-J like membrane chaperone protein; Provisional; Region: djlA; PRK09430 323098004680 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 323098004681 HSP70 interaction site [polypeptide binding]; other site 323098004682 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 323098004683 Pantoate-beta-alanine ligase; Region: PanC; cd00560 323098004684 pantoate--beta-alanine ligase; Region: panC; TIGR00018 323098004685 active site 323098004686 ATP-binding site [chemical binding]; other site 323098004687 pantoate-binding site; other site 323098004688 HXXH motif; other site 323098004689 Protein of unknown function (DUF1489); Region: DUF1489; cl11570 323098004690 GST_N family, unknown subfamily 1; composed of uncharacterized proteins, predominantly from bacteria, with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with...; Region: GST_N_1; cd03043 323098004691 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 323098004692 putative C-terminal domain interface [polypeptide binding]; other site 323098004693 putative GSH binding site (G-site) [chemical binding]; other site 323098004694 putative dimer interface [polypeptide binding]; other site 323098004695 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 323098004696 putative N-terminal domain interface [polypeptide binding]; other site 323098004697 putative dimer interface [polypeptide binding]; other site 323098004698 putative substrate binding pocket (H-site) [chemical binding]; other site 323098004699 Protein of unknown function (DUF3253); Region: DUF3253; pfam11625 323098004700 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 323098004701 putative active site [active] 323098004702 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 323098004703 non-specific DNA binding site [nucleotide binding]; other site 323098004704 salt bridge; other site 323098004705 sequence-specific DNA binding site [nucleotide binding]; other site 323098004706 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 323098004707 NodB motif; other site 323098004708 active site 323098004709 catalytic site [active] 323098004710 metal binding site [ion binding]; metal-binding site 323098004711 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 323098004712 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 323098004713 active site 323098004714 interdomain interaction site; other site 323098004715 putative metal-binding site [ion binding]; other site 323098004716 nucleotide binding site [chemical binding]; other site 323098004717 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 323098004718 domain I; other site 323098004719 DNA binding groove [nucleotide binding] 323098004720 phosphate binding site [ion binding]; other site 323098004721 domain II; other site 323098004722 domain III; other site 323098004723 nucleotide binding site [chemical binding]; other site 323098004724 catalytic site [active] 323098004725 domain IV; other site 323098004726 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 323098004727 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 323098004728 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 323098004729 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 323098004730 ribonuclease R; Region: RNase_R; TIGR02063 323098004731 RNB domain; Region: RNB; pfam00773 323098004732 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 323098004733 RNA binding site [nucleotide binding]; other site 323098004734 Protein of unknown function (DUF983); Region: DUF983; cl02211 323098004735 peptide chain release factor 2; Provisional; Region: PRK07342 323098004736 RF-1 domain; Region: RF-1; cl02875 323098004737 RF-1 domain; Region: RF-1; cl02875 323098004738 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 323098004739 Transglycosylase; Region: Transgly; cl07896 323098004740 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 323098004741 Winged helix-turn helix; Region: HTH_29; pfam13551 323098004742 Integrase core domain; Region: rve; cl01316 323098004743 Integrase core domain; Region: rve_3; cl15866 323098004744 Transposase domain (DUF772); Region: DUF772; cl15789 323098004745 AMIN domain; Region: AMIN; pfam11741 323098004746 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 323098004747 active site 323098004748 metal binding site [ion binding]; metal-binding site 323098004749 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 323098004750 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 323098004751 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 323098004752 thiamine monophosphate kinase; Provisional; Region: PRK05731 323098004753 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 323098004754 ATP binding site [chemical binding]; other site 323098004755 dimerization interface [polypeptide binding]; other site 323098004756 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 323098004757 putative RNA binding site [nucleotide binding]; other site 323098004758 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 323098004759 homopentamer interface [polypeptide binding]; other site 323098004760 active site 323098004761 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 323098004762 Lumazine binding domain; Region: Lum_binding; pfam00677 323098004763 Lumazine binding domain; Region: Lum_binding; pfam00677 323098004764 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 323098004765 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 323098004766 catalytic motif [active] 323098004767 Zn binding site [ion binding]; other site 323098004768 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 323098004769 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 323098004770 ATP cone domain; Region: ATP-cone; pfam03477 323098004771 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 323098004772 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 323098004773 dimer interface [polypeptide binding]; other site 323098004774 glycine-pyridoxal phosphate binding site [chemical binding]; other site 323098004775 active site 323098004776 folate binding site [chemical binding]; other site 323098004777 Domain of unknown function (DUF4062); Region: DUF4062; pfam13271 323098004778 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 323098004779 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 323098004780 Secretin and TonB N terminus short domain; Region: STN; cl06624 323098004781 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 323098004782 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 323098004783 N-terminal plug; other site 323098004784 ligand-binding site [chemical binding]; other site 323098004785 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 323098004786 FecR protein; Region: FecR; pfam04773 323098004787 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 323098004788 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 323098004789 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 323098004790 DNA binding residues [nucleotide binding] 323098004791 Acylphosphatase; Region: Acylphosphatase; cl00551 323098004792 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 323098004793 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 323098004794 ATP-grasp domain; Region: ATP-grasp_4; cl03087 323098004795 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 323098004796 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 323098004797 carboxyltransferase (CT) interaction site; other site 323098004798 biotinylation site [posttranslational modification]; other site 323098004799 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 323098004800 Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by...; Region: PRX_1cys; cd03016 323098004801 dimer interface [polypeptide binding]; other site 323098004802 decamer (pentamer of dimers) interface [polypeptide binding]; other site 323098004803 catalytic triad [active] 323098004804 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 323098004805 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase; Region: adh_III_F_hyde; TIGR02818 323098004806 substrate binding site [chemical binding]; other site 323098004807 catalytic Zn binding site [ion binding]; other site 323098004808 NAD binding site [chemical binding]; other site 323098004809 structural Zn binding site [ion binding]; other site 323098004810 dimer interface [polypeptide binding]; other site 323098004811 CHASE2 domain; Region: CHASE2; cl01732 323098004812 Adenylyl- / guanylyl cyclase, catalytic domain; Region: CYCc; smart00044 323098004813 cyclase homology domain; Region: CHD; cd07302 323098004814 nucleotidyl binding site; other site 323098004815 metal binding site [ion binding]; metal-binding site 323098004816 dimer interface [polypeptide binding]; other site 323098004817 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 323098004818 Tetratricopeptide repeat; Region: TPR_16; pfam13432 323098004819 binding surface 323098004820 TPR motif; other site 323098004821 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 323098004822 PAS domain S-box; Region: sensory_box; TIGR00229 323098004823 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 323098004824 putative active site [active] 323098004825 heme pocket [chemical binding]; other site 323098004826 PAS fold; Region: PAS_4; pfam08448 323098004827 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 323098004828 putative active site [active] 323098004829 heme pocket [chemical binding]; other site 323098004830 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 323098004831 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 323098004832 ATP binding site [chemical binding]; other site 323098004833 Mg2+ binding site [ion binding]; other site 323098004834 G-X-G motif; other site 323098004835 indolepyruvate ferredoxin oxidoreductase; Validated; Region: PRK09193 323098004836 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 323098004837 dimer interface [polypeptide binding]; other site 323098004838 PYR/PP interface [polypeptide binding]; other site 323098004839 TPP binding site [chemical binding]; other site 323098004840 substrate binding site [chemical binding]; other site 323098004841 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 323098004842 TPP-binding site [chemical binding]; other site 323098004843 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 323098004844 Inorganic pyrophosphatase [Energy production and conversion]; Region: OVP1; cl11452 323098004845 membrane-bound proton-translocating pyrophosphatase; Validated; Region: hppA; PRK00733 323098004846 aspartate aminotransferase; Provisional; Region: PRK05764 323098004847 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 323098004848 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098004849 homodimer interface [polypeptide binding]; other site 323098004850 catalytic residue [active] 323098004851 Peptidase family M48; Region: Peptidase_M48; cl12018 323098004852 Tetratricopeptide repeat; Region: TPR_16; pfam13432 323098004853 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 323098004854 TPR motif; other site 323098004855 binding surface 323098004856 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 323098004857 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 323098004858 catalytic residues [active] 323098004859 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 323098004860 trimer interface [polypeptide binding]; other site 323098004861 active site 323098004862 dimer interface [polypeptide binding]; other site 323098004863 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 323098004864 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 323098004865 carboxyltransferase (CT) interaction site; other site 323098004866 biotinylation site [posttranslational modification]; other site 323098004867 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 323098004868 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 323098004869 ATP-grasp domain; Region: ATP-grasp_4; cl03087 323098004870 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 323098004871 CHASE3 domain; Region: CHASE3; cl05000 323098004872 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]; Region: COG4251 323098004873 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 323098004874 dimer interface [polypeptide binding]; other site 323098004875 phosphorylation site [posttranslational modification] 323098004876 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 323098004877 ATP binding site [chemical binding]; other site 323098004878 Mg2+ binding site [ion binding]; other site 323098004879 G-X-G motif; other site 323098004880 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 323098004881 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 323098004882 active site 323098004883 phosphorylation site [posttranslational modification] 323098004884 intermolecular recognition site; other site 323098004885 dimerization interface [polypeptide binding]; other site 323098004886 Response regulator receiver domain; Region: Response_reg; pfam00072 323098004887 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 323098004888 active site 323098004889 phosphorylation site [posttranslational modification] 323098004890 intermolecular recognition site; other site 323098004891 dimerization interface [polypeptide binding]; other site 323098004892 Histidine kinase; Region: HisKA_2; cl06527 323098004893 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 323098004894 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 323098004895 ATP binding site [chemical binding]; other site 323098004896 Mg2+ binding site [ion binding]; other site 323098004897 G-X-G motif; other site 323098004898 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 323098004899 Uncharacterized protein conserved in bacteria (DUF2155); Region: DUF2155; cl01970 323098004900 FecR protein; Region: FecR; pfam04773 323098004901 NADH ubiquinone oxidoreductase subunit NDUFA12; Region: NDUFA12; cl01534 323098004902 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 323098004903 Domain of unknown function (DUF3597); Region: DUF3597; pfam12200 323098004904 Predicted integral membrane protein (DUF2189); Region: DUF2189; cl02291 323098004905 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 323098004906 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098004907 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 323098004908 active site 323098004909 ATP binding site [chemical binding]; other site 323098004910 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 323098004911 AMP-binding enzyme; Region: AMP-binding; cl15778 323098004912 Isoprenoid Biosynthesis enzymes, Class 1; Region: Isoprenoid_Biosyn_C1; cl00210 323098004913 substrate binding pocket [chemical binding]; other site 323098004914 aspartate-rich region 2; other site 323098004915 substrate-Mg2+ binding site; other site 323098004916 Mth938-like domain. The members of this family include: Mth938, 2P1, Xcr35, Rpa2829, and several uncharacterized sequences. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a...; Region: Mth938-like; cd00248 323098004917 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 323098004918 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 323098004919 Protein export membrane protein; Region: SecD_SecF; cl14618 323098004920 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 323098004921 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 323098004922 Protein export membrane protein; Region: SecD_SecF; cl14618 323098004923 Preprotein translocase subunit; Region: YajC; cl00806 323098004924 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098004925 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 323098004926 putative peptidoglycan binding site; other site 323098004927 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 323098004928 putative peptidoglycan binding site; other site 323098004929 Peptidase family M23; Region: Peptidase_M23; pfam01551 323098004930 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 323098004931 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 323098004932 S-adenosylmethionine binding site [chemical binding]; other site 323098004933 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 323098004934 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 323098004935 active site 323098004936 phosphorylation site [posttranslational modification] 323098004937 intermolecular recognition site; other site 323098004938 dimerization interface [polypeptide binding]; other site 323098004939 Survival protein SurE; Region: SurE; cl00448 323098004940 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 323098004941 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 323098004942 motif 1; other site 323098004943 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 323098004944 active site 323098004945 dimer interface [polypeptide binding]; other site 323098004946 motif 2; other site 323098004947 motif 3; other site 323098004948 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 323098004949 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 323098004950 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 323098004951 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 323098004952 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 323098004953 S-adenosylmethionine binding site [chemical binding]; other site 323098004954 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14353 323098004955 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 323098004956 Substrate binding site; other site 323098004957 Mg++ binding site; other site 323098004958 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 323098004959 active site 323098004960 substrate binding site [chemical binding]; other site 323098004961 CoA binding site [chemical binding]; other site 323098004962 Glycosyl hydrolases family 17; Region: Glyco_hydro_17; cl02191 323098004963 Glycosyl hydrolases family 17; Region: Glyco_hydro_17; cl02191 323098004964 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 323098004965 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 323098004966 active site 323098004967 Hypoxia induced protein conserved region; Region: HIG_1_N; pfam04588 323098004968 PcfJ-like protein; Region: PcfJ; pfam14284 323098004969 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 323098004970 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 323098004971 dimer interface [polypeptide binding]; other site 323098004972 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098004973 catalytic residue [active] 323098004974 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; cl00409 323098004975 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 323098004976 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 323098004977 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 323098004978 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; cd00317 323098004979 active site 323098004980 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; cd00317 323098004981 active site 323098004982 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 323098004983 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 323098004984 active site 323098004985 (T/H)XGH motif; other site 323098004986 DNA gyrase, A subunit; Region: gyrA; TIGR01063 323098004987 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 323098004988 CAP-like domain; other site 323098004989 active site 323098004990 primary dimer interface [polypeptide binding]; other site 323098004991 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 323098004992 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 323098004993 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 323098004994 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 323098004995 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 323098004996 MarC family integral membrane protein; Region: MarC; cl00919 323098004997 Putative transcriptional regulators (Ypuh-like); Region: DUF387; cl00612 323098004998 ScpA/B protein; Region: ScpA_ScpB; cl00598 323098004999 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 323098005000 Sporulation related domain; Region: SPOR; cl10051 323098005001 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 323098005002 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; cl04104 323098005003 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 323098005004 active site 323098005005 HIGH motif; other site 323098005006 KMSK motif region; other site 323098005007 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 323098005008 tRNA binding surface [nucleotide binding]; other site 323098005009 anticodon binding site; other site 323098005010 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 323098005011 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 323098005012 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 323098005013 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 323098005014 putative phosphate binding site [ion binding]; other site 323098005015 putative catalytic site [active] 323098005016 active site 323098005017 metal binding site A [ion binding]; metal-binding site 323098005018 DNA binding site [nucleotide binding] 323098005019 putative AP binding site [nucleotide binding]; other site 323098005020 putative metal binding site B [ion binding]; other site 323098005021 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 323098005022 Sel1 repeat; Region: Sel1; cl02723 323098005023 Sel1 repeat; Region: Sel1; cl02723 323098005024 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 323098005025 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098005026 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 323098005027 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 323098005028 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 323098005029 ligand binding site [chemical binding]; other site 323098005030 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 323098005031 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 323098005032 E3 interaction surface; other site 323098005033 lipoyl attachment site [posttranslational modification]; other site 323098005034 e3 binding domain; Region: E3_binding; pfam02817 323098005035 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 323098005036 pyruvate dehydrogenase subunit beta; Provisional; Region: PRK11892 323098005037 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 323098005038 E3 interaction surface; other site 323098005039 lipoyl attachment site [posttranslational modification]; other site 323098005040 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 323098005041 alpha subunit interface [polypeptide binding]; other site 323098005042 TPP binding site [chemical binding]; other site 323098005043 heterodimer interface [polypeptide binding]; other site 323098005044 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 323098005045 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 323098005046 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 323098005047 tetramer interface [polypeptide binding]; other site 323098005048 TPP-binding site [chemical binding]; other site 323098005049 heterodimer interface [polypeptide binding]; other site 323098005050 phosphorylation loop region [posttranslational modification] 323098005051 Septum formation initiator; Region: DivIC; cl11433 323098005052 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 323098005053 Phospholipid methyltransferase; Region: PEMT; cl00763 323098005054 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 323098005055 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 323098005056 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 323098005057 enolase; Provisional; Region: eno; PRK00077 323098005058 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 323098005059 dimer interface [polypeptide binding]; other site 323098005060 metal binding site [ion binding]; metal-binding site 323098005061 substrate binding pocket [chemical binding]; other site 323098005062 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 323098005063 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 323098005064 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 323098005065 putative substrate translocation pore; other site 323098005066 NeuB family; Region: NeuB; cl00496 323098005067 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 323098005068 PAAR motif; Region: PAAR_motif; cl15808 323098005069 CTP synthetase; Validated; Region: pyrG; PRK05380 323098005070 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 323098005071 Catalytic site [active] 323098005072 active site 323098005073 UTP binding site [chemical binding]; other site 323098005074 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 323098005075 active site 323098005076 putative oxyanion hole; other site 323098005077 catalytic triad [active] 323098005078 Preprotein translocase SecG subunit; Region: SecG; cl09123 323098005079 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 323098005080 substrate binding site [chemical binding]; other site 323098005081 dimer interface [polypeptide binding]; other site 323098005082 catalytic triad [active] 323098005083 SurA N-terminal domain; Region: SurA_N_3; cl07813 323098005084 PPIC-type PPIASE domain; Region: Rotamase; cl08278 323098005085 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 323098005086 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 323098005087 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 323098005088 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 323098005089 active site 323098005090 ribulose/triose binding site [chemical binding]; other site 323098005091 phosphate binding site [ion binding]; other site 323098005092 substrate (anthranilate) binding pocket [chemical binding]; other site 323098005093 product (indole) binding pocket [chemical binding]; other site 323098005094 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 323098005095 trimer interface [polypeptide binding]; other site 323098005096 dimer interface [polypeptide binding]; other site 323098005097 putative active site [active] 323098005098 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 323098005099 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 323098005100 dimer interface [polypeptide binding]; other site 323098005101 putative functional site; other site 323098005102 putative MPT binding site; other site 323098005103 LexA repressor; Validated; Region: PRK00215 323098005104 Helix-turn-helix domains; Region: HTH; cl00088 323098005105 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 323098005106 Catalytic site [active] 323098005107 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 323098005108 Competence protein; Region: Competence; cl00471 323098005109 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 323098005110 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 323098005111 active site 323098005112 HIGH motif; other site 323098005113 nucleotide binding site [chemical binding]; other site 323098005114 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 323098005115 KMSKS motif; other site 323098005116 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 323098005117 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 323098005118 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 323098005119 HIGH motif; other site 323098005120 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 323098005121 active site 323098005122 KMSKS motif; other site 323098005123 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 323098005124 dimer interface [polypeptide binding]; other site 323098005125 Citrate synthase; Region: Citrate_synt; pfam00285 323098005126 active site 323098005127 citrylCoA binding site [chemical binding]; other site 323098005128 NADH binding [chemical binding]; other site 323098005129 cationic pore residues; other site 323098005130 oxalacetate/citrate binding site [chemical binding]; other site 323098005131 coenzyme A binding site [chemical binding]; other site 323098005132 catalytic triad [active] 323098005133 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 323098005134 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 323098005135 Protein of unknown function (DUF1009); Region: DUF1009; cl09182 323098005136 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 323098005137 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 323098005138 active site 323098005139 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 323098005140 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 323098005141 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 323098005142 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 323098005143 trimer interface [polypeptide binding]; other site 323098005144 active site 323098005145 UDP-GlcNAc binding site [chemical binding]; other site 323098005146 lipid binding site [chemical binding]; lipid-binding site 323098005147 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 323098005148 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 323098005149 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 323098005150 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 323098005151 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 323098005152 Surface antigen; Region: Bac_surface_Ag; cl03097 323098005153 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 323098005154 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 323098005155 active site 323098005156 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 323098005157 protein binding site [polypeptide binding]; other site 323098005158 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 323098005159 putative substrate binding region [chemical binding]; other site 323098005160 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 323098005161 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 323098005162 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 