-- dump date 20140619_233225 -- class Genbank::misc_feature -- table misc_feature_note -- id note 123214000001 AAA-like domain; Region: AAA_10; pfam12846 123214000002 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 123214000003 TraM recognition site of TraD and TraG; Region: TraG-D_C; pfam12696 123214000004 Flagellin N-methylase; Region: FliB; pfam03692 123214000005 hypothetical protein; Validated; Region: PRK08116 123214000006 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 123214000007 Walker A motif; other site 123214000008 ATP binding site [chemical binding]; other site 123214000009 Walker B motif; other site 123214000010 arginine finger; other site 123214000011 Phage integrase, N-terminal SAM-like domain; Region: Phage_integr_N; cl12235 123214000012 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 123214000013 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 123214000014 active site 123214000015 Int/Topo IB signature motif; other site 123214000016 catalytic residues [active] 123214000017 DNA binding site [nucleotide binding] 123214000018 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4185 123214000019 AAA domain; Region: AAA_33; pfam13671 123214000020 conjugal transfer mating pair stabilization protein TraN; Reviewed; Region: PRK12355 123214000021 conjugal transfer mating pair stabilization protein TraN; Reviewed; Region: PRK12355 123214000022 Type-F conjugative transfer system pilin assembly protein; Region: TrbC_Ftype; cl09883 123214000023 TraU protein; Region: TraU; pfam06834 123214000024 RelB antitoxin; Region: RelB; cl01171 123214000025 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 123214000026 Conjugative relaxosome accessory transposon protein; Region: TraH; cl05580 123214000027 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 123214000028 catalytic residues [active] 123214000029 Putative helicase; Region: TraI_2; pfam07514 123214000030 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 123214000031 Zn2+ binding site [ion binding]; other site 123214000032 Mg2+ binding site [ion binding]; other site 123214000033 Type-F conjugative transfer system protein (TrbI_Ftype); Region: TrbI_Ftype; cl11515 123214000034 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 123214000035 type-IV secretion system protein TraC; Region: TraC-F-type; TIGR02746 123214000036 type IV conjugative transfer system lipoprotein TraV; Region: TraV; TIGR02747 123214000037 Type IV conjugative transfer system lipoprotein (TraV); Region: TraV; pfam09676 123214000038 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 123214000039 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 123214000040 dimer interface [polypeptide binding]; other site 123214000041 catalytic residues [active] 123214000042 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 123214000043 Bacterial SH3 domain; Region: SH3_3; pfam08239 123214000044 type IV conjugative transfer system protein TraE; Region: TraE_TIGR; TIGR02761 123214000045 type IV conjugative transfer system protein TraL; Region: TraL_TIGR; TIGR02762 123214000046 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 123214000047 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 123214000048 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 123214000049 DNA topoisomerase III; Provisional; Region: PRK07726 123214000050 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 123214000051 active site 123214000052 putative interdomain interaction site [polypeptide binding]; other site 123214000053 putative metal-binding site [ion binding]; other site 123214000054 putative nucleotide binding site [chemical binding]; other site 123214000055 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 123214000056 domain I; other site 123214000057 DNA binding groove [nucleotide binding] 123214000058 phosphate binding site [ion binding]; other site 123214000059 domain II; other site 123214000060 domain III; other site 123214000061 nucleotide binding site [chemical binding]; other site 123214000062 catalytic site [active] 123214000063 domain IV; other site 123214000064 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 123214000065 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 123214000066 Initiator Replication protein; Region: Rep_3; pfam01051 123214000067 Plasmid segregation protein ParM and similar proteins; Region: ParM_like; cd10227 123214000068 PRTRC system protein D; Region: PRTRC_D; TIGR03739 123214000069 Mg binding site [ion binding]; other site 123214000070 nucleotide binding site [chemical binding]; other site 123214000071 putative protofilament interface [polypeptide binding]; other site 123214000072 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 123214000073 oligomerisation interface [polypeptide binding]; other site 123214000074 mobile loop; other site 123214000075 roof hairpin; other site 123214000076 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 123214000077 [Protein-PII] uridylyltransferase; Region: UTase_glnD; TIGR01693 123214000078 metal binding triad; other site 123214000079 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 123214000080 CRISPR/Cas system-associated protein Cas3'' Region: Cas3''_I; cl17503 123214000081 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 123214000082 DNA mismatch repair protein MutL; Region: mutl; TIGR00585 123214000083 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 123214000084 ATP binding site [chemical binding]; other site 123214000085 Mg2+ binding site [ion binding]; other site 123214000086 G-X-G motif; other site 123214000087 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 123214000088 ATP binding site [chemical binding]; other site 123214000089 MutL C terminal dimerisation domain; Region: MutL_C; smart00853 