323098005163 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 323098005164 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 323098005165 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; cl00230 323098005166 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 323098005167 catalytic residue [active] 323098005168 putative FPP diphosphate binding site; other site 323098005169 putative FPP binding hydrophobic cleft; other site 323098005170 dimer interface [polypeptide binding]; other site 323098005171 putative IPP diphosphate binding site; other site 323098005172 ribosome recycling factor; Reviewed; Region: frr; PRK00083 323098005173 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 323098005174 hinge region; other site 323098005175 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 323098005176 putative nucleotide binding site [chemical binding]; other site 323098005177 uridine monophosphate binding site [chemical binding]; other site 323098005178 homohexameric interface [polypeptide binding]; other site 323098005179 elongation factor Ts; Provisional; Region: tsf; PRK09377 323098005180 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 323098005181 Elongation factor TS; Region: EF_TS; pfam00889 323098005182 Elongation factor TS; Region: EF_TS; pfam00889 323098005183 30S ribosomal protein S2/unknown domain fusion protein; Provisional; Region: rpsB; PRK12311 323098005184 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 323098005185 rRNA interaction site [nucleotide binding]; other site 323098005186 S8 interaction site; other site 323098005187 putative laminin-1 binding site; other site 323098005188 Uncharacterized conserved protein [Function unknown]; Region: COG3743 323098005189 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 323098005190 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 323098005191 Protein of unknown function, DUF655; Region: DUF655; pfam04919 323098005192 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 323098005193 generic binding surface I; other site 323098005194 generic binding surface II; other site 323098005195 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 323098005196 active site 323098005197 dimer interface [polypeptide binding]; other site 323098005198 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 323098005199 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 323098005200 Walker A/P-loop; other site 323098005201 ATP binding site [chemical binding]; other site 323098005202 Q-loop/lid; other site 323098005203 ABC transporter signature motif; other site 323098005204 Walker B; other site 323098005205 D-loop; other site 323098005206 H-loop/switch region; other site 323098005207 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 323098005208 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 323098005209 FtsX-like permease family; Region: FtsX; cl15850 323098005210 prolyl-tRNA synthetase; Provisional; Region: PRK12325 323098005211 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 323098005212 dimer interface [polypeptide binding]; other site 323098005213 motif 1; other site 323098005214 active site 323098005215 motif 2; other site 323098005216 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 323098005217 active site 323098005218 motif 3; other site 323098005219 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 323098005220 anticodon binding site; other site 323098005221 Reeler-like domain of YcnI and similar proteins; Region: YcnI_like; cd08545 323098005222 Protein of unknown function (DUF461); Region: DUF461; cl01071 323098005223 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 323098005224 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 323098005225 N-terminal plug; other site 323098005226 ligand-binding site [chemical binding]; other site 323098005227 Protein of unknown function (DUF2946); Region: DUF2946; pfam11162 323098005228 Protein of unknown function (DUF1467); Region: DUF1467; cl11569 323098005229 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 323098005230 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 323098005231 dimer interface [polypeptide binding]; other site 323098005232 substrate binding site [chemical binding]; other site 323098005233 metal binding site [ion binding]; metal-binding site 323098005234 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 323098005235 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 323098005236 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 323098005237 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 323098005238 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 323098005239 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 323098005240 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 323098005241 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 323098005242 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 323098005243 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 323098005244 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 323098005245 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 323098005246 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 323098005247 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 323098005248 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 323098005249 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 323098005250 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 323098005251 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 323098005252 4Fe-4S binding domain; Region: Fer4; cl02805 323098005253 4Fe-4S binding domain; Region: Fer4; cl02805 323098005254 NADH dehydrogenase; Region: NADHdh; cl00469 323098005255 NADH dehydrogenase subunit G; Validated; Region: PRK09130 323098005256 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 323098005257 catalytic loop [active] 323098005258 iron binding site [ion binding]; other site 323098005259 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; cl11210 323098005260 MopB_Res_Cmplx1_Nad11: The second domain of the Nad11/75-kDa subunit of the NADH-quinone oxidoreductase/respiratory complex I/NADH dehydrogenase-1(NDH-1) of eukaryotes and the Nqo3/G subunit of alphaproteobacteria NDH-1. The NADH-quinone oxidoreductase...; Region: MopB_Res-Cmplx1_Nad11; cd02773 323098005261 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 323098005262 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 323098005263 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 323098005264 SLBB domain; Region: SLBB; pfam10531 323098005265 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; cl11211 323098005266 NADH dehydrogenase subunit E; Provisional; Region: PRK12373 323098005267 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 323098005268 putative dimer interface [polypeptide binding]; other site 323098005269 [2Fe-2S] cluster binding site [ion binding]; other site 323098005270 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098005271 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 323098005272 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; pfam00346 323098005273 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl15771 323098005274 NADH dehydrogenase subunit B; Provisional; Region: PRK14820 323098005275 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl15792 323098005276 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 323098005277 Protein of unknown function (DUF2798); Region: DUF2798; pfam11391 323098005278 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 323098005279 IHF - DNA interface [nucleotide binding]; other site 323098005280 IHF dimer interface [polypeptide binding]; other site 323098005281 M20 Peptidase T specifically cleaves tripeptides; Region: M20_peptT; cd03892 323098005282 peptidase T; Region: peptidase-T; TIGR01882 323098005283 metal binding site [ion binding]; metal-binding site 323098005284 dimer interface [polypeptide binding]; other site 323098005285 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098005286 Methyltransferase domain; Region: Methyltransf_31; pfam13847 323098005287 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 323098005288 S-adenosylmethionine binding site [chemical binding]; other site 323098005289 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 323098005290 Found in ATP-dependent protease La (LON); Region: LON; smart00464 323098005291 The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; Region: BAR; cl12013 323098005292 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 323098005293 Walker A motif; other site 323098005294 ATP binding site [chemical binding]; other site 323098005295 Walker B motif; other site 323098005296 arginine finger; other site 323098005297 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 323098005298 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 323098005299 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 323098005300 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 323098005301 Walker A motif; other site 323098005302 ATP binding site [chemical binding]; other site 323098005303 Walker B motif; other site 323098005304 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 323098005305 Clp protease; Region: CLP_protease; pfam00574 323098005306 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 323098005307 oligomer interface [polypeptide binding]; other site 323098005308 active site residues [active] 323098005309 trigger factor; Provisional; Region: tig; PRK01490 323098005310 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 323098005311 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 323098005312 copper-resistance protein, CopA family; Region: copper_res_A; TIGR01480 323098005313 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 323098005314 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 323098005315 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 323098005316 YjeF-related protein N-terminus; Region: YjeF_N; cl00318 323098005317 putative carbohydrate kinase; Provisional; Region: PRK10565 323098005318 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 323098005319 putative substrate binding site [chemical binding]; other site 323098005320 putative ATP binding site [chemical binding]; other site 323098005321 Nitrogen regulatory protein P-II; Region: P-II; cl00412 323098005322 Nitrogen regulatory protein P-II; Region: P-II; smart00938 323098005323 glutamine synthetase; Provisional; Region: glnA; PRK09469 323098005324 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 323098005325 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 323098005326 Domain of unknown function DUF20; Region: UPF0118; pfam01594 323098005327 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 323098005328 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 323098005329 Helix-turn-helix domains; Region: HTH; cl00088 323098005330 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 323098005331 dimer interface [polypeptide binding]; other site 323098005332 allosteric magnesium binding site [ion binding]; other site 323098005333 active site 323098005334 aspartate-rich active site metal binding site; other site 323098005335 Schiff base residues; other site 323098005336 RDD family; Region: RDD; cl00746 323098005337 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 323098005338 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 323098005339 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 323098005340 manganese transport protein MntH; Reviewed; Region: PRK00701; cl15845 323098005341 Natural resistance-associated macrophage protein; Region: Nramp; pfam01566 323098005342 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 323098005343 ArsC family; Region: ArsC; pfam03960 323098005344 catalytic residues [active] 323098005345 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 323098005346 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 323098005347 CAP-like domain; other site 323098005348 active site 323098005349 primary dimer interface [polypeptide binding]; other site 323098005350 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 323098005351 Recombination protein O N terminal; Region: RecO_N; cl15812 323098005352 Recombination protein O C terminal; Region: RecO_C; pfam02565 323098005353 GTPase Era; Reviewed; Region: era; PRK00089 323098005354 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 323098005355 G1 box; other site 323098005356 GTP/Mg2+ binding site [chemical binding]; other site 323098005357 Switch I region; other site 323098005358 G2 box; other site 323098005359 Switch II region; other site 323098005360 G3 box; other site 323098005361 G4 box; other site 323098005362 G5 box; other site 323098005363 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 323098005364 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 323098005365 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 323098005366 dimerization interface [polypeptide binding]; other site 323098005367 active site 323098005368 metal binding site [ion binding]; metal-binding site 323098005369 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 323098005370 signal peptidase I; Provisional; Region: PRK10861 323098005371 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 323098005372 Catalytic site [active] 323098005373 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 323098005374 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 323098005375 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 323098005376 active site 323098005377 hydrophilic channel; other site 323098005378 dimerization interface [polypeptide binding]; other site 323098005379 catalytic residues [active] 323098005380 active site lid [active] 323098005381 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 323098005382 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 323098005383 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 323098005384 synthetase active site [active] 323098005385 NTP binding site [chemical binding]; other site 323098005386 metal binding site [ion binding]; metal-binding site 323098005387 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 323098005388 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 323098005389 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 323098005390 Uncharacterized conserved protein [Function unknown]; Region: COG1432 323098005391 LabA_like proteins; Region: LabA; cd10911 323098005392 putative metal binding site [ion binding]; other site 323098005393 Family-5 Uracil-DNA glycosylases (UDG), found in thermophilic organisms; Region: UDG_F5_TTUDGB_like; cd10031 323098005394 Fe-S cluster binding site [ion binding]; other site 323098005395 DNA binding site [nucleotide binding] 323098005396 active site 323098005397 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 323098005398 SmpB-tmRNA interface; other site 323098005399 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 323098005400 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 323098005401 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 323098005402 dihydrodipicolinate synthase; Region: dapA; TIGR00674 323098005403 dimer interface [polypeptide binding]; other site 323098005404 active site 323098005405 catalytic residue [active] 323098005406 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 323098005407 N-acetyl-D-glucosamine binding site [chemical binding]; other site 323098005408 catalytic residue [active] 323098005409 Helix-turn-helix domains; Region: HTH; cl00088 323098005410 Helix-turn-helix domains; Region: HTH; cl00088 323098005411 Winged helix-turn helix; Region: HTH_29; pfam13551 323098005412 Helix-turn-helix domains; Region: HTH; cl00088 323098005413 Integrase core domain; Region: rve; cl01316 323098005414 Integrase core domain; Region: rve_3; cl15866 323098005415 Porin subfamily; Region: Porin_2; pfam02530 323098005416 Transposase domain (DUF772); Region: DUF772; cl15789 323098005417 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cd09725 323098005418 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-C; cd09721 323098005419 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 323098005420 CRISPR/Cas system-associated RAMP superfamily protein Cas7; Region: Cas7_I-C; cd09689 323098005421 CRISPR-associated protein Cas8c/Csd1, subtype I-C/DVULG; Region: cas_Csd1; TIGR01863 323098005422 CRISPR/Cas system-associated protein Cas8c; Region: Cas8c_I-C; cd09757 323098005423 CRISPR-associated protein (Cas_Cas5); Region: Cas_Cas5d; pfam09704 323098005424 CRISPR/Cas system-associated RAMP superfamily protein Cas5; Region: Cas5_I-C; cd09752 323098005425 CRISPR/Cas system-associated protein Cas3''; Region: Cas3''_I; cd09641 323098005426 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098005427 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 323098005428 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 323098005429 catalytic residues [active] 323098005430 catalytic nucleophile [active] 323098005431 Presynaptic Site I dimer interface [polypeptide binding]; other site 323098005432 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 323098005433 Synaptic Flat tetramer interface [polypeptide binding]; other site 323098005434 Synaptic Site I dimer interface [polypeptide binding]; other site 323098005435 DNA binding site [nucleotide binding] 323098005436 Recombinase; Region: Recombinase; pfam07508 323098005437 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 323098005438 Helix-turn-helix domains; Region: HTH; cl00088 323098005439 Helix-turn-helix domains; Region: HTH; cl00088 323098005440 Winged helix-turn helix; Region: HTH_29; pfam13551 323098005441 Helix-turn-helix domains; Region: HTH; cl00088 323098005442 Integrase core domain; Region: rve; cl01316 323098005443 Integrase core domain; Region: rve_3; cl15866 323098005444 putative phosphoketolase; Provisional; Region: PRK05261 323098005445 Thiamine pyrophosphate (TPP) family, Phosphoketolase (PK) subfamily, TPP-binding module; PK catalyzes the conversion of D-xylulose 5-phosphate and phosphate to acetyl phosphate, D-glyceraldehyde-3-phosphate and H2O. This enzyme requires divalent...; Region: TPP_PK; cd02011 323098005446 TPP-binding site; other site 323098005447 D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase; Region: XFP; pfam03894 323098005448 XFP C-terminal domain; Region: XFP_C; pfam09363 323098005449 Acetokinase family; Region: Acetate_kinase; cl01029 323098005450 propionate/acetate kinase; Provisional; Region: PRK12379 323098005451 propanediol utilization phosphotransacylase; Provisional; Region: PRK15070 323098005452 Propanediol utilisation protein PduL; Region: PduL; pfam06130 323098005453 Propanediol utilisation protein PduL; Region: PduL; pfam06130 323098005454 heavy metal translocating P-type ATPase; Region: ATPase-IB_hvy; TIGR01525 323098005455 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 323098005456 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 323098005457 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 323098005458 catalytic residues [active] 323098005459 catalytic nucleophile [active] 323098005460 Presynaptic Site I dimer interface [polypeptide binding]; other site 323098005461 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 323098005462 Synaptic Flat tetramer interface [polypeptide binding]; other site 323098005463 Synaptic Site I dimer interface [polypeptide binding]; other site 323098005464 DNA binding site [nucleotide binding] 323098005465 Recombinase; Region: Recombinase; pfam07508 323098005466 Protein of unknown function (DUF2924); Region: DUF2924; pfam11149 323098005467 Domain of unknown function DUF87; Region: DUF87; pfam01935 323098005468 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]; Region: COG2405 323098005469 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 323098005470 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 323098005471 non-specific DNA binding site [nucleotide binding]; other site 323098005472 salt bridge; other site 323098005473 sequence-specific DNA binding site [nucleotide binding]; other site 323098005474 Domain of unknown function (DUF955); Region: DUF955; cl01076 323098005475 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 323098005476 AAA domain; Region: AAA_24; pfam13479 323098005477 Helix-turn-helix domains; Region: HTH; cl00088 323098005478 Winged helix-turn helix; Region: HTH_29; pfam13551 323098005479 Helix-turn-helix domains; Region: HTH; cl00088 323098005480 Integrase core domain; Region: rve; cl01316 323098005481 Integrase core domain; Region: rve_3; cl15866 323098005482 Helix-turn-helix domains; Region: HTH; cl00088 323098005483 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 323098005484 DNA binding residues [nucleotide binding] 323098005485 Winged helix-turn helix; Region: HTH_29; pfam13551 323098005486 Helix-turn-helix domains; Region: HTH; cl00088 323098005487 Helix-turn-helix domains; Region: HTH; cl00088 323098005488 Integrase core domain; Region: rve; cl01316 323098005489 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098005490 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 323098005491 FecR protein; Region: FecR; pfam04773 323098005492 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 323098005493 Bacterial Micro-Compartment (BMC)-like domain 1 repeat 1; Region: BMC_like_1_repeat1; cd07051 323098005494 putative hexamer interface [polypeptide binding]; other site 323098005495 putative hexagonal pore; other site 323098005496 Bacterial Micro-Compartment (BMC)-like domain 1 repeat 2; Region: BMC_like_1_repeat2; cd07052 323098005497 putative hexamer interface [polypeptide binding]; other site 323098005498 putative hexagonal pore; other site 323098005499 norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial...; Region: vWA_norD_type; cd01454 323098005500 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098005501 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 323098005502 ParA-like protein; Provisional; Region: PHA02518 323098005503 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 323098005504 P-loop; other site 323098005505 Magnesium ion binding site [ion binding]; other site 323098005506 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; cl00942 323098005507 aromatic arch; other site 323098005508 DCoH dimer interaction site [polypeptide binding]; other site 323098005509 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 323098005510 DCoH tetramer interaction site [polypeptide binding]; other site 323098005511 substrate binding site [chemical binding]; other site 323098005512 Carboxysome Shell 1 (CsoS1); Bacterial Micro-Compartment (BCM) domain; Region: BMC_CsoS1; cd07058 323098005513 Hexamer interface [polypeptide binding]; other site 323098005514 Hexagonal pore residue; other site 323098005515 Hexagonal pore; other site 323098005516 Carboxysome Shell 1 (CsoS1); Bacterial Micro-Compartment (BCM) domain; Region: BMC_CsoS1; cd07058 323098005517 Hexamer interface [polypeptide binding]; other site 323098005518 Hexagonal pore residue; other site 323098005519 Hexagonal pore; other site 323098005520 Ethanolamine utilisation protein and carboxysome structural protein domain family; Region: EutN_CcmL; cd01614 323098005521 Hexamer/Pentamer interface [polypeptide binding]; other site 323098005522 central pore; other site 323098005523 Ethanolamine utilisation protein and carboxysome structural protein domain family; Region: EutN_CcmL; cd01614 323098005524 Hexamer/Pentamer interface [polypeptide binding]; other site 323098005525 central pore; other site 323098005526 Carboxysome Shell Carbonic Anhydrase; Region: CsoSCA; cl07510 323098005527 Carboxysome shell peptide mid-region; Region: CsoS2_M; pfam12288 323098005528 Carboxysome shell peptide mid-region; Region: CsoS2_M; pfam12288 323098005529 Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco...; Region: RuBisCO_small; cd03527 323098005530 multimerization interface [polypeptide binding]; other site 323098005531 ribulose bisophosphate carboxylase; Reviewed; Region: rbcL; PRK04208 323098005532 Ribulose bisphosphate carboxylase large chain; Region: RuBisCO_large; cl08232 323098005533 dimer interface [polypeptide binding]; other site 323098005534 catalytic residue [active] 323098005535 metal binding site [ion binding]; metal-binding site 323098005536 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 323098005537 Helix-turn-helix domains; Region: HTH; cl00088 323098005538 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 323098005539 putative dimerization interface [polypeptide binding]; other site 323098005540 Nitrogen regulatory protein P-II; Region: P-II; cl00412 323098005541 Nitrogen regulatory protein P-II; Region: P-II; smart00938 323098005542 Uncharacterized protein conserved in bacteria (DUF2309); Region: DUF2309; pfam10070 323098005543 Uncharacterized protein conserved in bacteria (DUF2309); Region: DUF2309; pfam10070 323098005544 Uncharacterized protein conserved in bacteria (DUF2309); Region: DUF2309; pfam10070 323098005545 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 323098005546 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 323098005547 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 323098005548 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 323098005549 GatB domain; Region: GatB_Yqey; cl11497 323098005550 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 323098005551 Integrase core domain; Region: rve; cl01316 323098005552 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098005553 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 323098005554 Amidase; Region: Amidase; cl11426 323098005555 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 323098005556 Glu-tRNAGln amidotransferase C subunit; Region: Glu-tRNAGln; cl00495 323098005557 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 323098005558 CAAX protease self-immunity; Region: Abi; cl00558 323098005559 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 323098005560 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 323098005561 active site 323098005562 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 323098005563 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 323098005564 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098005565 dihydroorotase; Validated; Region: PRK09059 323098005566 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 323098005567 Dihydroorotase (DHOase), subgroup IIa; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This subgroup also contains proteins that lack the active site, like unc-33, a C; Region: DHOase_IIa; cd01317 323098005568 active site 323098005569 Glycerol-3-phosphate acyltransferase; Region: G3P_acyltransf; cl00410 323098005570 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 323098005571 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 323098005572 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 323098005573 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 323098005574 S-adenosylmethionine binding site [chemical binding]; other site 323098005575 replicative DNA helicase; Provisional; Region: PRK09165 323098005576 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 323098005577 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 323098005578 Walker A motif; other site 323098005579 ATP binding site [chemical binding]; other site 323098005580 Walker B motif; other site 323098005581 DNA binding loops [nucleotide binding] 323098005582 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 323098005583 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 323098005584 active site 323098005585 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 323098005586 dimer interface [polypeptide binding]; other site 323098005587 substrate binding site [chemical binding]; other site 323098005588 catalytic residues [active] 323098005589 DNA repair protein RadA; Provisional; Region: PRK11823 323098005590 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098005591 Walker A motif; other site 323098005592 ATP binding site [chemical binding]; other site 323098005593 Walker B motif; other site 323098005594 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 323098005595 Colicin V production protein; Region: Colicin_V; cl00567 323098005596 amidophosphoribosyltransferase; Provisional; Region: PRK09123 323098005597 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 323098005598 active site 323098005599 tetramer interface [polypeptide binding]; other site 323098005600 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 323098005601 active site 323098005602 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 323098005603 short chain dehydrogenase; Provisional; Region: PRK12829 323098005604 classical (c) SDRs; Region: SDR_c; cd05233 323098005605 NAD(P) binding site [chemical binding]; other site 323098005606 active site 323098005607 GTP-binding protein Der; Reviewed; Region: PRK00093 323098005608 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 323098005609 G1 box; other site 323098005610 GTP/Mg2+ binding site [chemical binding]; other site 323098005611 Switch I region; other site 323098005612 G2 box; other site 323098005613 Switch II region; other site 323098005614 G3 box; other site 323098005615 G4 box; other site 323098005616 G5 box; other site 323098005617 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 323098005618 G1 box; other site 323098005619 GTP/Mg2+ binding site [chemical binding]; other site 323098005620 Switch I region; other site 323098005621 G2 box; other site 323098005622 G3 box; other site 323098005623 Switch II region; other site 323098005624 G4 box; other site 323098005625 G5 box; other site 323098005626 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4649 323098005627 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 323098005628 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 323098005629 oligomerization interface [polypeptide binding]; other site 323098005630 active site 323098005631 metal binding site [ion binding]; metal-binding site 323098005632 Phospholipid methyltransferase; Region: PEMT; cl00763 323098005633 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 323098005634 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 323098005635 G1 box; other site 323098005636 putative GEF interaction site [polypeptide binding]; other site 323098005637 GTP/Mg2+ binding site [chemical binding]; other site 323098005638 Switch I region; other site 323098005639 G2 box; other site 323098005640 G3 box; other site 323098005641 Switch II region; other site 323098005642 G4 box; other site 323098005643 G5 box; other site 323098005644 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 323098005645 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 323098005646 Integrase core domain; Region: rve; cl01316 323098005647 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098005648 Winged helix-turn helix; Region: HTH_29; pfam13551 323098005649 Helix-turn-helix domains; Region: HTH; cl00088 323098005650 Helix-turn-helix domains; Region: HTH; cl00088 323098005651 Phosphate transporter family; Region: PHO4; cl00396 323098005652 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 323098005653 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 323098005654 ArsC family; Region: ArsC; pfam03960 323098005655 putative catalytic residues [active] 323098005656 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 323098005657 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 323098005658 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 323098005659 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 323098005660 active site 323098005661 dimer interface [polypeptide binding]; other site 323098005662 motif 1; other site 323098005663 motif 2; other site 323098005664 motif 3; other site 323098005665 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 323098005666 anticodon binding site; other site 323098005667 Nitroreductase-like family which includes NADH oxidase and arsenite oxidiase. NADH oxidase catalyses the oxidation of NAD(P)H and accepts a wide broad range of compounds as electron acceptors, such as nitrocompound. Arsenite oxidase in a...; Region: Arsenite_oxidase; cd02135 323098005668 putative FMN binding site [chemical binding]; other site 323098005669 Gram-negative bacterial tonB protein; Region: TonB; cl10048 323098005670 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 323098005671 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 323098005672 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 323098005673 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 323098005674 Walker A/P-loop; other site 323098005675 ATP binding site [chemical binding]; other site 323098005676 Q-loop/lid; other site 323098005677 ABC transporter signature motif; other site 323098005678 Walker B; other site 323098005679 D-loop; other site 323098005680 H-loop/switch region; other site 323098005681 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 323098005682 FtsX-like permease family; Region: FtsX; cl15850 323098005683 macrolide transporter subunit MacA; Provisional; Region: PRK11578 323098005684 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 323098005685 Helix-turn-helix domains; Region: HTH; cl00088 323098005686 Helix-turn-helix domains; Region: HTH; cl00088 323098005687 Winged helix-turn helix; Region: HTH_29; pfam13551 323098005688 Helix-turn-helix domains; Region: HTH; cl00088 323098005689 Integrase core domain; Region: rve; cl01316 323098005690 Integrase core domain; Region: rve_3; cl15866 323098005691 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 323098005692 Secretin and TonB N terminus short domain; Region: STN; cl06624 323098005693 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 323098005694 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 323098005695 N-terminal plug; other site 323098005696 ligand-binding site [chemical binding]; other site 323098005697 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 323098005698 FecR protein; Region: FecR; pfam04773 323098005699 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 323098005700 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 323098005701 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 323098005702 Protein of unknown function (DUF3016); Region: DUF3016; pfam11454 323098005703 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 323098005704 Gram-negative bacterial tonB protein; Region: TonB; cl10048 323098005705 Protein of unknown function (DUF3356); Region: DUF3356; pfam11836 323098005706 bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase; Provisional; Region: PRK11316 323098005707 Winged helix-turn helix; Region: HTH_29; pfam13551 323098005708 Helix-turn-helix domains; Region: HTH; cl00088 323098005709 Helix-turn-helix domains; Region: HTH; cl00088 323098005710 Integrase core domain; Region: rve; cl01316 323098005711 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098005712 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 323098005713 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 323098005714 ligand binding site [chemical binding]; other site 323098005715 flexible hinge region; other site 323098005716 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 323098005717 putative switch regulator; other site 323098005718 non-specific DNA interactions [nucleotide binding]; other site 323098005719 DNA binding site [nucleotide binding] 323098005720 sequence specific DNA binding site [nucleotide binding]; other site 323098005721 putative cAMP binding site [chemical binding]; other site 323098005722 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 323098005723 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 323098005724 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 323098005725 putative transporter; Provisional; Region: PRK11660 323098005726 Sulfate transporter family; Region: Sulfate_transp; cl15842 323098005727 Sulfate transporter family; Region: Sulfate_transp; cl15842 323098005728 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 323098005729 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 323098005730 Nitrate reductase alpha subunit [Energy production and conversion]; Region: NarG; COG5013 323098005731 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to...; Region: MopB_Nitrate-R-NarG-like; cd02750 323098005732 [4Fe-4S] binding site [ion binding]; other site 323098005733 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 323098005734 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 323098005735 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 323098005736 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 323098005737 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to...; Region: MopB_CT_Nitrate-R-NarG-like; cd02776 323098005738 molybdopterin cofactor binding site; other site 323098005739 Uncharacterized protein conserved in bacteria (DUF2309); Region: DUF2309; pfam10070 323098005740 Uncharacterized protein conserved in bacteria (DUF2309); Region: DUF2309; pfam10070 323098005741 Uncharacterized protein conserved in bacteria (DUF2309); Region: DUF2309; pfam10070 323098005742 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; cl15691 323098005743 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 323098005744 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 323098005745 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 323098005746 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 323098005747 N-terminal plug; other site 323098005748 ligand-binding site [chemical binding]; other site 323098005749 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 323098005750 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 323098005751 intersubunit interface [polypeptide binding]; other site 323098005752 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 323098005753 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 323098005754 Walker A/P-loop; other site 323098005755 ATP binding site [chemical binding]; other site 323098005756 Q-loop/lid; other site 323098005757 ABC transporter signature motif; other site 323098005758 Walker B; other site 323098005759 D-loop; other site 323098005760 H-loop/switch region; other site 323098005761 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 323098005762 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 323098005763 ABC-ATPase subunit interface; other site 323098005764 dimer interface [polypeptide binding]; other site 323098005765 putative PBP binding regions; other site 323098005766 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 323098005767 ligand-binding site [chemical binding]; other site 323098005768 Helix-turn-helix domains; Region: HTH; cl00088 323098005769 Integrase core domain; Region: rve; cl01316 323098005770 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098005771 HipA N-terminal domain; Region: Couple_hipA; cl11853 323098005772 HipA-like N-terminal domain; Region: HipA_N; pfam07805 323098005773 HipA-like C-terminal domain; Region: HipA_C; pfam07804 323098005774 Helix-turn-helix domains; Region: HTH; cl00088 323098005775 Helix-turn-helix domains; Region: HTH; cl00088 323098005776 Winged helix-turn helix; Region: HTH_29; pfam13551 323098005777 Helix-turn-helix domains; Region: HTH; cl00088 323098005778 Integrase core domain; Region: rve; cl01316 323098005779 Integrase core domain; Region: rve_3; cl15866 323098005780 Divergent AAA domain; Region: AAA_4; pfam04326 323098005781 Peptidase S8 family domain in Subtilisin-like proteins; Region: Peptidases_S8_Subtilisin_like_2; cd04847 323098005782 active site 323098005783 catalytic triad [active] 323098005784 type VI secretion ATPase, ClpV1 family; Region: VI_ClpV1; TIGR03345 323098005785 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 323098005786 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 323098005787 Walker A motif; other site 323098005788 ATP binding site [chemical binding]; other site 323098005789 Walker B motif; other site 323098005790 arginine finger; other site 323098005791 Protein of unknown function (DUF2274); Region: DUF2274; cl02406 323098005792 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 323098005793 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 323098005794 VirB7 interaction site; other site 323098005795 VirB8 protein; Region: VirB8; cl01500 323098005796 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 323098005797 Conjugal transfer/entry exclusion protein [Intracellular trafficking and secretion]; Region: COG5314; cl02193 323098005798 conjugal transfer ATPase TrbE; Provisional; Region: PRK13873 323098005799 conjugal transfer ATPase TrbE; Provisional; Region: PRK13873 323098005800 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098005801 Walker A/P-loop; other site 323098005802 ATP binding site [chemical binding]; other site 323098005803 Helix-turn-helix domains; Region: HTH; cl00088 323098005804 Winged helix-turn helix; Region: HTH_29; pfam13551 323098005805 Helix-turn-helix domains; Region: HTH; cl00088 323098005806 Integrase core domain; Region: rve; cl01316 323098005807 Integrase core domain; Region: rve_3; cl15866 323098005808 Helix-turn-helix domains; Region: HTH; cl00088 323098005809 Winged helix-turn helix; Region: HTH_29; pfam13551 323098005810 Helix-turn-helix domains; Region: HTH; cl00088 323098005811 Helix-turn-helix domains; Region: HTH; cl00088 323098005812 Integrase core domain; Region: rve; cl01316 323098005813 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098005814 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 323098005815 DNA binding site [nucleotide binding] 323098005816 active site 323098005817 Int/Topo IB signature motif; other site 323098005818 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 323098005819 Winged helix-turn helix; Region: HTH_29; pfam13551 323098005820 Helix-turn-helix domains; Region: HTH; cl00088 323098005821 Helix-turn-helix domains; Region: HTH; cl00088 323098005822 Integrase core domain; Region: rve; cl01316 323098005823 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098005824 Fic family protein [Function unknown]; Region: COG3177 323098005825 Fic/DOC family N-terminal; Region: Fic_N; pfam13784 323098005826 Fic/DOC family; Region: Fic; cl00960 323098005827 Glycogen debranching enzyme [Carbohydrate transport and metabolism]; Region: GDB1; COG3408 323098005828 Bacterial alpha-L-rhamnosidase; Region: Bac_rhamnosid; cl01801 323098005829 This family is most closely related to the GT1 family of glycosyltransferases. aviGT4 in Streptomyces viridochromogenes has been shown to be involved in biosynthesis of oligosaccharide antibiotic avilamycin A. Inactivation of aviGT4 resulted in a mutant...; Region: GT1_AviGT4_like; cd03802 323098005830 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 323098005831 putative ADP-binding pocket [chemical binding]; other site 323098005832 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 323098005833 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 323098005834 ring oligomerisation interface [polypeptide binding]; other site 323098005835 ATP/Mg binding site [chemical binding]; other site 323098005836 stacking interactions; other site 323098005837 hinge regions; other site 323098005838 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 323098005839 oligomerisation interface [polypeptide binding]; other site 323098005840 mobile loop; other site 323098005841 roof hairpin; other site 323098005842 Usg-like family; Region: Usg; cl11567 323098005843 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 323098005844 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation...; Region: ACD_IbpA-B_like; cd06470 323098005845 putative dimer interface [polypeptide binding]; other site 323098005846 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 323098005847 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 323098005848 putative dimer interface [polypeptide binding]; other site 323098005849 Helix-turn-helix domains; Region: HTH; cl00088 323098005850 putative transposase OrfB; Reviewed; Region: PHA02517 323098005851 HTH-like domain; Region: HTH_21; pfam13276 323098005852 Integrase core domain; Region: rve; cl01316 323098005853 Integrase core domain; Region: rve_3; cl15866 323098005854 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 323098005855 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 323098005856 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 323098005857 ParB-like nuclease domain; Region: ParBc; cl02129 323098005858 plasmid partitioning protein; Provisional; Region: PRK13832 323098005859 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 323098005860 metal binding site [ion binding]; metal-binding site 323098005861 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098005862 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098005863 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098005864 conjugative transfer relaxase protein TraI; Region: TraI_TIGR; TIGR02760 323098005865 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 323098005866 Protein of unknown function (DUF2493); Region: DUF2493; pfam10686 323098005867 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 323098005868 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 323098005869 ATP binding site [chemical binding]; other site 323098005870 putative Mg++ binding site [ion binding]; other site 323098005871 Protein of unknown function (DUF736); Region: DUF736; cl02303 323098005872 Helix-turn-helix domains; Region: HTH; cl00088 323098005873 Winged helix-turn helix; Region: HTH_29; pfam13551 323098005874 Helix-turn-helix domains; Region: HTH; cl00088 323098005875 Integrase core domain; Region: rve; cl01316 323098005876 Integrase core domain; Region: rve_3; cl15866 323098005877 Helix-turn-helix domains; Region: HTH; cl00088 323098005878 RNA polymerase sigma factor SigJ; Provisional; Region: PRK09636 323098005879 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 323098005880 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 323098005881 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 323098005882 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 323098005883 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 323098005884 integrase; Provisional; Region: PRK09692 323098005885 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 323098005886 active site 323098005887 Int/Topo IB signature motif; other site 323098005888 GMP synthase; Reviewed; Region: guaA; PRK00074 323098005889 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 323098005890 AMP/PPi binding site [chemical binding]; other site 323098005891 candidate oxyanion hole; other site 323098005892 catalytic triad [active] 323098005893 potential glutamine specificity residues [chemical binding]; other site 323098005894 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 323098005895 ATP Binding subdomain [chemical binding]; other site 323098005896 Ligand Binding sites [chemical binding]; other site 323098005897 Dimerization subdomain; other site 323098005898 ribosomal RNA small subunit methyltransferase RsmB; Region: rsmB; TIGR00563 323098005899 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; cl15754 323098005900 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 323098005901 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 323098005902 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 323098005903 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 323098005904 active site 323098005905 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 323098005906 putative transporter; Provisional; Region: PRK10504 323098005907 putative substrate translocation pore; other site 323098005908 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 323098005909 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 323098005910 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 323098005911 S-adenosylmethionine binding site [chemical binding]; other site 323098005912 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 323098005913 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; cl00727 323098005914 ABC transporter ATPase component; Reviewed; Region: PRK11147 323098005915 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 323098005916 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 323098005917 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098005918 HI0933-like protein; Region: HI0933_like; pfam03486 323098005919 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098005920 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 323098005921 putative active site [active] 323098005922 putative catalytic site [active] 323098005923 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098005924 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 323098005925 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 323098005926 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 323098005927 substrate binding site [chemical binding]; other site 323098005928 oxyanion hole (OAH) forming residues; other site 323098005929 trimer interface [polypeptide binding]; other site 323098005930 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; cl15762 323098005931 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 323098005932 Isobutyryl-CoA dehydrogenase; Region: IBD; cd01162 323098005933 substrate binding pocket [chemical binding]; other site 323098005934 FAD binding site [chemical binding]; other site 323098005935 catalytic base [active] 323098005936 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 323098005937 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 323098005938 tetrameric interface [polypeptide binding]; other site 323098005939 NAD binding site [chemical binding]; other site 323098005940 catalytic residues [active] 323098005941 acetyl-CoA acetyltransferase; Provisional; Region: PRK07516 323098005942 Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal...; Region: SCP-x_thiolase; cd00829 323098005943 active site 323098005944 SET domain; Region: SET; cl02566 323098005945 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 323098005946 Tim44-like domain; Region: Tim44; cl09208 323098005947 Protein of unknown function (DUF1491); Region: DUF1491; cl11568 323098005948 adenylosuccinate lyase; Provisional; Region: PRK07492 323098005949 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 323098005950 tetramer interface [polypeptide binding]; other site 323098005951 active site 323098005952 PilZ domain; Region: PilZ; cl01260 323098005953 PilZ domain; Region: PilZ; cl01260 323098005954 Phosphate-selective porin O and P; Region: Porin_O_P; cl01524 323098005955 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 323098005956 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 323098005957 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 323098005958 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 323098005959 trimer interface [polypeptide binding]; other site 323098005960 putative metal binding site [ion binding]; other site 323098005961 Protein of unknown function (DUF3126); Region: DUF3126; pfam11324 323098005962 serine acetyltransferase; Provisional; Region: cysE; PRK11132 323098005963 Serine acetyltransferase, N-terminal; Region: SATase_N; cl05762 323098005964 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 323098005965 trimer interface [polypeptide binding]; other site 323098005966 active site 323098005967 substrate binding site [chemical binding]; other site 323098005968 CoA binding site [chemical binding]; other site 323098005969 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 323098005970 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 323098005971 Zinc-finger domain; Region: zf-CHCC; cl01821 323098005972 salicylate hydroxylase; Provisional; Region: PRK06475 323098005973 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098005974 Thermophilic metalloprotease (M29); Region: Peptidase_M29; pfam02073 323098005975 DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1; Region: DsbA_HCCA_Iso; cd03022 323098005976 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 323098005977 putative catalytic residue [active] 323098005978 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 323098005979 active site 323098005980 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 323098005981 Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of...; Region: cinA; cd00885 323098005982 putative MPT binding site; other site 323098005983 Usg-like family; Region: Usg; cl11567 323098005984 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 323098005985 oligomerisation interface [polypeptide binding]; other site 323098005986 mobile loop; other site 323098005987 roof hairpin; other site 323098005988 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 323098005989 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 323098005990 ring oligomerisation interface [polypeptide binding]; other site 323098005991 ATP/Mg binding site [chemical binding]; other site 323098005992 stacking interactions; other site 323098005993 hinge regions; other site 323098005994 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl15769 323098005995 dolichyl-phosphate beta-D-mannosyltransferase; Region: PLN02726 323098005996 DPM1_like represents putative enzymes similar to eukaryotic DPM1; Region: DPM1_like; cd06442 323098005997 Ligand binding site; other site 323098005998 Putative Catalytic site; other site 323098005999 DXD motif; other site 323098006000 GtrA-like protein; Region: GtrA; cl00971 323098006001 Protein of unknown function DUF72; Region: DUF72; cl00777 323098006002 Protein of unknown function, DUF488; Region: DUF488; cl01246 323098006003 MoeA_like. This domain is similar to a domain found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. There this domain is presumed to bind molybdopterin. The exact function of this subgroup is...; Region: MoeA_like; cd03522 323098006004 putative MPT binding site; other site 323098006005 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 323098006006 Ligand binding site; other site 323098006007 metal-binding site 323098006008 XdhC Rossmann domain; Region: XdhC_C; pfam13478 323098006009 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 323098006010 Protein containing von Willebrand factor type A (vWA) domain [General function prediction only]; Region: CoxE; COG3552 323098006011 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 323098006012 metal ion-dependent adhesion site (MIDAS); other site 323098006013 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 323098006014 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 323098006015 Walker A motif; other site 323098006016 ATP binding site [chemical binding]; other site 323098006017 Walker B motif; other site 323098006018 arginine finger; other site 323098006019 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 323098006020 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; cl08390 323098006021 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 323098006022 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 323098006023 catalytic loop [active] 323098006024 iron binding site [ion binding]; other site 323098006025 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 323098006026 Carbon monoxide dehydrogenase subunit G (CoxG); Region: CoxG; cd05018 323098006027 putative hydrophobic ligand binding site [chemical binding]; other site 323098006028 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 323098006029 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 323098006030 TM-ABC transporter signature motif; other site 323098006031 Domain of unknown function (DUF3382); Region: DUF3382; pfam11862 323098006032 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 323098006033 TM-ABC transporter signature motif; other site 323098006034 leucine/isoleucine/valine transporter ATP-binding subunit; Provisional; Region: livG; PRK11300 323098006035 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 323098006036 Walker A/P-loop; other site 323098006037 ATP binding site [chemical binding]; other site 323098006038 Q-loop/lid; other site 323098006039 ABC transporter signature motif; other site 323098006040 Walker B; other site 323098006041 D-loop; other site 323098006042 H-loop/switch region; other site 323098006043 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 323098006044 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 323098006045 Walker A/P-loop; other site 323098006046 ATP binding site [chemical binding]; other site 323098006047 Q-loop/lid; other site 323098006048 ABC transporter signature motif; other site 323098006049 Walker B; other site 323098006050 D-loop; other site 323098006051 H-loop/switch region; other site 323098006052 leucine ABC transporter subunit substrate-binding protein LivK; Provisional; Region: PRK15404 323098006053 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 323098006054 dimerization interface [polypeptide binding]; other site 323098006055 ligand binding site [chemical binding]; other site 323098006056 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 323098006057 nylC-like family; composed of proteins with similarity to Flavobacterium endo-type 6-aminohexanoate-oligomer hydrolase (EIII), the product of the nylon oligomer degradation gene, nylC. EIII is an amide hydrolase that catalyzes the degradation of...; Region: nylC_like; cd02252 323098006058 nylC-like family; composed of proteins with similarity to Flavobacterium endo-type 6-aminohexanoate-oligomer hydrolase (EIII), the product of the nylon oligomer degradation gene, nylC. EIII is an amide hydrolase that catalyzes the degradation of...; Region: nylC_like; cd02252 323098006059 cleavage site 323098006060 Uncharacterized protein conserved in bacteria (DUF2320); Region: DUF2320; cl12051 323098006061 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 323098006062 substrate binding site [chemical binding]; other site 323098006063 hexamer interface [polypeptide binding]; other site 323098006064 metal binding site [ion binding]; metal-binding site 323098006065 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 323098006066 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 323098006067 N-terminal plug; other site 323098006068 ligand-binding site [chemical binding]; other site 323098006069 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 323098006070 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 323098006071 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 323098006072 putative active site [active] 323098006073 heme pocket [chemical binding]; other site 323098006074 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 323098006075 dimer interface [polypeptide binding]; other site 323098006076 phosphorylation site [posttranslational modification] 323098006077 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 323098006078 ATP binding site [chemical binding]; other site 323098006079 Mg2+ binding site [ion binding]; other site 323098006080 G-X-G motif; other site 323098006081 Fe-S metabolism associated domain; Region: SufE; cl00951 323098006082 Transposase domain (DUF772); Region: DUF772; cl15789 323098006083 Winged helix-turn helix; Region: HTH_29; pfam13551 323098006084 Integrase core domain; Region: rve; cl01316 323098006085 Integrase core domain; Region: rve_3; cl15866 323098006086 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 323098006087 DnaA box-binding interface [nucleotide binding]; other site 323098006088 Predicted transcriptional regulator [Transcription]; Region: COG4957 323098006089 ROS/MUCR transcriptional regulator protein; Region: ROS_MUCR; pfam05443 323098006090 Interleukin 11; Region: IL11; pfam07400 323098006091 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 323098006092 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_3; cd05680 