123214000090 menaquinone biosynthesis decarboxylase, SCO4490 family; Region: mena_SCO4490; TIGR03701 123214000091 Chain length determinant protein; Region: Wzz; cl15801 123214000092 AAA domain; Region: AAA_32; pfam13654 123214000093 lon-related putative ATP-dependent protease; Region: lon_rel; TIGR00764 123214000094 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 123214000095 Protein of unknown function (DUF2914); Region: DUF2914; pfam11141 123214000096 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 123214000097 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 123214000098 active site 123214000099 substrate binding site [chemical binding]; other site 123214000100 cosubstrate binding site; other site 123214000101 catalytic site [active] 123214000102 alpha-glucosidase; Provisional; Region: PRK10137 123214000103 Trehalase; Region: Trehalase; cl17346 123214000104 Protein of unknown function, DUF547; Region: DUF547; pfam04784 123214000105 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 123214000106 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 123214000107 dimerization interface [polypeptide binding]; other site 123214000108 putative ATP binding site [chemical binding]; other site 123214000109 putative NTPase; Provisional; Region: PRK13695 123214000110 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 123214000111 putative active site; other site 123214000112 catalytic triad [active] 123214000113 putative dimer interface [polypeptide binding]; other site 123214000114 Uncharacterized protein family UPF0047; Region: UPF0047; pfam01894 123214000115 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 123214000116 active site 123214000117 D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not...; Region: Dtyr_deacylase; cd00563 123214000118 putative active site [active] 123214000119 dimerization interface [polypeptide binding]; other site 123214000120 putative tRNAtyr binding site [nucleotide binding]; other site 123214000121 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 123214000122 alpha,alpha-trehalose-phosphate synthase [UDP-forming]; Region: trehalose_OtsA; TIGR02400 123214000123 active site 123214000124 homotetramer interface [polypeptide binding]; other site 123214000125 GTP-binding protein Der; Reviewed; Region: PRK00093 123214000126 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 123214000127 G1 box; other site 123214000128 GTP/Mg2+ binding site [chemical binding]; other site 123214000129 Switch I region; other site 123214000130 G2 box; other site 123214000131 Switch II region; other site 123214000132 G3 box; other site 123214000133 G4 box; other site 123214000134 G5 box; other site 123214000135 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 123214000136 G1 box; other site 123214000137 GTP/Mg2+ binding site [chemical binding]; other site 123214000138 Switch I region; other site 123214000139 G2 box; other site 123214000140 G3 box; other site 123214000141 Switch II region; other site 123214000142 G4 box; other site 123214000143 G5 box; other site 123214000144 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 123214000145 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 123214000146 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 123214000147 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214000148 metal binding site [ion binding]; metal-binding site 123214000149 active site 123214000150 I-site; other site 123214000151 Pyruvate kinase [Carbohydrate transport and metabolism]; Region: PykF; COG0469 123214000152 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; cl17342 123214000153 domain interfaces; other site 123214000154 active site 123214000155 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 123214000156 metal binding site 2 [ion binding]; metal-binding site 123214000157 putative DNA binding helix; other site 123214000158 metal binding site 1 [ion binding]; metal-binding site 123214000159 dimer interface [polypeptide binding]; other site 123214000160 structural Zn2+ binding site [ion binding]; other site 123214000161 Sulfite oxidase and related enzymes [General function prediction only]; Region: COG2041 123214000162 bacterial and archael members of the sulfite oxidase (SO) family of molybdopterin binding domains. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and...; Region: arch_bact_SO_family_Moco; cd02109 123214000163 Moco binding site; other site 123214000164 metal coordination site [ion binding]; other site 123214000165 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 123214000166 Peptidase M20 acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (ArgE/DapE)-like; Region: M20_ArgE_DapE_like; cd08659 123214000167 metal binding site [ion binding]; metal-binding site 123214000168 dimer interface [polypeptide binding]; other site 123214000169 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 123214000170 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 123214000171 Coenzyme A binding pocket [chemical binding]; other site 123214000172 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 123214000173 FeS/SAM binding site; other site 123214000174 Radical SAM superfamily; Region: Radical_SAM; pfam04055 123214000175 GMP synthase; Reviewed; Region: guaA; PRK00074 123214000176 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 123214000177 AMP/PPi binding site [chemical binding]; other site 123214000178 candidate oxyanion hole; other site 123214000179 catalytic triad [active] 123214000180 potential glutamine specificity residues [chemical binding]; other site 123214000181 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 123214000182 ATP Binding subdomain [chemical binding]; other site 123214000183 Ligand Binding sites [chemical binding]; other site 123214000184 Dimerization subdomain; other site 123214000185 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214000186 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 123214000187 NAD(P) binding site [chemical binding]; other site 123214000188 active site 123214000189 ABC transporter G family member; Provisional; Region: PLN03140 123214000190 V-type ATP synthase subunit C; Provisional; Region: PRK01198; cl00660 123214000191 Archaeal/vacuolar-type H+-ATPase subunit I [Energy production and conversion]; Region: NtpI; COG1269 123214000192 ATP synthase (F/14-kDa) subunit; Region: ATP-synt_F; pfam01990 123214000193 V-type ATP synthase subunit A; Provisional; Region: PRK04192 123214000194 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 123214000195 V/A-type ATP synthase catalytic subunit A. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi...; Region: V_A-ATPase_A; cd01134 123214000196 Walker A motif/ATP binding site; other site 123214000197 Walker B motif; other site 123214000198 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 123214000199 V-type ATP synthase subunit B; Provisional; Region: PRK04196 123214000200 V/A-type ATP synthase (non-catalytic) subunit B. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi...; Region: V_A-ATPase_B; cd01135 123214000201 Walker A motif homologous position; other site 123214000202 Walker B motif; other site 123214000203 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 123214000204 ATP synthase subunit D; Region: ATP-synt_D; pfam01813 123214000205 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 123214000206 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 123214000207 RNA binding site [nucleotide binding]; other site 123214000208 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 123214000209 RNA binding site [nucleotide binding]; other site 123214000210 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 123214000211 RNA binding site [nucleotide binding]; other site 123214000212 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 123214000213 RNA binding site [nucleotide binding]; other site 123214000214 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 123214000215 RNA binding site [nucleotide binding]; other site 123214000216 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 123214000217 RNA binding site [nucleotide binding]; other site 123214000218 Ca2+/Na+ antiporter [Inorganic ion transport and metabolism]; Region: ECM27; COG0530 123214000219 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 123214000220 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 123214000221 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 123214000222 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 123214000223 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 123214000224 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 123214000225 putative active site [active] 123214000226 FOG: CBS domain [General function prediction only]; Region: COG0517 123214000227 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_9; cd04622 123214000228 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 123214000229 M20 Peptidase Aminoacylase 1 family; Region: M20_Acy1; cd03886 123214000230 metal binding site [ion binding]; metal-binding site 123214000231 dimer interface [polypeptide binding]; other site 123214000232 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 123214000233 AAA domain; Region: AAA_14; pfam13173 123214000234 copper-resistance protein, CopA family; Region: copper_res_A; TIGR01480 123214000235 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 123214000236 Multicopper oxidase; Region: Cu-oxidase; pfam00394 123214000237 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 123214000238 Copper resistance protein B precursor (CopB); Region: CopB; pfam05275 123214000239 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 123214000240 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 123214000241 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 123214000242 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 123214000243 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 123214000244 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 123214000245 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 123214000246 rod shape-determining protein MreC; Provisional; Region: PRK13922 123214000247 rod shape-determining protein MreC; Region: MreC; pfam04085 123214000248 rod shape-determining protein MreB; Provisional; Region: PRK13927 123214000249 MreB and similar proteins; Region: MreB_like; cd10225 123214000250 nucleotide binding site [chemical binding]; other site 123214000251 Mg binding site [ion binding]; other site 123214000252 putative protofilament interaction site [polypeptide binding]; other site 123214000253 RodZ interaction site [polypeptide binding]; other site 123214000254 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 123214000255 dihydrodipicolinate synthase; Region: dapA; TIGR00674 123214000256 dimer interface [polypeptide binding]; other site 123214000257 active site 123214000258 catalytic residue [active] 123214000259 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 123214000260 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 123214000261 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 123214000262 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 123214000263 inhibitor-cofactor binding pocket; inhibition site 123214000264 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214000265 catalytic residue [active] 123214000266 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 123214000267 homopentamer interface [polypeptide binding]; other site 123214000268 active site 123214000269 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 123214000270 putative RNA binding site [nucleotide binding]; other site 123214000271 Calcineurin-like phosphoesterase superfamily domain; Region: Metallophos_2; pfam12850 123214000272 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 123214000273 active site 123214000274 metal binding site [ion binding]; metal-binding site 123214000275 Preprotein translocase subunit; Region: YajC; pfam02699 123214000276 poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA; Region: PGA_TPR_OMP; TIGR03939 123214000277 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:...; Region: TRX_Fd_family; cd02980 123214000278 dimer interface [polypeptide binding]; other site 123214000279 [2Fe-2S] cluster binding site [ion binding]; other site 123214000280 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 123214000281 FAD binding site [chemical binding]; other site 123214000282 Predicted HD superfamily hydrolase [General function prediction only]; Region: COG1418 123214000283 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 123214000284 Zn2+ binding site [ion binding]; other site 123214000285 Mg2+ binding site [ion binding]; other site 123214000286 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 123214000287 5,10-methenyltetrahydrofolate synthetase; Region: MTHFS_bact; TIGR02727 123214000288 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 123214000289 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 123214000290 putative tRNA-binding site [nucleotide binding]; other site 123214000291 B3/4 domain; Region: B3_4; pfam03483 123214000292 tRNA synthetase B5 domain; Region: B5; smart00874 123214000293 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 123214000294 dimer interface [polypeptide binding]; other site 123214000295 motif 1; other site 123214000296 motif 3; other site 123214000297 motif 2; other site 123214000298 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 123214000299 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 123214000300 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 123214000301 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 123214000302 dimer interface [polypeptide binding]; other site 123214000303 motif 1; other site 123214000304 active site 123214000305 motif 2; other site 123214000306 motif 3; other site 123214000307 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 123214000308 23S rRNA binding site [nucleotide binding]; other site 123214000309 L21 binding site [polypeptide binding]; other site 123214000310 L13 binding site [polypeptide binding]; other site 123214000311 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 123214000312 Cytochrome C' Region: Cytochrom_C_2; cl01610 123214000313 Cytochrome c554 and c-prime; Region: Cytochrome_C554; pfam13435 123214000314 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cl03439 123214000315 heme-binding residues [chemical binding]; other site 123214000316 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 123214000317 active site 123214000318 dimerization interface [polypeptide binding]; other site 123214000319 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...; Region: RuvC_resolvase; cd00529 123214000320 active site 123214000321 putative DNA-binding cleft [nucleotide binding]; other site 123214000322 dimer interface [polypeptide binding]; other site 123214000323 hypothetical protein; Validated; Region: PRK00110 123214000324 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]; Region: COG2231 123214000325 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 123214000326 minor groove reading motif; other site 123214000327 helix-hairpin-helix signature motif; other site 123214000328 substrate binding pocket [chemical binding]; other site 123214000329 active site 123214000330 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 123214000331 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 123214000332 putative acyl-acceptor binding pocket; other site 123214000333 LytB protein; Region: LYTB; cl00507 123214000334 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 123214000335 PilZ domain; Region: PilZ; pfam07238 123214000336 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 123214000337 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 123214000338 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 123214000339 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 123214000340 ligand binding site [chemical binding]; other site 123214000341 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 123214000342 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 123214000343 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 123214000344 ligand binding site [chemical binding]; other site 123214000345 Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase; Region: PUA; smart00359 123214000346 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 123214000347 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 123214000348 putative RNA binding site [nucleotide binding]; other site 123214000349 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 123214000350 S-adenosylmethionine binding site [chemical binding]; other site 123214000351 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 123214000352 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 123214000353 S-adenosylmethionine binding site [chemical binding]; other site 123214000354 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 123214000355 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 123214000356 hinge; other site 123214000357 active site 123214000358 RNA polymerase sigma factor RpoD, C-terminal domain; Region: RpoD_Cterm; TIGR02393 123214000359 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 