323098006093 metal binding site [ion binding]; metal-binding site 323098006094 putative dimer interface [polypeptide binding]; other site 323098006095 Protein of unknown function (DUF2029); Region: DUF2029; cl09812 323098006096 Domain of unknown function DUF87; Region: DUF87; pfam01935 323098006097 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 323098006098 Domain of unknown function (DUF4332); Region: DUF4332; pfam14229 323098006099 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 323098006100 dihydropteroate synthase; Region: DHPS; TIGR01496 323098006101 substrate binding pocket [chemical binding]; other site 323098006102 dimer interface [polypeptide binding]; other site 323098006103 inhibitor binding site; inhibition site 323098006104 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 323098006105 homooctamer interface [polypeptide binding]; other site 323098006106 active site 323098006107 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 323098006108 catalytic center binding site [active] 323098006109 ATP binding site [chemical binding]; other site 323098006110 methylmalonyl-CoA mutase, heterodimeric type, beta chain; Region: mmCoA_mut_beta; TIGR00642 323098006111 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Beta subunit-like subfamily; contains bacterial proteins similar to the beta subunit of MCMs from Propionbacterium shermanni and Streptomyces cinnamonensis, which are alpha/beta...; Region: MM_CoA_mutase_beta; cd03677 323098006112 heterodimer interface [polypeptide binding]; other site 323098006113 substrate interaction site [chemical binding]; other site 323098006114 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 323098006115 methylmalonyl-CoA mutase; Reviewed; Region: PRK09426 323098006116 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Alpha subunit-like subfamily; contains proteins similar to the alpha subunit of Propionbacterium shermanni MCM, as well as human and E. coli MCM. Members of this subfamily contain...; Region: MM_CoA_mutase_alpha_like; cd03679 323098006117 active site 323098006118 substrate binding site [chemical binding]; other site 323098006119 coenzyme B12 binding site [chemical binding]; other site 323098006120 methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom...; Region: MM_CoA_mut_B12_BD; cd02071 323098006121 B12 binding site [chemical binding]; other site 323098006122 cobalt ligand [ion binding]; other site 323098006123 Domain of unknown function (DUF4163); Region: DUF4163; pfam13739 323098006124 Protein of unknown function (DUF3298); Region: DUF3298; pfam11738 323098006125 membrane ATPase/protein kinase; Provisional; Region: PRK09435 323098006126 The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and...; Region: ArgK-like; cd03114 323098006127 Walker A; other site 323098006128 Pyroglutamyl peptidase (PGP) type I, also known as pyrrolidone carboxyl peptidase (pcp) type I: Enzymes responsible for cleaving pyroglutamate (pGlu) from the N-terminal end of specialized proteins. The N-terminal pGlu protects these proteins from...; Region: Peptidase_C15; cd00501 323098006129 putative substrate binding pocket [chemical binding]; other site 323098006130 AC domain interface; other site 323098006131 catalytic triad [active] 323098006132 AB domain interface; other site 323098006133 interchain disulfide; other site 323098006134 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 323098006135 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 323098006136 putative substrate translocation pore; other site 323098006137 twin-arg-translocated uncharacterized repeat protein; Region: RR_plus_rpt_1; TIGR03808 323098006138 putative cofactor-binding repeat; Region: RR_fam_repeat; TIGR03807 323098006139 TIGR03809 family protein; Region: TIGR03809 323098006140 CsbD-like; Region: CsbD; cl15799 323098006141 Peptidase S8 family domain, uncharacterized subfamily 4; Region: Peptidases_S8_4; cd05561 323098006142 active site 323098006143 catalytic triad [active] 323098006144 RNA polymerase sigma factor; Provisional; Region: PRK12515 323098006145 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 323098006146 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 323098006147 DNA binding residues [nucleotide binding] 323098006148 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; cl15419 323098006149 enoyl-CoA hydratase; Provisional; Region: PRK05862 323098006150 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 323098006151 substrate binding site [chemical binding]; other site 323098006152 oxyanion hole (OAH) forming residues; other site 323098006153 trimer interface [polypeptide binding]; other site 323098006154 Acetyl-CoA hydrolase [Energy production and conversion]; Region: ACH1; COG0427 323098006155 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 323098006156 threonine dehydratase; Provisional; Region: PRK07334 323098006157 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 323098006158 tetramer interface [polypeptide binding]; other site 323098006159 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098006160 catalytic residue [active] 323098006161 C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains; Region: ACT_ThrD-II-like; cd04886 323098006162 DNA polymerase III DnaE; Reviewed; Region: dnaE; PRK06920 323098006163 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 323098006164 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 323098006165 generic binding surface II; other site 323098006166 generic binding surface I; other site 323098006167 DNA Polymerase Y-family; Region: PolY_like; cd03468 323098006168 active site 323098006169 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 323098006170 DNA binding site [nucleotide binding] 323098006171 Cell division inhibitor SulA; Region: SulA; cl01880 323098006172 putative DNA modification/repair radical SAM protein; Region: rSAM_link_UDG; TIGR03916 323098006173 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 323098006174 FeS/SAM binding site; other site 323098006175 Domain of unknown function (DUF4130; Region: DUF4130; cl14836 323098006176 Integrase core domain; Region: rve; cl01316 323098006177 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098006178 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 323098006179 Fe-S cluster binding site [ion binding]; other site 323098006180 active site 323098006181 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 323098006182 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 323098006183 metal binding site [ion binding]; metal-binding site 323098006184 putative dimer interface [polypeptide binding]; other site 323098006185 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 323098006186 Ornithine/acetylornithine aminotransferase [Amino acid transport and metabolism]; Region: ArgD; COG4992 323098006187 inhibitor-cofactor binding pocket; inhibition site 323098006188 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098006189 catalytic residue [active] 323098006190 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; cl01951 323098006191 hopanoid biosynthesis associated RND transporter like protein HpnN; Region: HpnN; TIGR03480 323098006192 Protein export membrane protein; Region: SecD_SecF; cl14618 323098006193 LytB protein; Region: LYTB; cl00507 323098006194 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 323098006195 hopanoid biosynthesis associated radical SAM protein HpnH; Region: HpnH; TIGR03470 323098006196 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 323098006197 FeS/SAM binding site; other site 323098006198 Domain of unknown function (DUF3463); Region: DUF3463; pfam11946 323098006199 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 323098006200 squalene-hopene cyclase; Region: hopene_cyclase; TIGR01507 323098006201 Squalene cyclase (SQCY) domain subgroup 1; found in class II terpene cyclases that have an alpha 6 - alpha 6 barrel fold. Squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY) are integral membrane proteins that catalyze a cationic cyclization...; Region: SQCY_1; cd02892 323098006202 Active site cavity [active] 323098006203 squalene-associated FAD-dependent desaturase; Region: HpnE; TIGR03467 323098006204 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 323098006205 active site lid residues [active] 323098006206 substrate binding pocket [chemical binding]; other site 323098006207 catalytic residues [active] 323098006208 substrate-Mg2+ binding site; other site 323098006209 aspartate-rich region 1; other site 323098006210 aspartate-rich region 2; other site 323098006211 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 323098006212 active site lid residues [active] 323098006213 substrate binding pocket [chemical binding]; other site 323098006214 catalytic residues [active] 323098006215 substrate-Mg2+ binding site; other site 323098006216 aspartate-rich region 1; other site 323098006217 aspartate-rich region 2; other site 323098006218 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 323098006219 Fe-S oxidoreductase [Energy production and conversion]; Region: COG1032 323098006220 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 323098006221 B12 binding site [chemical binding]; other site 323098006222 Domain of unknown function (DUF4070); Region: DUF4070; pfam13282 323098006223 amidase; Provisional; Region: PRK07056 323098006224 Amidase; Region: Amidase; cl11426 323098006225 Phosphoenolpyruvate carboxylase; Region: PEPcase; cl14656 323098006226 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 323098006227 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; cl12078 323098006228 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 323098006229 OsmC-like protein; Region: OsmC; cl00767 323098006230 FAD dependent oxidoreductase; Region: DAO; pfam01266 323098006231 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098006232 sarcosine oxidase, beta subunit family, heterotetrameric form; Region: soxB; TIGR01373 323098006233 multidrug efflux protein; Reviewed; Region: PRK09579 323098006234 Protein export membrane protein; Region: SecD_SecF; cl14618 323098006235 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 323098006236 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 323098006237 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 323098006238 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 323098006239 Helix-turn-helix domains; Region: HTH; cl00088 323098006240 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 323098006241 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 323098006242 NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Region: NAD_bind_1_Glu_DH; cd01076 323098006243 NAD(P) binding site [chemical binding]; other site 323098006244 phenylpropionate dioxygenase ferredoxin reductase subunit; Provisional; Region: PRK09754 323098006245 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 323098006246 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 323098006247 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 323098006248 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 323098006249 FkbR2 is a Streptomyces hygroscopicus protein with a hot dog fold that belongs to a conserved family of proteins found in prokaryotes and archaea but not in eukaryotes. FkbR2 has sequence similarity to (R)-specific enoyl-CoA hydratase, the peroxisomal...; Region: FkbR2; cd03451 323098006250 putative active site [active] 323098006251 putative catalytic site [active] 323098006252 Uncharacterized protein conserved in bacteria (DUF2218); Region: DUF2218; cl01424 323098006253 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 323098006254 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 323098006255 N-terminal plug; other site 323098006256 ligand-binding site [chemical binding]; other site 323098006257 putative acetyltransferase YhhY; Provisional; Region: PRK10140 323098006258 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 323098006259 Coenzyme A binding pocket [chemical binding]; other site 323098006260 Secretin and TonB N terminus short domain; Region: STN; cl06624 323098006261 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 323098006262 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 323098006263 N-terminal plug; other site 323098006264 ligand-binding site [chemical binding]; other site 323098006265 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 323098006266 FecR protein; Region: FecR; pfam04773 323098006267 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 323098006268 A predicted NlpC/p60-like peptidase; Region: BtrH; pfam14399 323098006269 acyl-CoA synthetase; Validated; Region: PRK08308 323098006270 AMP-binding enzyme; Region: AMP-binding; cl15778 323098006271 IucA / IucC family; Region: IucA_IucC; pfam04183 323098006272 Ferric iron reductase FhuF-like transporter; Region: FhuF; pfam06276 323098006273 Siderophore synthetase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: RhbC; COG4264 323098006274 IucA / IucC family; Region: IucA_IucC; pfam04183 323098006275 Ferric iron reductase FhuF-like transporter; Region: FhuF; pfam06276 323098006276 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 323098006277 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 323098006278 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 323098006279 DNA binding residues [nucleotide binding] 323098006280 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 323098006281 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 323098006282 Gram-negative bacterial tonB protein; Region: TonB; cl10048 323098006283 Glucoamylase and related glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: SGA1; COG3387 323098006284 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 323098006285 short chain dehydrogenase; Provisional; Region: PRK07109 323098006286 classical (c) SDR, subgroup 3; Region: SDR_c3; cd05360 323098006287 putative NAD(P) binding site [chemical binding]; other site 323098006288 active site 323098006289 Cytochrome c oxidase caa3 assembly factor (Caa3_CtaG); Region: Caa3_CtaG; cl09173 323098006290 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 323098006291 cytochrome c oxidase, subunit II; Region: CoxB; TIGR02866 323098006292 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 323098006293 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 323098006294 Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons...; Region: Ubiquinol_Oxidase_I; cd01662 323098006295 D-pathway; other site 323098006296 Putative ubiquinol binding site [chemical binding]; other site 323098006297 Low-spin heme (heme b) binding site [chemical binding]; other site 323098006298 Putative water exit pathway; other site 323098006299 Binuclear center (heme o3/CuB) [ion binding]; other site 323098006300 K-pathway; other site 323098006301 Putative proton exit pathway; other site 323098006302 Heme-copper oxidase subunit III. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane. The...; Region: Heme_Cu_Oxidase_III_like; cl00211 323098006303 Subunit I/III interface [polypeptide binding]; other site 323098006304 Predicted membrane protein (DUF2231); Region: DUF2231; cl01730 323098006305 Protein of unknown function (DUF2946); Region: DUF2946; pfam11162 323098006306 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 323098006307 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 323098006308 N-terminal plug; other site 323098006309 ligand-binding site [chemical binding]; other site 323098006310 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 323098006311 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 323098006312 Peptidase propeptide and YPEB domain; Region: PepSY; cl15815 323098006313 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 323098006314 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 323098006315 N-Dimethylarginine dimethylaminohydrolase [Amino acid transport and metabolism]; Region: COG1834 323098006316 Amidinotransferase; Region: Amidinotransf; cl12043 323098006317 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 323098006318 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 323098006319 Walker A/P-loop; other site 323098006320 ATP binding site [chemical binding]; other site 323098006321 Q-loop/lid; other site 323098006322 ABC transporter signature motif; other site 323098006323 Walker B; other site 323098006324 D-loop; other site 323098006325 H-loop/switch region; other site 323098006326 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 323098006327 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 323098006328 ABC-ATPase subunit interface; other site 323098006329 dimer interface [polypeptide binding]; other site 323098006330 putative PBP binding regions; other site 323098006331 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 323098006332 intersubunit interface [polypeptide binding]; other site 323098006333 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 323098006334 Haem utilisation ChuX/HutX; Region: ChuX_HutX; cl01509 323098006335 hypothetical protein; Provisional; Region: PRK06185 323098006336 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098006337 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098006338 Helix-turn-helix domains; Region: HTH; cl00088 323098006339 Winged helix-turn helix; Region: HTH_29; pfam13551 323098006340 Helix-turn-helix domains; Region: HTH; cl00088 323098006341 Integrase core domain; Region: rve; cl01316 323098006342 Integrase core domain; Region: rve_3; cl15866 323098006343 Helix-turn-helix domains; Region: HTH; cl00088 323098006344 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 323098006345 Protein of unknown function (DUF3489); Region: DUF3489; pfam11994 323098006346 Protein of unknown function (DUF2924); Region: DUF2924; pfam11149 323098006347 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 323098006348 catalytic residues [active] 323098006349 catalytic nucleophile [active] 323098006350 Presynaptic Site I dimer interface [polypeptide binding]; other site 323098006351 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 323098006352 Synaptic Flat tetramer interface [polypeptide binding]; other site 323098006353 Synaptic Site I dimer interface [polypeptide binding]; other site 323098006354 DNA binding site [nucleotide binding] 323098006355 Recombinase; Region: Recombinase; pfam07508 323098006356 2-isopropylmalate synthase; Validated; Region: PRK00915 323098006357 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 323098006358 active site 323098006359 catalytic residues [active] 323098006360 metal binding site [ion binding]; metal-binding site 323098006361 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 323098006362 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098006363 sulfate ABC transporter, ATP-binding protein; Region: 3a0106s01; TIGR00968 323098006364 Walker A/P-loop; other site 323098006365 ATP binding site [chemical binding]; other site 323098006366 Q-loop/lid; other site 323098006367 ABC transporter signature motif; other site 323098006368 Walker B; other site 323098006369 D-loop; other site 323098006370 H-loop/switch region; other site 323098006371 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 323098006372 dimer interface [polypeptide binding]; other site 323098006373 conserved gate region; other site 323098006374 putative PBP binding loops; other site 323098006375 ABC-ATPase subunit interface; other site 323098006376 NMT1-like family; Region: NMT1_2; cl15260 323098006377 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 323098006378 ketol-acid reductoisomerase; Provisional; Region: PRK05479 323098006379 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098006380 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 323098006381 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 323098006382 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 323098006383 putative valine binding site [chemical binding]; other site 323098006384 dimer interface [polypeptide binding]; other site 323098006385 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 323098006386 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK09107 323098006387 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 323098006388 PYR/PP interface [polypeptide binding]; other site 323098006389 dimer interface [polypeptide binding]; other site 323098006390 TPP binding site [chemical binding]; other site 323098006391 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 323098006392 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 323098006393 TPP-binding site [chemical binding]; other site 323098006394 dimer interface [polypeptide binding]; other site 323098006395 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 323098006396 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098006397 phosphoserine phosphatase SerB; Region: serB; TIGR00338 323098006398 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 323098006399 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 323098006400 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 323098006401 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 323098006402 protein binding site [polypeptide binding]; other site 323098006403 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 323098006404 protein binding site [polypeptide binding]; other site 323098006405 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; cl01275 323098006406 FtsH protease regulator HflC; Provisional; Region: PRK11029 323098006407 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 323098006408 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 323098006409 HflK protein; Region: hflK; TIGR01933 323098006410 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 323098006411 folate binding site [chemical binding]; other site 323098006412 NADP+ binding site [chemical binding]; other site 323098006413 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 323098006414 dimerization interface [polypeptide binding]; other site 323098006415 active site 323098006416 Stringent starvation protein B; Region: SspB; cl01120 323098006417 fumarate hydratase; Reviewed; Region: fumC; PRK00485 323098006418 Class II fumarases; Region: Fumarase_classII; cd01362 323098006419 active site 323098006420 tetramer interface [polypeptide binding]; other site 323098006421 Domain of unknown function (DUF4169); Region: DUF4169; pfam13770 323098006422 Ribbon-helix-helix domain; Region: RHH_4; cl01775 323098006423 Ribbon-helix-helix domain; Region: RHH_4; cl01775 323098006424 Helix-turn-helix domains; Region: HTH; cl00088 323098006425 Helix-turn-helix domains; Region: HTH; cl00088 323098006426 Winged helix-turn helix; Region: HTH_29; pfam13551 323098006427 Helix-turn-helix domains; Region: HTH; cl00088 323098006428 Integrase core domain; Region: rve; cl01316 323098006429 Integrase core domain; Region: rve_3; cl15866 323098006430 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 323098006431 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098006432 Family description; Region: UvrD_C_2; cl15862 323098006433 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 323098006434 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 323098006435 Walker A/P-loop; other site 323098006436 ATP binding site [chemical binding]; other site 323098006437 Q-loop/lid; other site 323098006438 ABC transporter signature motif; other site 323098006439 Walker B; other site 323098006440 D-loop; other site 323098006441 H-loop/switch region; other site 323098006442 ABC-2 type transporter; Region: ABC2_membrane; cl11417 323098006443 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 323098006444 Phytoene dehydrogenase and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG1233 323098006445 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098006446 ribosomal protein L11 methyltransferase; Reviewed; Region: prmA; PRK00517 323098006447 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 323098006448 S-adenosylmethionine binding site [chemical binding]; other site 323098006449 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 323098006450 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 323098006451 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 323098006452 active site 323098006453 Integrase core domain; Region: rve; cl01316 323098006454 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098006455 Winged helix-turn helix; Region: HTH_29; pfam13551 323098006456 Helix-turn-helix domains; Region: HTH; cl00088 323098006457 Helix-turn-helix domains; Region: HTH; cl00088 323098006458 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 323098006459 DNA-binding site [nucleotide binding]; DNA binding site 323098006460 RNA-binding motif; other site 323098006461 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 323098006462 S-adenosyl-L-homocysteine hydrolase (AdoHycase) catalyzes the hydrolysis of S-adenosyl-L-homocysteine (AdoHyc) to form adenosine (Ado) and homocysteine (Hcy). The equilibrium lies far on the side of AdoHyc synthesis, but in nature the removal of Ado and...; Region: AdoHcyase; cd00401 323098006463 oligomerization interface [polypeptide binding]; other site 323098006464 active site 323098006465 NAD+ binding site [chemical binding]; other site 323098006466 S-adenosylmethionine synthetase; Validated; Region: PRK05250 323098006467 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 323098006468 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 323098006469 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 323098006470 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 323098006471 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098006472 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 323098006473 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098006474 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 323098006475 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 323098006476 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 323098006477 putative active site [active] 323098006478 putative substrate binding site [chemical binding]; other site 323098006479 putative cosubstrate binding site; other site 323098006480 catalytic site [active] 323098006481 The members of this subfamily catalyze the formation of a phosphodiester bond between a membrane-associated undecaprenyl-phosphate (Und-P) molecule and N-acetylhexosamine 1-phosphate, which is usually donated by a soluble UDP-N-acetylhexosamine precursor; Region: GT_WbpL_WbcO_like; cd06854 323098006482 Mg++ binding site [ion binding]; other site 323098006483 putative catalytic motif [active] 323098006484 putative substrate binding site [chemical binding]; other site 323098006485 GDP-fucose synthetase, extended (e) SDRs; Region: GDP_FS_SDR_e; cd05239 323098006486 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 323098006487 NADP binding site [chemical binding]; other site 323098006488 active site 323098006489 putative substrate binding site [chemical binding]; other site 323098006490 GDP-mannose 4,6-dehydratase; Region: gmd; TIGR01472 323098006491 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 323098006492 NADP-binding site; other site 323098006493 homotetramer interface [polypeptide binding]; other site 323098006494 substrate binding site [chemical binding]; other site 323098006495 homodimer interface [polypeptide binding]; other site 323098006496 active site 323098006497 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 323098006498 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 323098006499 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 323098006500 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098006501 NAD(P) binding site [chemical binding]; other site 323098006502 active site 323098006503 Glutamate-1-semialdehyde aminotransferase [Coenzyme metabolism]; Region: HemL; COG0001 323098006504 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 323098006505 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 323098006506 catalytic residue [active] 323098006507 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 323098006508 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 323098006509 substrate binding site [chemical binding]; other site 323098006510 glutamase interaction surface [polypeptide binding]; other site 323098006511 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13141 323098006512 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 323098006513 putative active site [active] 323098006514 oxyanion strand; other site 323098006515 catalytic triad [active] 323098006516 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_III; cd01996 323098006517 Ligand Binding Site [chemical binding]; other site 323098006518 flagellin modification protein A; Provisional; Region: PRK09186 323098006519 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098006520 NAD(P) binding site [chemical binding]; other site 323098006521 active site 323098006522 FOG: CBS domain [General function prediction only]; Region: COG0517 323098006523 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain associated with the NTP (Nucleotidyl transferase) domain downstream. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently...; Region: CBS_pair_NTP_transferase_assoc; cd04607 323098006524 NTP_trnasferase_like_2 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_2; cd06426 323098006525 Substrate binding site; other site 323098006526 metal-binding site 323098006527 Putative Acyltransferase (AT), Left-handed parallel beta-Helix (LbH) domain; This group is composed of mostly uncharacterized proteins containing an N-terminal helical subdomain followed by a LbH domain. The alignment contains 6 turns, each containing...; Region: LbH_AT_putative; cd03360 323098006528 putative trimer interface [polypeptide binding]; other site 323098006529 putative CoA binding site [chemical binding]; other site 323098006530 N-acetylneuraminate synthase; Region: NeuB_NnaB; TIGR03569 323098006531 NeuB family; Region: NeuB; cl00496 323098006532 SAF domain; Region: SAF; cl00555 323098006533 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 323098006534 ligand binding site; other site 323098006535 tetramer interface; other site 323098006536 UDP-N-acetyl-D-glucosamine 2-epimerase, UDP-hydrolysing; Region: NeuC_NnaA; TIGR03568 323098006537 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 323098006538 active site 323098006539 homodimer interface [polypeptide binding]; other site 323098006540 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098006541 extended (e) SDRs; Region: SDR_e; cd08946 323098006542 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 323098006543 NAD(P) binding site [chemical binding]; other site 323098006544 active site 323098006545 substrate binding site [chemical binding]; other site 323098006546 aminotransferase, LLPSF_NHT_00031 family; Region: NHT_00031; TIGR04181 323098006547 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 323098006548 inhibitor-cofactor binding pocket; inhibition site 323098006549 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098006550 catalytic residue [active] 323098006551 Arna decarboxylase_like, extended (e) SDRs; Region: Arna_like_SDR_e; cd05257 323098006552 NAD dependent epimerase/dehydratase, LLPSF_EDH_00030 family; Region: EDH_00030; TIGR04180 323098006553 NAD binding site [chemical binding]; other site 323098006554 substrate binding site [chemical binding]; other site 323098006555 active site 323098006556 Helix-turn-helix domains; Region: HTH; cl00088 323098006557 putative transposase OrfB; Reviewed; Region: PHA02517 323098006558 Helix-turn-helix domains; Region: HTH; cl00088 323098006559 Integrase core domain; Region: rve; cl01316 323098006560 Integrase core domain; Region: rve_3; cl15866 323098006561 Helix-turn-helix domains; Region: HTH; cl00088 323098006562 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 323098006563 S-adenosylmethionine binding site [chemical binding]; other site 323098006564 O-Antigen ligase; Region: Wzy_C; cl04850 323098006565 Integrase core domain; Region: rve; cl01316 323098006566 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098006567 Transposase domain (DUF772); Region: DUF772; cl15789 323098006568 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 323098006569 Alanine-glyoxylate aminotransferase (AGAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to alanine-glyoxylate aminotransferase (AGAT); Region: AGAT_like; cd06451 323098006570 homodimer interface [polypeptide binding]; other site 323098006571 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098006572 catalytic residue [active] 323098006573 HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life; Region: HINT_subgroup; cd01277 323098006574 HIT family signature motif; other site 323098006575 catalytic residue [active] 323098006576 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 323098006577 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 323098006578 ligand binding site [chemical binding]; other site 323098006579 flexible hinge region; other site 323098006580 Helix-turn-helix domains; Region: HTH; cl00088 323098006581 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK05964 323098006582 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 323098006583 inhibitor-cofactor binding pocket; inhibition site 323098006584 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098006585 catalytic residue [active] 323098006586 AAA domain; Region: AAA_26; pfam13500 323098006587 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098006588 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 323098006589 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 323098006590 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 323098006591 catalytic residue [active] 323098006592 Stress responsive A/B Barrel Domain; Region: Dabb; cl15807 323098006593 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 323098006594 Quinolinate synthetase A protein; Region: NadA; cl00420 323098006595 L-aspartate oxidase; Provisional; Region: PRK07512 323098006596 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098006597 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 323098006598 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK06106 323098006599 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 323098006600 dimerization interface [polypeptide binding]; other site 323098006601 active site 323098006602 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 323098006603 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 323098006604 metal binding site [ion binding]; metal-binding site 323098006605 active site 323098006606 I-site; other site 323098006607 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 323098006608 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 323098006609 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 323098006610 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 323098006611 DNA binding residues [nucleotide binding] 323098006612 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 323098006613 pseudouridine synthase, RluA family; Region: rluA_subfam; TIGR00005 323098006614 RNA binding surface [nucleotide binding]; other site 323098006615 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 323098006616 active site 323098006617 Helix-turn-helix domains; Region: HTH; cl00088 323098006618 putative transposase OrfB; Reviewed; Region: PHA02517 323098006619 Helix-turn-helix domains; Region: HTH; cl00088 323098006620 Integrase core domain; Region: rve; cl01316 323098006621 Integrase core domain; Region: rve_3; cl15866 323098006622 Helix-turn-helix domains; Region: HTH; cl00088 323098006623 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 323098006624 Integrase core domain; Region: rve; cl01316 323098006625 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098006626 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 323098006627 lytic murein transglycosylase; Region: MltB_2; TIGR02283 323098006628 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 323098006629 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 323098006630 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 323098006631 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 323098006632 RNA polymerase sigma factor RpoD, C-terminal domain; Region: RpoD_Cterm; TIGR02393 323098006633 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 323098006634 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 323098006635 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 323098006636 DNA binding residues [nucleotide binding] 323098006637 DNA primase, catalytic core; Region: dnaG; TIGR01391 323098006638 CHC2 zinc finger; Region: zf-CHC2; cl15369 323098006639 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 323098006640 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 323098006641 active site 323098006642 metal binding site [ion binding]; metal-binding site 323098006643 interdomain interaction site; other site 323098006644 Chlorite dismutase; Region: Chlor_dismutase; cl01280 323098006645 N-formylglutamate amidohydrolase; Region: FGase; cl01522 323098006646 GatB domain; Region: GatB_Yqey; cl11497 323098006647 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 323098006648 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; cl03056 323098006649 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 323098006650 catalytic site [active] 323098006651 subunit interface [polypeptide binding]; other site 323098006652 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 323098006653 Ferritin-like domain; Region: Ferritin; pfam00210 323098006654 dimerization interface [polypeptide binding]; other site 323098006655 DPS ferroxidase diiron center [ion binding]; other site 323098006656 ion pore; other site 323098006657 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 323098006658 S-adenosylmethionine binding site [chemical binding]; other site 323098006659 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 323098006660 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 323098006661 ATP-grasp domain; Region: ATP-grasp_4; cl03087 323098006662 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 323098006663 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 323098006664 ATP-grasp domain; Region: ATP-grasp_4; cl03087 323098006665 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 323098006666 IMP binding site; other site 323098006667 dimer interface [polypeptide binding]; other site 323098006668 interdomain contacts; other site 323098006669 partial ornithine binding site; other site 323098006670 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 323098006671 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 323098006672 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 323098006673 DoxX; Region: DoxX; cl00976 323098006674 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 323098006675 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 323098006676 putative DNA binding site [nucleotide binding]; other site 323098006677 putative Zn2+ binding site [ion binding]; other site 323098006678 Helix-turn-helix domains; Region: HTH; cl00088 323098006679 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 323098006680 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 323098006681 Transcriptional regulator [Transcription]; Region: LysR; COG0583 323098006682 Helix-turn-helix domains; Region: HTH; cl00088 323098006683 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 323098006684 putative effector binding pocket; other site 323098006685 dimerization interface [polypeptide binding]; other site 323098006686 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 323098006687 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 323098006688 P-loop; other site 323098006689 Magnesium ion binding site [ion binding]; other site 323098006690 Extensin-like protein C-terminus; Region: Extensin-like_C; pfam06904 323098006691 Domain of unknown function (DUF4403); Region: DUF4403; pfam14356 323098006692 Dodecin; Region: Dodecin; cl01328 323098006693 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 323098006694 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 323098006695 N-acetyl-D-glucosamine binding site [chemical binding]; other site 323098006696 catalytic residue [active] 323098006697 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 323098006698 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 323098006699 thiS-thiF/thiG interaction site; other site 323098006700 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 323098006701 ThiS interaction site; other site 323098006702 putative active site [active] 323098006703 tetramer interface [polypeptide binding]; other site 323098006704 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 323098006705 active site 323098006706 thiamine phosphate binding site [chemical binding]; other site 323098006707 pyrophosphate binding site [ion binding]; other site 323098006708 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 323098006709 ThiC-associated domain; Region: ThiC-associated; pfam13667 323098006710 ThiC family; Region: ThiC; cl08031 323098006711 Protein of unknown function (DUF3829); Region: DUF3829; pfam12889 323098006712 Helix-turn-helix domains; Region: HTH; cl00088 323098006713 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 323098006714 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 323098006715 Transposase domain (DUF772); Region: DUF772; cl15789 323098006716 Transposase domain (DUF772); Region: DUF772; cl15789 323098006717 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 323098006718 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 323098006719 heme binding site [chemical binding]; other site 323098006720 ferroxidase pore; other site 323098006721 ferroxidase diiron center [ion binding]; other site 323098006722 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 323098006723 lytic murein transglycosylase; Region: MltB_2; TIGR02283 323098006724 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 323098006725 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 323098006726 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 323098006727 Trans-aconitate methyltransferase [General function prediction only]; Region: Tam; COG4106 323098006728 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 323098006729 S-adenosylmethionine binding site [chemical binding]; other site 323098006730 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 323098006731 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 323098006732 Protein of unknown function (DUF497); Region: DUF497; cl01108 323098006733 Protein of unknown function (DUF3680); Region: DUF3680; cl02189 323098006734 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 323098006735 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098006736 Walker A/P-loop; other site 323098006737 ATP binding site [chemical binding]; other site 323098006738 Q-loop/lid; other site 323098006739 ABC transporter signature motif; other site 323098006740 Walker B; other site 323098006741 D-loop; other site 323098006742 H-loop/switch region; other site 323098006743 ABC transporter; Region: ABC_tran_2; pfam12848 323098006744 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 323098006745 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 323098006746 3-mercaptopyruvate sulfurtransferase; Region: PLN02723 323098006747 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 323098006748 active site residue [active] 323098006749 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 323098006750 active site residue [active] 323098006751 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 323098006752 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 323098006753 PAS fold; Region: PAS_7; pfam12860 323098006754 Cysteine-rich CWC; Region: Cys_rich_CWC; pfam14375 323098006755 excinuclease ABC subunit B; Provisional; Region: PRK05298 323098006756 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 323098006757 ATP binding site [chemical binding]; other site 323098006758 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 323098006759 nucleotide binding region [chemical binding]; other site 323098006760 ATP-binding site [chemical binding]; other site 323098006761 Ultra-violet resistance protein B; Region: UvrB; pfam12344 323098006762 UvrB/uvrC motif; Region: UVR; pfam02151 323098006763 Transposase domain (DUF772); Region: DUF772; cl15789 323098006764 Transposase domain (DUF772); Region: DUF772; cl15789 323098006765 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 323098006766 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 323098006767 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 323098006768 active site 323098006769 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 323098006770 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 323098006771 Uncharacterized conserved protein [Function unknown]; Region: COG1565 323098006772 Putative S-adenosyl-L-methionine-dependent methyltransferase; Region: Methyltransf_28; pfam02636 323098006773 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 323098006774 Membrane fusogenic activity; Region: BMFP; cl01115 323098006775 YdeM is a Bacillus subtilis protein that belongs to a family of prokaryotic proteins of unkown function. YdeM has sequence similarity to the hot-dog fold of (R)-specific enoyl-CoA hydratase. Other enzymes with this fold include the peroxisomal...; Region: YdeM; cd03454 323098006776 putative active site [active] 323098006777 putative catalytic site [active] 323098006778 YdeM is a Bacillus subtilis protein that belongs to a family of prokaryotic proteins of unkown function. YdeM has sequence similarity to the hot-dog fold of (R)-specific enoyl-CoA hydratase. Other enzymes with this fold include the peroxisomal...; Region: YdeM; cd03454 323098006779 putative active site [active] 323098006780 putative catalytic site [active] 323098006781 Domain of unknown function (DUF4282); Region: DUF4282; pfam14110 323098006782 GTP-binding protein YchF; Reviewed; Region: PRK09601 323098006783 YchF GTPase; Region: YchF; cd01900 323098006784 G1 box; other site 323098006785 GTP/Mg2+ binding site [chemical binding]; other site 323098006786 Switch I region; other site 323098006787 G2 box; other site 323098006788 Switch II region; other site 323098006789 G3 box; other site 323098006790 G4 box; other site 323098006791 G5 box; other site 323098006792 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 323098006793 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 323098006794 putative active site [active] 323098006795 catalytic residue [active] 323098006796 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 323098006797 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 323098006798 5S rRNA interface [nucleotide binding]; other site 323098006799 CTC domain interface [polypeptide binding]; other site 323098006800 L16 interface [polypeptide binding]; other site 323098006801 Putative bacterial sensory transduction regulator; Region: YbjN; cl15834 323098006802 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 323098006803 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098006804 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 323098006805 NAD+-dependent alpha-aminoadipic semialdehyde dehydrogenase, ALDH family members 7A1 and 7B; Region: ALDH_F7_AASADH; cd07130 323098006806 tetrameric interface [polypeptide binding]; other site 323098006807 NAD binding site [chemical binding]; other site 323098006808 catalytic residues [active] 323098006809 ornithine--oxo-acid transaminase; Provisional; Region: rocD; PRK04073 323098006810 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 323098006811 inhibitor-cofactor binding pocket; inhibition site 323098006812 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098006813 catalytic residue [active] 323098006814 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 323098006815 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 323098006816 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 323098006817 ATP binding site [chemical binding]; other site 323098006818 Mg2+ binding site [ion binding]; other site 323098006819 G-X-G motif; other site 323098006820 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 323098006821 active site 323098006822 phosphorylation site [posttranslational modification] 323098006823 intermolecular recognition site; other site 323098006824 dimerization interface [polypeptide binding]; other site 323098006825 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 323098006826 DNA binding site [nucleotide binding] 323098006827 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 323098006828 Helix-turn-helix domains; Region: HTH; cl00088 323098006829 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 323098006830 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 323098006831 homodimer interface [polypeptide binding]; other site 323098006832 substrate-cofactor binding pocket; other site 323098006833 catalytic residue [active] 323098006834 multidrug efflux protein; Reviewed; Region: PRK01766 323098006835 MatE; Region: MatE; cl10513 323098006836 MatE; Region: MatE; cl10513 323098006837 HemK family putative methylases; Region: hemK_fam; TIGR00536 323098006838 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 323098006839 S-adenosylmethionine binding site [chemical binding]; other site 323098006840 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 323098006841 MoaE homodimer interface [polypeptide binding]; other site 323098006842 MoaD interaction [polypeptide binding]; other site 323098006843 active site residues [active] 323098006844 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 323098006845 MoaE interaction surface [polypeptide binding]; other site 323098006846 MoeB interaction surface [polypeptide binding]; other site 323098006847 thiocarboxylated glycine; other site 323098006848 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 323098006849 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 323098006850 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 323098006851 GIY-YIG motif/motif A; other site 323098006852 active site 323098006853 catalytic site [active] 323098006854 putative DNA binding site [nucleotide binding]; other site 323098006855 metal binding site [ion binding]; metal-binding site 323098006856 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 323098006857 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 323098006858 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 323098006859 Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far. This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases). Plant T2 RNases are expressed during leaf...; Region: RNase_T2_prok; cd01062 323098006860 B1 nucleotide binding pocket [chemical binding]; other site 323098006861 B2 nucleotide binding pocket [chemical binding]; other site 323098006862 CAS motifs; other site 323098006863 active site 323098006864 Protein of unknown function (DUF3617); Region: DUF3617; pfam12276 323098006865 histidyl-tRNA synthetase; Region: hisS; TIGR00442 323098006866 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 323098006867 dimer interface [polypeptide binding]; other site 323098006868 motif 1; other site 323098006869 motif 2; other site 323098006870 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 323098006871 active site 323098006872 motif 3; other site 323098006873 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 323098006874 anticodon binding site; other site 323098006875 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 323098006876 putative active site [active] 323098006877 Predicted membrane protein [Function unknown]; Region: COG4655 323098006878 TadE-like protein; Region: TadE; cl10688 323098006879 Putative Tad-like Flp pilus-assembly; Region: Tad_C; pfam09977 323098006880 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 323098006881 TadE-like protein; Region: TadE; cl10688 323098006882 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 323098006883 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 323098006884 inhibitor-cofactor binding pocket; inhibition site 323098006885 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098006886 catalytic residue [active] 323098006887 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 323098006888 Predicted sugar phosphatases of the HAD superfamily [Carbohydrate transport and metabolism]; Region: NagD; COG0647 323098006889 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 323098006890 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 323098006891 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 323098006892 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 323098006893 active site 323098006894 phosphorylation site [posttranslational modification] 323098006895 intermolecular recognition site; other site 323098006896 dimerization interface [polypeptide binding]; other site 323098006897 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 323098006898 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 323098006899 active site 323098006900 Riboflavin kinase; Region: Flavokinase; cl03312 323098006901 isoleucyl-tRNA synthetase; Provisional; Region: ileS; PRK13804 323098006902 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 323098006903 active site 323098006904 HIGH motif; other site 323098006905 nucleotide binding site [chemical binding]; other site 323098006906 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 323098006907 active site 323098006908 KMSKS motif; other site 323098006909 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 323098006910 tRNA binding surface [nucleotide binding]; other site 323098006911 anticodon binding site; other site 323098006912 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 323098006913 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 323098006914 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 323098006915 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 323098006916 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 323098006917 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 323098006918 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 323098006919 RF-1 domain; Region: RF-1; cl02875 323098006920 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 323098006921 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 323098006922 MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is...; Region: MutL_Trans; cd00782 323098006923 ATP binding site [chemical binding]; other site 323098006924 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 323098006925 Methyltransferase domain; Region: Methyltransf_31; pfam13847 323098006926 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 323098006927 S-adenosylmethionine binding site [chemical binding]; other site 323098006928 104 kDa microneme/rhoptry antigen; Provisional; Region: PTZ00449 323098006929 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 323098006930 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 323098006931 RNA binding surface [nucleotide binding]; other site 323098006932 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 323098006933 active site 323098006934 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 323098006935 nucleoside/Zn binding site; other site 323098006936 dimer interface [polypeptide binding]; other site 323098006937 catalytic motif [active] 323098006938 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 323098006939 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 323098006940 ATP-grasp domain; Region: ATP-grasp_4; cl03087 323098006941 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 323098006942 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 323098006943 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 323098006944 generic binding surface II; other site 323098006945 generic binding surface I; other site 323098006946 Uncharacterized protein conserved in bacteria (DUF2093); Region: DUF2093; cl11535 323098006947 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 323098006948 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 323098006949 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 323098006950 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 323098006951 putative acyl-acceptor binding pocket; other site 323098006952 Domain of unknown function (DUF4170); Region: DUF4170; pfam13773 323098006953 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in cysteine...; Region: CysQ; cd01638 323098006954 active site 323098006955 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 323098006956 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 323098006957 UbiA prenyltransferase family; Region: UbiA; cl00337 323098006958 alpha-ketoglutarate decarboxylase; Reviewed; Region: kgd; PRK12270 323098006959 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385; cl00611 323098006960 RNA methyltransferase; Region: Methyltrans_RNA; pfam04452 323098006961 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: hisZ; PRK12295 323098006962 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 323098006963 dimer interface [polypeptide binding]; other site 323098006964 motif 1; other site 323098006965 motif 2; other site 323098006966 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 323098006967 active site 323098006968 motif 3; other site 323098006969 ATP phosphoribosyltransferase; Reviewed; Region: hisG; PRK00489 323098006970 ATP phosphoribosyltransferase; Region: HisG; cl15266 323098006971 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 323098006972 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 323098006973 Ligand binding site; other site 323098006974 Putative Catalytic site; other site 323098006975 DXD motif; other site 323098006976 YdjC-like protein; Region: YdjC; cl01344 323098006977 Uncharacterized protein conserved in bacteria (DUF2076); Region: DUF2076; cl01353 323098006978 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 323098006979 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 323098006980 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 323098006981 oligomerisation interface [polypeptide binding]; other site 323098006982 mobile loop; other site 323098006983 roof hairpin; other site 323098006984 chaperonin GroEL; Reviewed; Region: groEL; PRK12852 323098006985 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 323098006986 ring oligomerisation interface [polypeptide binding]; other site 323098006987 ATP/Mg binding site [chemical binding]; other site 323098006988 stacking interactions; other site 323098006989 hinge regions; other site 323098006990 META domain; Region: META; cl01245 323098006991 glycolate oxidase iron-sulfur subunit; Provisional; Region: glcF; PRK11274 323098006992 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 323098006993 Cysteine-rich domain; Region: CCG; pfam02754 323098006994 Cysteine-rich domain; Region: CCG; pfam02754 323098006995 glycolate oxidase FAD binding subunit; Provisional; Region: glcE; PRK11282 323098006996 FAD binding domain; Region: FAD_binding_4; pfam01565 323098006997 glycolate oxidase subunit GlcD; Provisional; Region: PRK11230 323098006998 FAD binding domain; Region: FAD_binding_4; pfam01565 323098006999 Cytochrome c; Region: Cytochrom_C; cl11414 323098007000 Helix-turn-helix domains; Region: HTH; cl00088 323098007001 Protein of unknown function (DUF1236); Region: DUF1236; pfam06823 323098007002 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 323098007003 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 323098007004 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 323098007005 dimer interface [polypeptide binding]; other site 323098007006 motif 1; other site 323098007007 active site 323098007008 motif 2; other site 323098007009 motif 3; other site 323098007010 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 323098007011 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 323098007012 tandem repeat interface [polypeptide binding]; other site 323098007013 oligomer interface [polypeptide binding]; other site 323098007014 active site residues [active] 323098007015 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 323098007016 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 323098007017 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 323098007018 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 323098007019 substrate binding pocket [chemical binding]; other site 323098007020 chain length determination region; other site 323098007021 substrate-Mg2+ binding site; other site 323098007022 catalytic residues [active] 323098007023 aspartate-rich region 1; other site 323098007024 active site lid residues [active] 323098007025 aspartate-rich region 2; other site 323098007026 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK14608 323098007027 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 323098007028 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 323098007029 binding surface 323098007030 TPR motif; other site 323098007031 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]; Region: COG2956 323098007032 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 323098007033 binding surface 323098007034 TPR motif; other site 323098007035 TPR repeat; Region: TPR_11; pfam13414 323098007036 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 323098007037 binding surface 323098007038 TPR motif; other site 323098007039 TPR repeat; Region: TPR_11; pfam13414 323098007040 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 323098007041 binding surface 323098007042 TPR motif; other site 323098007043 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098007044 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 323098007045 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 323098007046 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 323098007047 Fe-S cluster binding site [ion binding]; other site 323098007048 active site 323098007049 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl15769 323098007050 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 323098007051 RNA/DNA hybrid binding site [nucleotide binding]; other site 323098007052 active site 323098007053 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 323098007054 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 323098007055 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 323098007056 FeS/SAM binding site; other site 323098007057 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 323098007058 MPT binding site; other site 323098007059 trimer interface [polypeptide binding]; other site 323098007060 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; cl00988 323098007061 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 323098007062 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098007063 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 323098007064 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 323098007065 C-terminal domain interface [polypeptide binding]; other site 323098007066 GSH binding site (G-site) [chemical binding]; other site 323098007067 dimer interface [polypeptide binding]; other site 323098007068 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 323098007069 N-terminal domain interface [polypeptide binding]; other site 323098007070 dimer interface [polypeptide binding]; other site 323098007071 substrate binding pocket (H-site) [chemical binding]; other site 323098007072 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 323098007073 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 323098007074 minor groove reading motif; other site 323098007075 helix-hairpin-helix signature motif; other site 323098007076 active site 323098007077 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 323098007078 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 323098007079 DNA binding and oxoG recognition site [nucleotide binding] 323098007080 Protein of unknown function (DUF721); Region: DUF721; cl02324 323098007081 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 323098007082 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 323098007083 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 323098007084 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large; Region: ABC_SMC_barmotin; cd03278 323098007085 Walker A/P-loop; other site 323098007086 ATP binding site [chemical binding]; other site 323098007087 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; cl05797 323098007088 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 323098007089 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large; Region: ABC_SMC_barmotin; cd03278 323098007090 ABC transporter signature motif; other site 323098007091 Walker B; other site 323098007092 D-loop; other site 323098007093 H-loop/switch region; other site 323098007094 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098007095 Protein of unknown function (DUF454); Region: DUF454; cl01063 323098007096 LemA family; Region: LemA; cl00742 323098007097 Peptidase family M48; Region: Peptidase_M48; cl12018 323098007098 Adenine/guanine phosphoribosyltransferases and related PRPP-binding proteins [Nucleotide transport and metabolism]; Region: Apt; COG0503 323098007099 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 323098007100 active site 323098007101 anthranilate synthase; Provisional; Region: PRK13566 323098007102 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 323098007103 chorismate binding enzyme; Region: Chorismate_bind; cl10555 323098007104 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 323098007105 glutamine binding [chemical binding]; other site 323098007106 catalytic triad [active] 323098007107 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 323098007108 substrate binding site [chemical binding]; other site 323098007109 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 323098007110 cytochrome b; Provisional; Region: CYTB; MTH00156 323098007111 Qi binding site; other site 323098007112 intrachain domain interface; other site 323098007113 interchain domain interface [polypeptide binding]; other site 323098007114 heme bH binding site [chemical binding]; other site 323098007115 heme bL binding site [chemical binding]; other site 323098007116 Qo binding site; other site 323098007117 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 323098007118 interchain domain interface [polypeptide binding]; other site 323098007119 intrachain domain interface; other site 323098007120 Qi binding site; other site 323098007121 Qo binding site; other site 323098007122 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 323098007123 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 323098007124 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 323098007125 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 323098007126 [2Fe-2S] cluster binding site [ion binding]; other site 323098007127 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 323098007128 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 323098007129 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 323098007130 FeS/SAM binding site; other site 323098007131 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 323098007132 active site 323098007133 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl00433 323098007134 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 323098007135 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 323098007136 active site 323098007137 NTP binding site [chemical binding]; other site 323098007138 metal binding triad [ion binding]; metal-binding site 323098007139 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 323098007140 putative active site [active] 323098007141 putative CoA binding site [chemical binding]; other site 323098007142 nudix motif; other site 323098007143 metal binding site [ion binding]; metal-binding site 323098007144 Protein of unknown function (DUF1285); Region: DUF1285; cl01571 323098007145 MoxR-like ATPases [General function prediction only]; Region: COG0714 323098007146 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098007147 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 323098007148 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 323098007149 A4 beta-galactosidase middle domain: a type 1 glutamine amidotransferase (GATase1)-like domain; Region: A4_beta-galactosidase_middle_domain; cd03143 323098007150 Domain of unknown function (DUF4159); Region: DUF4159; pfam13709 323098007151 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 323098007152 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 323098007153 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; cl00284 323098007154 Predicted acetyltransferase [General function prediction only]; Region: COG3153 323098007155 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 323098007156 Coenzyme A binding pocket [chemical binding]; other site 323098007157 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_21; cd04680 323098007158 nudix motif; other site 323098007159 Predicted phosphohydrolases [General function prediction only]; Region: Icc; COG1409 323098007160 Bacillus subtilis YydB and related proteins, metallophosphatase domain; Region: MPP_YydB; cd07400 323098007161 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 323098007162 Protein of unknown function, DUF486; Region: DUF486; cl01236 323098007163 Protein of unknown function (DUF3297); Region: DUF3297; pfam11730 323098007164 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 323098007165 catalytic residues [active] 323098007166 dimer interface [polypeptide binding]; other site 323098007167 bifunctional transaldolase/phosoglucose isomerase; Validated; Region: PRK09533 323098007168 Transaldolase-like proteins from plants and bacteria; Region: Transaldolase_like; cd00955 323098007169 putative active site [active] 323098007170 catalytic residue [active] 323098007171 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 323098007172 active site 323098007173 dimer interface [polypeptide binding]; other site 323098007174 SIS_TAL_PGI: Transaldolase (TAL)/ Phosphoglucose isomerase (PGI). This group represents the SIS (Sugar ISomerase) PGI domain, of a multifunctional protein (TAL-PGI ) having both TAL and PGI activities. TAL_PGI contains an N-terminal TAL domain and a...; Region: SIS_TAL_PGI; cd05798 323098007175 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098007176 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK12490 323098007177 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 323098007178 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 323098007179 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 323098007180 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 323098007181 putative active site [active] 323098007182 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 323098007183 Gluconate kinase [Carbohydrate transport and metabolism]; Region: GntK; COG3265 323098007184 ATP-binding site [chemical binding]; other site 323098007185 Gluconate-6-phosphate binding site [chemical binding]; other site 323098007186 Glucoamylase and related glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: SGA1; COG3387 323098007187 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 323098007188 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 323098007189 metal binding site [ion binding]; metal-binding site 323098007190 active site 323098007191 I-site; other site 323098007192 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 323098007193 nitrite reductase, copper-containing; Region: Cu_nitrite_red; TIGR02376 323098007194 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 323098007195 Cytochrome c; Region: Cytochrom_C; cl11414 323098007196 Cytochrome c; Region: Cytochrom_C; cl11414 323098007197 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 323098007198 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 323098007199 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 323098007200 TPR motif; other site 323098007201 binding surface 323098007202 Helix-turn-helix domains; Region: HTH; cl00088 323098007203 Rrf2 family protein; Region: rrf2_super; TIGR00738 323098007204 putative monovalent cation/H+ antiporter subunit A; Reviewed; Region: PRK12648 323098007205 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 323098007206 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 323098007207 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 323098007208 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 323098007209 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12666 323098007210 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 323098007211 Na+/H+ ion antiporter subunit; Region: MNHE; cl00807 323098007212 Multiple resistance and pH regulation protein F (MrpF / PhaF); Region: MrpF_PhaF; cl09154 323098007213 Na+/H+ antiporter subunit; Region: PhaG_MnhG_YufB; cl00583 323098007214 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 323098007215 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 323098007216 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 323098007217 short chain dehydrogenase; Provisional; Region: PRK06701 323098007218 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098007219 NAD(P) binding site [chemical binding]; other site 323098007220 active site 323098007221 Isochorismatase family; Region: Isochorismatase; pfam00857 323098007222 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cd00431 323098007223 catalytic triad [active] 323098007224 conserved cis-peptide bond; other site 323098007225 YciF bacterial stress response protein, ferritin-like iron-binding domain; Region: YciF; cd07909 323098007226 dimerization interface [polypeptide binding]; other site 323098007227 metal binding site [ion binding]; metal-binding site 323098007228 Helix-turn-helix domains; Region: HTH; cl00088 323098007229 Winged helix-turn helix; Region: HTH_29; pfam13551 323098007230 Helix-turn-helix domains; Region: HTH; cl00088 323098007231 Integrase core domain; Region: rve; cl01316 323098007232 Integrase core domain; Region: rve_3; cl15866 323098007233 Helix-turn-helix domains; Region: HTH; cl00088 323098007234 Hydroxyneurosporene synthase (CrtC); Region: CrtC; cl12101 323098007235 FtsX-like permease family; Region: FtsX; cl15850 323098007236 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 323098007237 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 323098007238 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 323098007239 Walker A/P-loop; other site 323098007240 ATP binding site [chemical binding]; other site 323098007241 Q-loop/lid; other site 323098007242 ABC transporter signature motif; other site 323098007243 Walker B; other site 323098007244 D-loop; other site 323098007245 H-loop/switch region; other site 323098007246 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 323098007247 Helix-turn-helix domains; Region: HTH; cl00088 323098007248 Helix-turn-helix domains; Region: HTH; cl00088 323098007249 Winged helix-turn helix; Region: HTH_29; pfam13551 323098007250 Helix-turn-helix domains; Region: HTH; cl00088 323098007251 Integrase core domain; Region: rve; cl01316 323098007252 Integrase core domain; Region: rve_3; cl15866 323098007253 Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: ECM4; COG0435 323098007254 C-terminal, alpha helical domain of Class Omega-like Glutathione S-transferases; Region: GST_C_Omega_like; cd03190 323098007255 putative dimer interface [polypeptide binding]; other site 323098007256 N-terminal domain interface [polypeptide binding]; other site 323098007257 putative substrate binding pocket (H-site) [chemical binding]; other site 323098007258 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 323098007259 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 323098007260 NMT1/THI5 like; Region: NMT1; pfam09084 323098007261 cyclic beta-1,2-glucan ABC transporter; Provisional; Region: PRK13657 323098007262 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 323098007263 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098007264 Walker A/P-loop; other site 323098007265 ATP binding site [chemical binding]; other site 323098007266 Q-loop/lid; other site 323098007267 ABC transporter signature motif; other site 323098007268 Walker B; other site 323098007269 D-loop; other site 323098007270 H-loop/switch region; other site 323098007271 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 323098007272 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 323098007273 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 323098007274 Ligand Binding Site [chemical binding]; other site 323098007275 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 323098007276 AMP-binding enzyme; Region: AMP-binding; cl15778 323098007277 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 323098007278 Bacterial protein of unknown function (DUF924); Region: DUF924; cl01561 323098007279 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 323098007280 catalytic triad [active] 323098007281 dimer interface [polypeptide binding]; other site 323098007282 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 323098007283 RNA/DNA hybrid binding site [nucleotide binding]; other site 323098007284 active site 323098007285 Homoserine Kinase, type II. Homoserine kinase 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: HomoserineK_II; cd05153 323098007286 Phosphotransferase enzyme family; Region: APH; pfam01636 323098007287 putative active site [active] 323098007288 putative substrate binding site [chemical binding]; other site 323098007289 ATP binding site [chemical binding]; other site 323098007290 LytB protein; Region: LYTB; cl00507 323098007291 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 323098007292 Protein of unknown function (DUF1013); Region: DUF1013; cl11533 323098007293 hypothetical protein; Provisional; Region: PRK08185 323098007294 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1; Region: TBP_aldolase_IIB; cd00947 323098007295 intersubunit interface [polypeptide binding]; other site 323098007296 active site 323098007297 zinc binding site [ion binding]; other site 323098007298 Na+ binding site [ion binding]; other site 323098007299 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098007300 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 323098007301 metal binding site [ion binding]; metal-binding site 323098007302 active site 323098007303 Helix-turn-helix domains; Region: HTH; cl00088 323098007304 Transcriptional regulator [Transcription]; Region: LysR; COG0583 323098007305 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 323098007306 putative dimerization interface [polypeptide binding]; other site 323098007307 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 323098007308 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 323098007309 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 323098007310 FAD binding domain; Region: FAD_binding_4; pfam01565 323098007311 Uncharacterized ACR, COG2135; Region: DUF159; cl03646 323098007312 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_15; cd04673 323098007313 nudix motif; other site 323098007314 Protein of unknown function (DUF2385); Region: DUF2385; cl11490 323098007315 dihydroorotase; Validated; Region: PRK09060 323098007316 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 323098007317 Dihydroorotase (DHOase), subgroup IIb; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This group contains the archeal members of the DHOase family; Region: DHOase_IIb; cd01318 323098007318 active site 323098007319 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 323098007320 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 323098007321 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 323098007322 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 323098007323 Cell Wall Hydrolase; Region: Hydrolase_2; pfam07486 323098007324 pyruvate phosphate dikinase; Provisional; Region: PRK09279 323098007325 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 323098007326 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 323098007327 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 323098007328 FtsH Extracellular; Region: FtsH_ext; pfam06480 323098007329 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 323098007330 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 323098007331 Walker A motif; other site 323098007332 ATP binding site [chemical binding]; other site 323098007333 Walker B motif; other site 323098007334 arginine finger; other site 323098007335 Peptidase family M41; Region: Peptidase_M41; pfam01434 323098007336 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 323098007337 Ligand Binding Site [chemical binding]; other site 323098007338 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 323098007339 active site 323098007340 metal binding site [ion binding]; metal-binding site 323098007341 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 323098007342 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 323098007343 ligand binding site [chemical binding]; other site 323098007344 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 323098007345 PAS fold; Region: PAS_7; pfam12860 323098007346 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 323098007347 metal binding site [ion binding]; metal-binding site 323098007348 active site 323098007349 I-site; other site 323098007350 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 323098007351 translocation protein TolB; Provisional; Region: tolB; PRK05137 323098007352 TolB amino-terminal domain; Region: TolB_N; cl00639 323098007353 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 323098007354 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 323098007355 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 323098007356 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 323098007357 TolA protein; Region: tolA_full; TIGR02794 323098007358 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 323098007359 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 323098007360 Protein of unknown function (DUF2852); Region: DUF2852; pfam11014 323098007361 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 323098007362 Helix-turn-helix domains; Region: HTH; cl00088 323098007363 WHG domain; Region: WHG; pfam13305 323098007364 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 323098007365 active site 323098007366 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 323098007367 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 323098007368 Walker A motif; other site 323098007369 ATP binding site [chemical binding]; other site 323098007370 Walker B motif; other site 323098007371 arginine finger; other site 323098007372 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 323098007373 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 323098007374 RuvA N terminal domain; Region: RuvA_N; pfam01330 323098007375 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 323098007376 active site 323098007377 putative DNA-binding cleft [nucleotide binding]; other site 323098007378 dimer interface [polypeptide binding]; other site 323098007379 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 323098007380 MgtE intracellular N domain; Region: MgtE_N; cl15244 323098007381 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 323098007382 Divalent cation transporter; Region: MgtE; cl00786 323098007383 Transcriptional regulator; Region: Transcrip_reg; cl00361 323098007384 Deinococcus radiodurans DR1281 and related proteins, metallophosphatase domain; Region: MPP_DR1281; cd07382 323098007385 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 323098007386 putative active site [active] 323098007387 metal binding site [ion binding]; metal-binding site 323098007388 homodimer binding site [polypeptide binding]; other site 323098007389 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 323098007390 Cell division protein ZapA; Region: ZapA; cl01146 323098007391 Domain of unknown function (DUF4164); Region: DUF4164; pfam13747 323098007392 transketolase; Reviewed; Region: PRK05899 323098007393 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 323098007394 TPP-binding site [chemical binding]; other site 323098007395 dimer interface [polypeptide binding]; other site 323098007396 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 323098007397 PYR/PP interface [polypeptide binding]; other site 323098007398 dimer interface [polypeptide binding]; other site 323098007399 TPP binding site [chemical binding]; other site 323098007400 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098007401 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 323098007402 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 323098007403 Phosphoglycerate kinase; Region: PGK; pfam00162 323098007404 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; cd00318 323098007405 substrate binding site [chemical binding]; other site 323098007406 hinge regions; other site 323098007407 ADP binding site [chemical binding]; other site 323098007408 catalytic site [active] 323098007409 Fructose-1,6-bisphosphate aldolase; Region: FBP_aldolase_I_a; cd00948 323098007410 active site 323098007411 intersubunit interface [polypeptide binding]; other site 323098007412 catalytic residue [active] 323098007413 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 323098007414 active site 323098007415 pyrophosphate binding site [ion binding]; other site 323098007416 thiamine phosphate binding site [chemical binding]; other site 323098007417 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 323098007418 Sel1 repeat; Region: Sel1; cl02723 323098007419 Sel1 repeat; Region: Sel1; cl02723 323098007420 Sel1 repeat; Region: Sel1; cl02723 323098007421 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 323098007422 active site 323098007423 dimerization interface [polypeptide binding]; other site 323098007424 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 323098007425 Protein export membrane protein; Region: SecD_SecF; cl14618 323098007426 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 323098007427 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 323098007428 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 323098007429 hypothetical protein; Validated; Region: PRK09039 323098007430 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 323098007431 ligand binding site [chemical binding]; other site 323098007432 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 323098007433 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 323098007434 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 323098007435 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 323098007436 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098007437 Walker A/P-loop; other site 323098007438 ATP binding site [chemical binding]; other site 323098007439 Q-loop/lid; other site 323098007440 ABC transporter signature motif; other site 323098007441 Walker B; other site 323098007442 D-loop; other site 323098007443 H-loop/switch region; other site 323098007444 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 323098007445 Protein of unknown function (DUF1465); Region: DUF1465; cl11562 323098007446 Protein of unknown function (DUF1192); Region: DUF1192; cl11573 323098007447 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 323098007448 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 323098007449 NAD(P) binding site [chemical binding]; other site 323098007450 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 323098007451 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 323098007452 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 323098007453 putative active site [active] 323098007454 PAS fold; Region: PAS_3; pfam08447 323098007455 heme pocket [chemical binding]; other site 323098007456 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 323098007457 metal binding site [ion binding]; metal-binding site 323098007458 active site 323098007459 I-site; other site 323098007460 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 323098007461 Uncharacterized ACR, COG1678; Region: DUF179; cl00731 323098007462 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 323098007463 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 323098007464 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098007465 3-hydroxybutyrate dehydrogenase; Region: PHB_DH; TIGR01963 323098007466 NAD(P) binding site [chemical binding]; other site 323098007467 active site 323098007468 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 323098007469 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 323098007470 Part of the ABC transporter complex cysAWTP involved in sulfate import. Responsible for energy coupling to the transport system. The complex is composed of two ATP-binding proteins (cysA), two transmembrane proteins (cysT and cysW), and a...; Region: ABC_CysA_sulfate_importer; cd03296 323098007471 Walker A/P-loop; other site 323098007472 ATP binding site [chemical binding]; other site 323098007473 Q-loop/lid; other site 323098007474 ABC transporter signature motif; other site 323098007475 Walker B; other site 323098007476 D-loop; other site 323098007477 H-loop/switch region; other site 323098007478 TOBE-like domain; Region: TOBE_3; pfam12857 323098007479 sulfate transport protein; Provisional; Region: cysT; CHL00187 323098007480 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 323098007481 dimer interface [polypeptide binding]; other site 323098007482 conserved gate region; other site 323098007483 putative PBP binding loops; other site 323098007484 ABC-ATPase subunit interface; other site 323098007485 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 323098007486 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 323098007487 dimer interface [polypeptide binding]; other site 323098007488 conserved gate region; other site 323098007489 putative PBP binding loops; other site 323098007490 ABC-ATPase subunit interface; other site 323098007491 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 323098007492 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 323098007493 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 323098007494 Active Sites [active] 323098007495 Siroheme synthase (precorrin-2 oxidase/ferrochelatase domain) [Coenzyme metabolism]; Region: CysG; COG1648 323098007496 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098007497 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098007498 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 323098007499 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 323098007500 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 323098007501 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 323098007502 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 323098007503 Active Sites [active] 323098007504 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 323098007505 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional; Region: PRK05506 323098007506 G1 box; other site 323098007507 putative GEF interaction site [polypeptide binding]; other site 323098007508 GTP/Mg2+ binding site [chemical binding]; other site 323098007509 Switch I region; other site 323098007510 G2 box; other site 323098007511 CysD dimerization site [polypeptide binding]; other site 323098007512 G3 box; other site 323098007513 Switch II region; other site 323098007514 G4 box; other site 323098007515 G5 box; other site 323098007516 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 323098007517 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 323098007518 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 323098007519 ligand-binding site [chemical binding]; other site 323098007520 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 323098007521 active site 323098007522 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 323098007523 Protein of unknown function (DUF805); Region: DUF805; cl01224 323098007524 two-component response regulator; Provisional; Region: PRK09191 323098007525 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 323098007526 active site 323098007527 phosphorylation site [posttranslational modification] 323098007528 intermolecular recognition site; other site 323098007529 dimerization interface [polypeptide binding]; other site 323098007530 RNA polymerase sigma factor; Provisional; Region: PRK12540 323098007531 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 323098007532 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 323098007533 DNA binding residues [nucleotide binding] 323098007534 CHASE domain; Region: CHASE; cl01369 323098007535 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 323098007536 Histidine kinase; Region: HisKA_2; cl06527 323098007537 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 323098007538 MiaB-like tRNA modifying enzyme; Region: MiaB-like-C; TIGR01579 323098007539 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 323098007540 FeS/SAM binding site; other site 323098007541 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 323098007542 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 323098007543 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 323098007544 GyrI-like small molecule binding domain; Region: GyrI-like; cl01368 323098007545 Protein of unknown function (DUF541); Region: SIMPL; cl01077 323098007546 signal recognition particle protein; Provisional; Region: PRK10867 323098007547 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 323098007548 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 323098007549 P loop; other site 323098007550 GTP binding site [chemical binding]; other site 323098007551 Signal peptide binding domain; Region: SRP_SPB; pfam02978 323098007552 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 323098007553 RimM N-terminal domain; Region: RimM; pfam01782 323098007554 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK13828 323098007555 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 323098007556 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 323098007557 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 323098007558 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 323098007559 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 323098007560 substrate binding site [chemical binding]; other site 323098007561 ligand binding site [chemical binding]; other site 323098007562 Possibl zinc metallo-peptidase; Region: DUF1025; cl01577 323098007563 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 323098007564 substrate binding site [chemical binding]; other site 323098007565 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_cladeB; cd00884 323098007566 active site clefts [active] 323098007567 zinc binding site [ion binding]; other site 323098007568 dimer interface [polypeptide binding]; other site 323098007569 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 323098007570 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098007571 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 323098007572 tartrate dehydrogenase; Provisional; Region: PRK08194 323098007573 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 323098007574 Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the...; Region: Cu-Zn_Superoxide_Dismutase; cd00305 323098007575 E-class dimer interface [polypeptide binding]; other site 323098007576 P-class dimer interface [polypeptide binding]; other site 323098007577 active site 323098007578 Cu2+ binding site [ion binding]; other site 323098007579 Zn2+ binding site [ion binding]; other site 323098007580 malonyl-CoA synthase; Validated; Region: PRK07514 323098007581 AMP-binding enzyme; Region: AMP-binding; cl15778 323098007582 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 323098007583 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 323098007584 Iron-sulfur protein interface; other site 323098007585 proximal quinone binding site [chemical binding]; other site 323098007586 SdhD (CybS) interface [polypeptide binding]; other site 323098007587 proximal heme binding site [chemical binding]; other site 323098007588 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit-like; composed of predominantly uncharacterized bacterial proteins with similarity to the E. coli SdhD subunit. One characterized protein is the respiratory...; Region: SQR_TypeC_SdhD_like; cd03495 323098007589 putative SdhC subunit interface [polypeptide binding]; other site 323098007590 putative proximal heme binding site [chemical binding]; other site 323098007591 putative Iron-sulfur protein interface [polypeptide binding]; other site 323098007592 putative proximal quinone binding site; other site 323098007593 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 323098007594 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098007595 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 323098007596 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 323098007597 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 323098007598 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 323098007599 ligand binding site [chemical binding]; other site 323098007600 Argininosuccinate synthase [Amino acid transport and metabolism]; Region: ArgG; COG0137 323098007601 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 323098007602 ANP binding site [chemical binding]; other site 323098007603 Substrate Binding Site II [chemical binding]; other site 323098007604 Substrate Binding Site I [chemical binding]; other site 323098007605 PAP2_like_6 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which mainly contains bacterial proteins, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_6; cd03396 323098007606 active site 323098007607 Predicted Fe-S-cluster redox enzyme [General function prediction only]; Region: COG0820 323098007608 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 323098007609 FeS/SAM binding site; other site 323098007610 Invasion associated locus B (IalB) protein; Region: IalB; cl02207 323098007611 Protein of unknown function (DUF1232); Region: DUF1232; cl01318 323098007612 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 323098007613 aromatic arch; other site 323098007614 DCoH dimer interaction site [polypeptide binding]; other site 323098007615 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 323098007616 DCoH tetramer interaction site [polypeptide binding]; other site 323098007617 substrate binding site [chemical binding]; other site 323098007618 Ferredoxin [Energy production and conversion]; Region: COG1146 323098007619 4Fe-4S binding domain; Region: Fer4; cl02805 323098007620 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 323098007621 Protein of unknown function, DUF488; Region: DUF488; cl01246 323098007622 heat shock protein 90; Provisional; Region: PRK05218 323098007623 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 323098007624 ATP binding site [chemical binding]; other site 323098007625 Mg2+ binding site [ion binding]; other site 323098007626 G-X-G motif; other site 323098007627 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 323098007628 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 323098007629 FlgD Ig-like domain; Region: FlgD_ig; cl15790 323098007630 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 323098007631 ApbE family; Region: ApbE; cl00643 323098007632 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 323098007633 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 323098007634 FMN binding site [chemical binding]; other site 323098007635 active site 323098007636 catalytic residues [active] 323098007637 substrate binding site [chemical binding]; other site 323098007638 Winged helix-turn helix; Region: HTH_29; pfam13551 323098007639 Integrase core domain; Region: rve; cl01316 323098007640 Integrase core domain; Region: rve_3; cl15866 323098007641 Helix-turn-helix domains; Region: HTH; cl00088 323098007642 Winged helix-turn helix; Region: HTH_29; pfam13551 323098007643 Helix-turn-helix domains; Region: HTH; cl00088 323098007644 Integrase core domain; Region: rve; cl01316 323098007645 Integrase core domain; Region: rve_3; cl15866 323098007646 Helix-turn-helix domains; Region: HTH; cl00088 323098007647 Transposase domain (DUF772); Region: DUF772; cl15789 323098007648 Transposase domain (DUF772); Region: DUF772; cl15789 323098007649 Transposase domain (DUF772); Region: DUF772; cl15789 323098007650 Transposase domain (DUF772); Region: DUF772; cl15789 323098007651 Uncharacterized conserved protein (DUF2190); Region: DUF2190; cl02289 323098007652 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 323098007653 Domain of unknown function (DUF3883); Region: DUF3883; pfam13020 323098007654 Phage protein Gp37/Gp68; Region: Gp37_Gp68; cl15384 323098007655 Integrase core domain; Region: rve; cl01316 323098007656 Integrase core domain; Region: rve_3; cl15866 323098007657 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 323098007658 catalytic residues [active] 323098007659 catalytic nucleophile [active] 323098007660 Recombinase; Region: Recombinase; pfam07508 323098007661 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 323098007662 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098007663 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 323098007664 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 323098007665 Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide...; Region: CASc; cl00042 323098007666 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 323098007667 Integrase core domain; Region: rve; cl01316 323098007668 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098007669 Winged helix-turn helix; Region: HTH_29; pfam13551 323098007670 Helix-turn-helix domains; Region: HTH; cl00088 323098007671 Helix-turn-helix domains; Region: HTH; cl00088 323098007672 Integrase core domain; Region: rve; cl01316 323098007673 Integrase core domain; Region: rve; cl01316 323098007674 Integrase core domain; Region: rve_3; cl15866 323098007675 Relaxase/Mobilisation nuclease domain; Region: Relaxase; cl01584 323098007676 Protein of unknown function (DUF3363); Region: DUF3363; pfam11843 323098007677 Glycosyl transferases, related to UDP-glucuronosyltransferase [Carbohydrate transport and metabolism / Signal transduction mechanisms]; Region: COG1819 323098007678 This family includes the Gtfs, a group of homologous glycosyltransferases involved in the final stages of the biosynthesis of antibiotics vancomycin and related chloroeremomycin. Gtfs transfer sugar moieties from an activated NDP-sugar donor to the...; Region: GT1_Gtf_like; cd03784 323098007679 homodimer interface [polypeptide binding]; other site 323098007680 active site 323098007681 TDP-binding site; other site 323098007682 acceptor substrate-binding pocket; other site 323098007683 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 323098007684 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 323098007685 Protein of unknown function (DUF1778); Region: DUF1778; cl01845 323098007686 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 323098007687 conjugal transfer coupling protein TraG; Provisional; Region: PRK13876 323098007688 PRTRC system ParB family protein; Region: PRTRC_parB; TIGR03734 323098007689 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 323098007690 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 323098007691 generic binding surface I; other site 323098007692 generic binding surface II; other site 323098007693 Transposase domain (DUF772); Region: DUF772; cl15789 323098007694 Transposase domain (DUF772); Region: DUF772; cl15789 323098007695 Helix-turn-helix domains; Region: HTH; cl00088 323098007696 Helix-turn-helix domains; Region: HTH; cl00088 323098007697 putative transposase OrfB; Reviewed; Region: PHA02517 323098007698 Helix-turn-helix domains; Region: HTH; cl00088 323098007699 Integrase core domain; Region: rve; cl01316 323098007700 Integrase core domain; Region: rve_3; cl15866 323098007701 Helix-turn-helix domains; Region: HTH; cl00088 323098007702 Winged helix-turn helix; Region: HTH_29; pfam13551 323098007703 Helix-turn-helix domains; Region: HTH; cl00088 323098007704 Integrase core domain; Region: rve; cl01316 323098007705 Integrase core domain; Region: rve_3; cl15866 323098007706 Helix-turn-helix domains; Region: HTH; cl00088 323098007707 HipA N-terminal domain; Region: Couple_hipA; cl11853 323098007708 HipA-like N-terminal domain; Region: HipA_N; pfam07805 323098007709 HipA-like C-terminal domain; Region: HipA_C; pfam07804 323098007710 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 323098007711 Prokaryotic E2 family A; Region: Prok-E2_A; pfam14457 323098007712 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098007713 ATP binding site [chemical binding]; other site 323098007714 Mpr1p, Pad1p N-terminal (MPN) domains; Region: MPN; cl13996 323098007715 Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) [Coenzyme metabolism / Translation, ribosomal structure and biogenesis]; Region: RimK; COG0189 323098007716 Helix-turn-helix domains; Region: HTH; cl00088 323098007717 putative transposase OrfB; Reviewed; Region: PHA02517 323098007718 Helix-turn-helix domains; Region: HTH; cl00088 323098007719 Integrase core domain; Region: rve; cl01316 323098007720 Integrase core domain; Region: rve_3; cl15866 323098007721 Helix-turn-helix domains; Region: HTH; cl00088 323098007722 Secretin and TonB N terminus short domain; Region: STN; cl06624 323098007723 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 323098007724 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 323098007725 N-terminal plug; other site 323098007726 ligand-binding site [chemical binding]; other site 323098007727 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 323098007728 FecR protein; Region: FecR; pfam04773 323098007729 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 323098007730 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 323098007731 DNA binding residues [nucleotide binding] 323098007732 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 323098007733 Helix-turn-helix domains; Region: HTH; cl00088 323098007734 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 323098007735 dimer interface [polypeptide binding]; other site 323098007736 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 323098007737 ribonucleotide-diphosphate reductase subunit beta; Provisional; Region: nrdF2; PRK13966 323098007738 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 323098007739 dimer interface [polypeptide binding]; other site 323098007740 putative radical transfer pathway; other site 323098007741 diiron center [ion binding]; other site 323098007742 tyrosyl radical; other site 323098007743 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07207 323098007744 ATP cone domain; Region: ATP-cone; pfam03477 323098007745 ATP cone domain; Region: ATP-cone; pfam03477 323098007746 Class I ribonucleotide reductase; Region: RNR_I; cd01679 323098007747 active site 323098007748 dimer interface [polypeptide binding]; other site 323098007749 catalytic residues [active] 323098007750 effector binding site; other site 323098007751 R2 peptide binding site; other site 323098007752 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 323098007753 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 323098007754 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 323098007755 THF binding site; other site 323098007756 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 323098007757 substrate binding site [chemical binding]; other site 323098007758 THF binding site; other site 323098007759 zinc-binding site [ion binding]; other site 323098007760 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 323098007761 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 323098007762 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 323098007763 substrate binding pocket [chemical binding]; other site 323098007764 membrane-bound complex binding site; other site 323098007765 hinge residues; other site 323098007766 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098007767 DsrE/DsrF-like family; Region: DrsE; cl00672 323098007768 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 323098007769 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 323098007770 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 323098007771 active site residue [active] 323098007772 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 323098007773 metal binding site [ion binding]; metal-binding site 323098007774 active site 323098007775 I-site; other site 323098007776 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 323098007777 Copper binding periplasmic protein CusF; Region: CusF_Ec; cl02363 323098007778 Winged helix-turn helix; Region: HTH_29; pfam13551 323098007779 Integrase core domain; Region: rve; cl01316 323098007780 Integrase core domain; Region: rve_3; cl15866 323098007781 Cysteine-rich 4 helical bundle widely conserved in bacteria; Region: DUF326; cd08026 323098007782 dimerization interface [polypeptide binding]; other site 323098007783 Protein of unknown function (DUF2946); Region: DUF2946; pfam11162 323098007784 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 323098007785 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 323098007786 N-terminal plug; other site 323098007787 ligand-binding site [chemical binding]; other site 323098007788 Sialidases or neuraminidases function to bind and hydrolyze terminal sialic acid residues from various glycoconjugates as well as playing roles in pathogenesis, bacterial nutrition and cellular interactions. They have a six-bladed, beta-propeller fold...; Region: Sialidase; cl01922 323098007789 BNR repeat-like domain; Region: BNR_2; pfam13088 323098007790 Asp-box motif; other site 323098007791 Sialidases or neuraminidases function to bind and hydrolyze terminal sialic acid residues from various glycoconjugates as well as playing roles in pathogenesis, bacterial nutrition and cellular interactions. They have a six-bladed, beta-propeller fold...; Region: Sialidase; cl01922 323098007792 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 323098007793 catalytic residues [active] 323098007794 High-affinity nickel-transport protein; Region: NicO; cl00964 323098007795 Protein of unknown function (DUF1007); Region: DUF1007; cl01487 323098007796 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 323098007797 dimerization interface [polypeptide binding]; other site 323098007798 putative DNA binding site [nucleotide binding]; other site 323098007799 putative Zn2+ binding site [ion binding]; other site 323098007800 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 323098007801 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 323098007802 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 323098007803 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 323098007804 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 323098007805 transcriptional regulatory protein TctD; Provisional; Region: PRK15479 323098007806 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 323098007807 active site 323098007808 phosphorylation site [posttranslational modification] 323098007809 intermolecular recognition site; other site 323098007810 dimerization interface [polypeptide binding]; other site 323098007811 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 323098007812 DNA binding site [nucleotide binding] 323098007813 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 323098007814 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 323098007815 dimerization interface [polypeptide binding]; other site 323098007816 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 323098007817 dimer interface [polypeptide binding]; other site 323098007818 phosphorylation site [posttranslational modification] 323098007819 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 323098007820 ATP binding site [chemical binding]; other site 323098007821 Mg2+ binding site [ion binding]; other site 323098007822 G-X-G motif; other site 323098007823 Predicted membrane protein (DUF2231); Region: DUF2231; cl01730 323098007824 Winged helix-turn helix; Region: HTH_29; pfam13551 323098007825 Integrase core domain; Region: rve; cl01316 323098007826 Integrase core domain; Region: rve_3; cl15866 323098007827 Winged helix-turn helix; Region: HTH_29; pfam13551 323098007828 Integrase core domain; Region: rve; cl01316 323098007829 Integrase core domain; Region: rve_3; cl15866 323098007830 Transposase domain (DUF772); Region: DUF772; cl15789 323098007831 Transposase domain (DUF772); Region: DUF772; cl15789 323098007832 Integrase core domain; Region: rve; cl01316 323098007833 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098007834 Transposase domain (DUF772); Region: DUF772; cl15789 323098007835 Transposase domain (DUF772); Region: DUF772; cl15789 323098007836 Transposase domain (DUF772); Region: DUF772; cl15789 323098007837 Transposase domain (DUF772); Region: DUF772; cl15789 323098007838 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 323098007839 probable Rubsico expression protein CbbX; Region: cbbX_cfxQ; TIGR02880 323098007840 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 323098007841 Walker A motif; other site 323098007842 ATP binding site [chemical binding]; other site 323098007843 Walker B motif; other site 323098007844 arginine finger; other site 323098007845 Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco...; Region: RuBisCO_small; cd03527 323098007846 multimerization interface [polypeptide binding]; other site 323098007847 ribulose bisophosphate carboxylase; Reviewed; Region: rbcL; PRK04208 323098007848 Ribulose bisphosphate carboxylase large chain, Form I; Region: RuBisCO_large_I; cd08212 323098007849 homodimer interface [polypeptide binding]; other site 323098007850 active site 323098007851 heterodimer interface [polypeptide binding]; other site 323098007852 catalytic residue [active] 323098007853 metal binding site [ion binding]; metal-binding site 323098007854 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 323098007855 Helix-turn-helix domains; Region: HTH; cl00088 323098007856 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 323098007857 putative dimerization interface [polypeptide binding]; other site 323098007858 Nitrogen regulatory protein P-II; Region: P-II; smart00938 323098007859 Nitrogen regulatory protein P-II; Region: P-II; cl00412 323098007860 Carboxysome Shell Carbonic Anhydrase; Region: CsoSCA; cl07510 323098007861 ParB-like nuclease domain; Region: ParBc; cl02129 323098007862 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 323098007863 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 323098007864 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 323098007865 protein binding site [polypeptide binding]; other site 323098007866 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 323098007867 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation...; Region: ACD_IbpA-B_like; cd06470 323098007868 putative dimer interface [polypeptide binding]; other site 323098007869 alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins; Region: alpha-crystallin-Hsps_p23-like; cl00175 323098007870 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation...; Region: ACD_IbpA-B_like; cd06470 323098007871 putative dimer interface [polypeptide binding]; other site 323098007872 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 323098007873 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 323098007874 putative dimer interface [polypeptide binding]; other site 323098007875 Helix-turn-helix domains; Region: HTH; cl00088 323098007876 putative transposase OrfB; Reviewed; Region: PHA02517 323098007877 Helix-turn-helix domains; Region: HTH; cl00088 323098007878 Integrase core domain; Region: rve; cl01316 323098007879 Integrase core domain; Region: rve_3; cl15866 323098007880 Helix-turn-helix domains; Region: HTH; cl00088 323098007881 Protein of unknown function (DUF3489); Region: DUF3489; pfam11994 323098007882 Protein of unknown function (DUF2924); Region: DUF2924; pfam11149 323098007883 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 323098007884 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 323098007885 catalytic residues [active] 323098007886 catalytic nucleophile [active] 323098007887 Presynaptic Site I dimer interface [polypeptide binding]; other site 323098007888 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 323098007889 Synaptic Flat tetramer interface [polypeptide binding]; other site 323098007890 Synaptic Site I dimer interface [polypeptide binding]; other site 323098007891 DNA binding site [nucleotide binding] 323098007892 Recombinase; Region: Recombinase; pfam07508 323098007893 Response regulator receiver domain; Region: Response_reg; pfam00072 323098007894 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 323098007895 active site 323098007896 phosphorylation site [posttranslational modification] 323098007897 intermolecular recognition site; other site 323098007898 dimerization interface [polypeptide binding]; other site 323098007899 N-formylglutamate amidohydrolase; Region: FGase; cl01522 323098007900 Winged helix-turn helix; Region: HTH_29; pfam13551 323098007901 Helix-turn-helix domains; Region: HTH; cl00088 323098007902 Helix-turn-helix domains; Region: HTH; cl00088 323098007903 Integrase core domain; Region: rve; cl01316 323098007904 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098007905 Predominantly bacterial family of Mg++ dependend phosphatases, related to inositol monophosphatases. These enzymes may dephosphorylate fructose-1,6-bisphosphate, inositol monophospate, 3'-phosphoadenosine-5'-phosphate, or similar substrates; Region: Bacterial_IMPase_like_1; cd01641 323098007906 active site 323098007907 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 323098007908 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 323098007909 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 323098007910 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation...; Region: ACD_IbpA-B_like; cd06470 323098007911 putative dimer interface [polypeptide binding]; other site 323098007912 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 323098007913 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 323098007914 active site 323098007915 dimer interface [polypeptide binding]; other site 323098007916 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 323098007917 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 323098007918 active site 323098007919 FMN binding site [chemical binding]; other site 323098007920 substrate binding site [chemical binding]; other site 323098007921 3Fe-4S cluster binding site [ion binding]; other site 323098007922 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 323098007923 domain interface; other site 323098007924 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 323098007925 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098007926 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; cl01053 323098007927 active site 323098007928 oxyanion hole [active] 323098007929 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; cl01053 323098007930 catalytic triad [active] 323098007931 Transglycosylase SLT domain; Region: SLT_2; pfam13406 323098007932 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 323098007933 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 323098007934 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 323098007935 active site 323098007936 tetramer interface; other site 323098007937 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229 323098007938 methionine sulfoxide reductase B; Provisional; Region: PRK00222; cl15841 323098007939 Domain of unknown function (DUF4112); Region: DUF4112; pfam13430 323098007940 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 323098007941 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 323098007942 GDP-binding site [chemical binding]; other site 323098007943 ACT binding site; other site 323098007944 IMP binding site; other site 323098007945 Carboxypeptidase C (cathepsin A) [Amino acid transport and metabolism]; Region: COG2939 323098007946 Serine carboxypeptidase; Region: Peptidase_S10; cl08270 323098007947 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK13581 323098007948 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098007949 C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-xct; cd04902 323098007950 putative L-serine binding site [chemical binding]; other site 323098007951 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 323098007952 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 323098007953 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 323098007954 catalytic residue [active] 323098007955 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 323098007956 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 323098007957 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 323098007958 Major Facilitator Superfamily; Region: MFS_1; pfam07690 323098007959 putative substrate translocation pore; other site 323098007960 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14315 323098007961 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 323098007962 active site 323098007963 substrate binding site [chemical binding]; other site 323098007964 metal binding site [ion binding]; metal-binding site 323098007965 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 323098007966 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 323098007967 G1 box; other site 323098007968 GTP/Mg2+ binding site [chemical binding]; other site 323098007969 Switch I region; other site 323098007970 G2 box; other site 323098007971 G3 box; other site 323098007972 Switch II region; other site 323098007973 G4 box; other site 323098007974 G5 box; other site 323098007975 Nucleoside recognition; Region: Gate; cl00486 323098007976 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 323098007977 Nucleoside recognition; Region: Gate; cl00486 323098007978 FeoA domain; Region: FeoA; cl00838 323098007979 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 323098007980 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 323098007981 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 323098007982 shikimate binding site; other site 323098007983 NAD(P) binding site [chemical binding]; other site 323098007984 Elongation factor G (EF-G) family; Region: EF-G_bact; cd04170 323098007985 elongation factor G; Reviewed; Region: PRK12740 323098007986 G1 box; other site 323098007987 putative GEF interaction site [polypeptide binding]; other site 323098007988 GTP/Mg2+ binding site [chemical binding]; other site 323098007989 Switch I region; other site 323098007990 G2 box; other site 323098007991 G3 box; other site 323098007992 Switch II region; other site 323098007993 G4 box; other site 323098007994 G5 box; other site 323098007995 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 323098007996 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 323098007997 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 323098007998 Protein of unknown function (DUF992); Region: DUF992; pfam06186 323098007999 aspartate aminotransferase; Provisional; Region: PRK05764 323098008000 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 323098008001 pyridoxal 5'-phosphate binding site [chemical binding]; other site 323098008002 homodimer interface [polypeptide binding]; other site 323098008003 catalytic residue [active] 323098008004 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 323098008005 GST_N family, unknown subfamily 4; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_4; cd03056 323098008006 putative C-terminal domain interface [polypeptide binding]; other site 323098008007 putative GSH binding site (G-site) [chemical binding]; other site 323098008008 putative dimer interface [polypeptide binding]; other site 323098008009 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 323098008010 N-terminal domain interface [polypeptide binding]; other site 323098008011 dimer interface [polypeptide binding]; other site 323098008012 substrate binding pocket (H-site) [chemical binding]; other site 323098008013 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 323098008014 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 323098008015 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 323098008016 tetramer interface [polypeptide binding]; other site 323098008017 active site 323098008018 Mg2+/Mn2+ binding site [ion binding]; other site 323098008019 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 323098008020 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 323098008021 non-specific DNA binding site [nucleotide binding]; other site 323098008022 salt bridge; other site 323098008023 sequence-specific DNA binding site [nucleotide binding]; other site 323098008024 Predicted transcriptional regulator [General function prediction only]; Region: COG3800 323098008025 Domain of unknown function (DUF955); Region: DUF955; cl01076 323098008026 Predicted transcriptional regulator (DUF2083); Region: DUF2083; pfam09856 323098008027 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 323098008028 Cytochrome c; Region: Cytochrom_C; cl11414 323098008029 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 323098008030 Moco binding site; other site 323098008031 metal coordination site [ion binding]; other site 323098008032 Domain of unknown function (DUF1993); Region: DUF1993; cl01567 323098008033 glycerol-3-phosphate dehydrogenase; Reviewed; Region: glpD; PRK12266 323098008034 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098008035 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 323098008036 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 323098008037 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 323098008038 substrate binding site [chemical binding]; other site 323098008039 oxyanion hole (OAH) forming residues; other site 323098008040 trimer interface [polypeptide binding]; other site 323098008041 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098008042 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 323098008043 acetyl-CoA acetyltransferase; Provisional; Region: PRK08170 323098008044 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 323098008045 dimer interface [polypeptide binding]; other site 323098008046 active site 323098008047 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 323098008048 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 323098008049 active site 323098008050 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 323098008051 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 323098008052 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 323098008053 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 323098008054 dimer interface [polypeptide binding]; other site 323098008055 putative CheW interface [polypeptide binding]; other site 323098008056 CsbD-like; Region: CsbD; cl15799 323098008057 putative rhodanese-related sulfurtransferase; Provisional; Region: PRK00142 323098008058 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 323098008059 active site residue [active] 323098008060 SlyX; Region: SlyX; cl01090 323098008061 Protein of unknown function (DUF3422); Region: DUF3422; cl02073 323098008062 putative enoyl-[acyl-carrier-protein] reductase II; Region: enACPred_II; TIGR03151 323098008063 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 323098008064 FMN binding site [chemical binding]; other site 323098008065 substrate binding site [chemical binding]; other site 323098008066 putative catalytic residue [active] 323098008067 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098008068 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098008069 Tetratricopeptide repeat; Region: TPR_12; pfam13424 323098008070 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 323098008071 binding surface 323098008072 TPR motif; other site 323098008073 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 323098008074 binding surface 323098008075 Tetratricopeptide repeat; Region: TPR_12; pfam13424 323098008076 TPR motif; other site 323098008077 Tetratricopeptide repeat; Region: TPR_12; pfam13424 323098008078 Tetratricopeptide repeat; Region: TPR_12; pfam13424 323098008079 Tetratricopeptide repeat; Region: TPR_12; pfam13424 323098008080 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 323098008081 binding surface 323098008082 TPR motif; other site 323098008083 Tetratricopeptide repeat; Region: TPR_12; pfam13424 323098008084 Tetratricopeptide repeat; Region: TPR_12; pfam13424 323098008085 Formate/nitrite transporter; Region: Form_Nir_trans; cl00927 323098008086 Winged helix-turn helix; Region: HTH_29; pfam13551 323098008087 Helix-turn-helix domains; Region: HTH; cl00088 323098008088 Helix-turn-helix domains; Region: HTH; cl00088 323098008089 Integrase core domain; Region: rve; cl01316 323098008090 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 323098008091 Helix-turn-helix domains; Region: HTH; cl00088 323098008092 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 323098008093 Transposase domain (DUF772); Region: DUF772; cl15789 323098008094 Transposase domain (DUF772); Region: DUF772; cl15789 323098008095 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 323098008096 active site 323098008097 metal binding site [ion binding]; metal-binding site 323098008098 hypothetical protein; Validated; Region: PRK07586 323098008099 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 323098008100 PYR/PP interface [polypeptide binding]; other site 323098008101 dimer interface [polypeptide binding]; other site 323098008102 TPP binding site [chemical binding]; other site 323098008103 Thiamine pyrophosphate (TPP) family, BFDC subfamily, TPP-binding module; composed of proteins similar to Pseudomonas putida benzoylformate decarboxylase (BFDC). P. putida BFDC plays a role in the mandelate pathway, catalyzing the conversion of...; Region: TPP_BFDC; cd02002 323098008104 TPP-binding site [chemical binding]; other site 323098008105 dimer interface [polypeptide binding]; other site 323098008106 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 323098008107 isovaleryl-CoA dehydrogenase; Region: PLN02519 323098008108 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 323098008109 substrate binding site [chemical binding]; other site 323098008110 FAD binding site [chemical binding]; other site 323098008111 catalytic base [active] 323098008112 YcjX-like family, DUF463; Region: DUF463; cl01193 323098008113 Domain of unknown function (DUF697); Region: DUF697; cl12064 323098008114 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 323098008115 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl15769 323098008116 sulfite oxidase; Provisional; Region: PLN00177 323098008117 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 323098008118 Moco binding site; other site 323098008119 metal coordination site [ion binding]; other site 323098008120 Cytochrome c; Region: Cytochrom_C; cl11414 323098008121 alpha,alpha-trehalose-phosphate synthase [UDP-forming]; Region: trehalose_OtsA; TIGR02400 323098008122 Trehalose-6-Phosphate Synthase (TPS) is a glycosyltransferase that catalyses the synthesis of alpha,alpha-1,1-trehalose-6-phosphate from glucose-6-phosphate using a UDP-glucose donor. It is a key enzyme in the trehalose synthesis pathway. Trehalose is a...; Region: GT1_TPS; cd03788 323098008123 active site 323098008124 homotetramer interface [polypeptide binding]; other site 323098008125 Glucoamylase and related glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: SGA1; COG3387 323098008126 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 323098008127 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 323098008128 benzoate transport; Region: 2A0115; TIGR00895 323098008129 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 323098008130 putative substrate translocation pore; other site 323098008131 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 323098008132 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 323098008133 ligand binding site [chemical binding]; other site 323098008134 Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide...; Region: CASc; cl00042 323098008135 TPR repeat; Region: TPR_11; pfam13414 323098008136 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 323098008137 binding surface 323098008138 TPR motif; other site 323098008139 TPR repeat; Region: TPR_11; pfam13414 323098008140 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 323098008141 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 323098008142 Protein export membrane protein; Region: SecD_SecF; cl14618 323098008143 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 323098008144 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 323098008145 ligand binding site [chemical binding]; other site 323098008146 flexible hinge region; other site 323098008147 Helix-turn-helix domains; Region: HTH; cl00088 323098008148 putative assembly protein; Provisional; Region: PRK10833 323098008149 AsmA-like C-terminal region; Region: AsmA_2; cl15864 323098008150 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 323098008151 Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide...; Region: CASc; cl00042 323098008152 substrate pocket [chemical binding]; other site 323098008153 active site 323098008154 dimer interface [polypeptide binding]; other site 323098008155 proteolytic cleavage site; other site 323098008156 Transposase domain (DUF772); Region: DUF772; cl15789 323098008157 Transposase domain (DUF772); Region: DUF772; cl15789 323098008158 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 323098008159 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 323098008160 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 323098008161 GAF domain; Region: GAF_2; pfam13185 323098008162 GAF domain; Region: GAF; cl15785 323098008163 cyclase homology domain; Region: CHD; cd07302 323098008164 nucleotidyl binding site; other site 323098008165 metal binding site [ion binding]; metal-binding site 323098008166 dimer interface [polypeptide binding]; other site 323098008167 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 323098008168 non-specific DNA binding site [nucleotide binding]; other site 323098008169 salt bridge; other site 323098008170 sequence-specific DNA binding site [nucleotide binding]; other site 323098008171 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4782 323098008172 Alpha/beta hydrolase of unknown function (DUF900); Region: DUF900; pfam05990 323098008173 Secretin and TonB N terminus short domain; Region: STN; cl06624 323098008174 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 323098008175 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 323098008176 N-terminal plug; other site 323098008177 ligand-binding site [chemical binding]; other site 323098008178 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 323098008179 FecR protein; Region: FecR; pfam04773 323098008180 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 323098008181 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 323098008182 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 323098008183 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 323098008184 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 323098008185 ABC-ATPase subunit interface; other site 323098008186 dimer interface [polypeptide binding]; other site 323098008187 putative PBP binding regions; other site 323098008188 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 323098008189 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 323098008190 Walker A/P-loop; other site 323098008191 ATP binding site [chemical binding]; other site 323098008192 Q-loop/lid; other site 323098008193 ABC transporter signature motif; other site 323098008194 Walker B; other site 323098008195 D-loop; other site 323098008196 H-loop/switch region; other site 323098008197 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 323098008198 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 323098008199 intersubunit interface [polypeptide binding]; other site 323098008200 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 323098008201 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 323098008202 N-terminal plug; other site 323098008203 ligand-binding site [chemical binding]; other site 323098008204 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 323098008205 Helix-turn-helix domains; Region: HTH; cl00088 323098008206 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 323098008207 Major Facilitator Superfamily; Region: MFS_1; pfam07690 323098008208 putative substrate translocation pore; other site 323098008209 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 323098008210 DNA-binding site [nucleotide binding]; DNA binding site 323098008211 RNA-binding motif; other site 323098008212 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11904 323098008213 Proline dehydrogenase; Region: Pro_dh; cl03282 323098008214 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 323098008215 Glutamate binding site [chemical binding]; other site 323098008216 NAD binding site [chemical binding]; other site 323098008217 catalytic residues [active] 323098008218 RNA polymerase sigma factor; Provisional; Region: PRK12515 323098008219 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 323098008220 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 323098008221 DNA binding residues [nucleotide binding] 323098008222 Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]; Region: CitB; COG4565 323098008223 Domain of unknown function (DUF3369); Region: DUF3369; pfam11849 323098008224 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 323098008225 dimer interface [polypeptide binding]; other site 323098008226 phosphorylation site [posttranslational modification] 323098008227 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 323098008228 ATP binding site [chemical binding]; other site 323098008229 Mg2+ binding site [ion binding]; other site 323098008230 G-X-G motif; other site 323098008231 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5394 323098008232 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 323098008233 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 323098008234 putative acyltransferase; Provisional; Region: PRK05790 323098008235 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 323098008236 dimer interface [polypeptide binding]; other site 323098008237 active site 323098008238 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 323098008239 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 323098008240 NAD(P) binding site [chemical binding]; other site 323098008241 homotetramer interface [polypeptide binding]; other site 323098008242 homodimer interface [polypeptide binding]; other site 323098008243 active site 323098008244 aromatic amino acid exporter; Provisional; Region: PRK11689 323098008245 EamA-like transporter family; Region: EamA; cl01037 323098008246 muropeptide transporter; Validated; Region: ampG; PRK11010 323098008247 muropeptide transporter; Reviewed; Region: ampG; PRK11902 323098008248 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 323098008249 active site 323098008250 catalytic residues [active] 323098008251 metal binding site [ion binding]; metal-binding site 323098008252 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 323098008253 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 323098008254 putative active site [active] 323098008255 substrate binding site [chemical binding]; other site 323098008256 putative cosubstrate binding site; other site 323098008257 catalytic site [active] 323098008258 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 323098008259 substrate binding site [chemical binding]; other site 323098008260 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 323098008261 PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1); Region: PseudoU_synth_EcTruA; cd02570 323098008262 dimerization interface 3.5A [polypeptide binding]; other site 323098008263 active site 323098008264 nucleosidase; Provisional; Region: PRK05634 323098008265 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 323098008266 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 323098008267 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 323098008268 metal binding site [ion binding]; metal-binding site 323098008269 dimer interface [polypeptide binding]; other site 323098008270 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 323098008271 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (also called THP succinyltransferase): THDP N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA; Region: LbH_THP_succinylT; cd03350 323098008272 trimer interface [polypeptide binding]; other site 323098008273 active site 323098008274 substrate binding site [chemical binding]; other site 323098008275 CoA binding site [chemical binding]; other site 323098008276 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 323098008277 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 323098008278 AAK_NAGK-C: N-Acetyl-L-glutamate kinase - cyclic (NAGK-C) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in some bacteria and photosynthetic organisms using the...; Region: AAK_NAGK-C; cd04250 323098008279 feedback inhibition sensing region; other site 323098008280 homohexameric interface [polypeptide binding]; other site 323098008281 nucleotide binding site [chemical binding]; other site 323098008282 N-acetyl-L-glutamate binding site [chemical binding]; other site 323098008283 Protein of unknown function (DUF423); Region: DUF423; cl01008 323098008284 Predicted GTPase [General function prediction only]; Region: COG0218 323098008285 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 323098008286 G1 box; other site 323098008287 GTP/Mg2+ binding site [chemical binding]; other site 323098008288 Switch I region; other site 323098008289 G2 box; other site 323098008290 G3 box; other site 323098008291 Switch II region; other site 323098008292 G4 box; other site 323098008293 G5 box; other site 323098008294 membrane protein insertase; Provisional; Region: PRK01318 323098008295 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 323098008296 Ribonuclease P; Region: Ribonuclease_P; cl00457 323098008297 Ribosomal protein L34; Region: Ribosomal_L34; cl00370 323098008298 sensory histidine kinase AtoS; Provisional; Region: PRK11360 323098008299 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 323098008300 ATP binding site [chemical binding]; other site 323098008301 Mg2+ binding site [ion binding]; other site 323098008302 G-X-G motif; other site 323098008303 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 323098008304 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 323098008305 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 323098008306 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 323098008307 FecR protein; Region: FecR; pfam04773 323098008308 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 323098008309 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 323098008310 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 323098008311 PIN domain of ribonucleases (toxins), VapC, FitB, and PAE0151 of bacterial and archaeal toxin/antitoxin-like operons, and other similar homologs; Region: PIN_VapC-like; cd09861 323098008312 putative active site [active] 323098008313 Helix-turn-helix domains; Region: HTH; cl00088 323098008314 Winged helix-turn helix; Region: HTH_29; pfam13551 323098008315 Helix-turn-helix domains; Region: HTH; cl00088 323098008316 Integrase core domain; Region: rve; cl01316 323098008317 Integrase core domain; Region: rve_3; cl15866 323098008318 Helix-turn-helix domains; Region: HTH; cl00088 323098008319 Phospholipid methyltransferase; Region: PEMT; cl00763 323098008320 Bacteriocin-protection, YdeI or OmpD-Associated; Region: OmdA; pfam13376 323098008321 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 323098008322 Ribbon-helix-helix protein, copG family; Region: RHH_1; cl15783 323098008323 Peptidase propeptide and YPEB domain; Region: PepSY; cl15815 323098008324 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 323098008325 Helix-turn-helix domains; Region: HTH; cl00088 323098008326 putative transposase OrfB; Reviewed; Region: PHA02517 323098008327 Helix-turn-helix domains; Region: HTH; cl00088 323098008328 Integrase core domain; Region: rve; cl01316 323098008329 Integrase core domain; Region: rve_3; cl15866 323098008330 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 323098008331 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 323098008332 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 323098008333 trimer interface [polypeptide binding]; other site 323098008334 active site 323098008335 UDP-GlcNAc binding site [chemical binding]; other site 323098008336 lipid binding site [chemical binding]; lipid-binding site 323098008337 Helix-turn-helix domains; Region: HTH; cl00088 323098008338 Helix-turn-helix domains; Region: HTH; cl00088 323098008339 putative transposase OrfB; Reviewed; Region: PHA02517 323098008340 Helix-turn-helix domains; Region: HTH; cl00088 323098008341 Integrase core domain; Region: rve; cl01316 323098008342 Integrase core domain; Region: rve_3; cl15866 323098008343 Protein of unknown function, DUF488; Region: DUF488; cl01246 323098008344 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 323098008345 catalytic residues [active] 323098008346 catalytic nucleophile [active] 323098008347 Recombinase; Region: Recombinase; pfam07508 323098008348 Uncharacterized protein conserved in bacteria (DUF2136); Region: DUF2136; cl01912 323098008349 Predicted transcription regulator containing HTH domain [Transcription]; Region: COG5499 323098008350 Helix-turn-helix domains; Region: HTH; cl00088 323098008351 Winged helix-turn helix; Region: HTH_29; pfam13551 323098008352 Helix-turn-helix domains; Region: HTH; cl00088 323098008353 Integrase core domain; Region: rve; cl01316 323098008354 Integrase core domain; Region: rve_3; cl15866 323098008355 Helix-turn-helix domains; Region: HTH; cl00088 323098008356 Transposase domain (DUF772); Region: DUF772; cl15789 323098008357 Transposase domain (DUF772); Region: DUF772; cl15789 323098008358 Helix-turn-helix domains; Region: HTH; cl00088 323098008359 Virulence protein [General function prediction only]; Region: COG3943 323098008360 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 323098008361 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 323098008362 Domain of unknown function (DUF4263); Region: DUF4263; pfam14082 323098008363 HAD-superfamily hydrolase, subfamily IIB; Region: HAD-SF-IIB; TIGR01484 323098008364 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 323098008365 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 323098008366 dimerization interface [polypeptide binding]; other site 323098008367 putative DNA binding site [nucleotide binding]; other site 323098008368 putative Zn2+ binding site [ion binding]; other site 323098008369 Low molecular weight phosphatase family; Region: LMWPc; cl00105 323098008370 active site 323098008371 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 323098008372 ArsC family; Region: ArsC; pfam03960 323098008373 catalytic residues [active] 323098008374 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 323098008375 Membrane transport protein; Region: Mem_trans; cl09117 323098008376 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 323098008377 FixH; Region: FixH; cl01254 323098008378 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 323098008379 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 323098008380 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 323098008381 Protein of unknown function, DUF; Region: DUF411; cl01142 323098008382 Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators; Region: HTH_CadR-PbrR-like; cd04785 323098008383 DNA binding residues [nucleotide binding] 323098008384 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 323098008385 dimer interface [polypeptide binding]; other site 323098008386 putative metal binding site [ion binding]; other site 323098008387 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 323098008388 zinc/cadmium/mercury/lead-transporting ATPase; Provisional; Region: zntA; PRK11033 323098008389 metal-binding site [ion binding] 323098008390 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 323098008391 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 323098008392 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 323098008393 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 323098008394 DNA binding site [nucleotide binding] 323098008395 active site 323098008396 Int/Topo IB signature motif; other site 323098008397 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 323098008398 catalytic residues [active] 323098008399 catalytic nucleophile [active] 323098008400 Recombinase; Region: Recombinase; pfam07508 323098008401 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 323098008402 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 323098008403 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 323098008404 Zn2+ binding site [ion binding]; other site 323098008405 Mg2+ binding site [ion binding]; other site 323098008406 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384