123214000360 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 123214000361 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 123214000362 DNA binding residues [nucleotide binding] 123214000363 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 123214000364 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 123214000365 dimer interface [polypeptide binding]; other site 123214000366 anticodon binding site; other site 123214000367 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...; Region: AspRS_core; cd00777 123214000368 homodimer interface [polypeptide binding]; other site 123214000369 motif 1; other site 123214000370 active site 123214000371 motif 2; other site 123214000372 GAD domain; Region: GAD; pfam02938 123214000373 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...; Region: AspRS_core; cd00777 123214000374 motif 3; other site 123214000375 Tetratricopeptide repeat; Region: TPR_12; pfam13424 123214000376 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 123214000377 binding surface 123214000378 TPR motif; other site 123214000379 Tetratricopeptide repeat; Region: TPR_12; pfam13424 123214000380 haloacid dehalogenase superfamily, subfamily IA, variant 1 with third motif having Dx(3-4)D or Dx(3-4)E; Region: HAD-SF-IA-v1; TIGR01549 123214000381 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 123214000382 motif II; other site 123214000383 argininosuccinate lyase; Provisional; Region: PRK00855 123214000384 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 123214000385 active sites [active] 123214000386 tetramer interface [polypeptide binding]; other site 123214000387 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 123214000388 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214000389 metal binding site [ion binding]; metal-binding site 123214000390 active site 123214000391 I-site; other site 123214000392 competence damage-inducible protein A; Provisional; Region: PRK00549 123214000393 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 123214000394 putative MPT binding site; other site 123214000395 Competence-damaged protein; Region: CinA; pfam02464 123214000396 SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. In this subgroup, SpoIVFB (sporulation protein, stage IV cell...; Region: S2P-M50_SpoIVFB_CBS; cd06164 123214000397 Peptidase family M50; Region: Peptidase_M50; pfam02163 123214000398 active site 123214000399 putative substrate binding region [chemical binding]; other site 123214000400 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 123214000401 FOG: CBS domain [General function prediction only]; Region: COG0517 123214000402 Uncharacterized metal-binding protein (DUF2227); Region: DUF2227; pfam09988 123214000403 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 123214000404 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 123214000405 ligand binding site [chemical binding]; other site 123214000406 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 123214000407 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 123214000408 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 123214000409 P loop; other site 123214000410 GTP binding site [chemical binding]; other site 123214000411 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 123214000412 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 123214000413 Glutamate-cysteine ligase family 2(GCS2); Region: GCS2; cl00954 123214000414 carboxylate-amine ligase, YbdK family; Region: gshA_cyan_rel; TIGR02050 123214000415 Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]; Region: NfeD; COG1030 123214000416 Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Region: Clp_protease_NfeD_1; cd07020 123214000417 dimer interface [polypeptide binding]; other site 123214000418 active site residues [active] 123214000419 PRA1 family protein; Region: PRA1; cl02137 123214000420 NfeD-like C-terminal, partner-binding; Region: NfeD; pfam01957 123214000421 carbon-monoxide dehydrogenase, catalytic subunit; Region: CO_DH_cata; TIGR01702 123214000422 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 123214000423 ACS interaction site; other site 123214000424 CODH interaction site; other site 123214000425 metal cluster binding site [ion binding]; other site 123214000426 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 123214000427 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 123214000428 catalytic residue [active] 123214000429 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 123214000430 lipoyl attachment site [posttranslational modification]; other site 123214000431 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 123214000432 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 123214000433 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 123214000434 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 123214000435 active site 123214000436 catalytic residues [active] 123214000437 metal binding site [ion binding]; metal-binding site 123214000438 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 123214000439 Memo (mediator of ErbB2-driven cell motility) is co-precipitated with the C terminus of ErbB2, a protein involved in cell motility; Region: MEMO_like; cd07361 123214000440 putative ligand binding pocket/active site [active] 123214000441 putative metal binding site [ion binding]; other site 123214000442 AmmeMemoRadiSam system protein A; Region: AmmeMemoSam_A; TIGR04335 123214000443 AMMECR1; Region: AMMECR1; pfam01871 123214000444 Ferritin-like domain; Region: Ferritin; pfam00210 123214000445 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 123214000446 dinuclear metal binding motif [ion binding]; other site 123214000447 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 123214000448 active site clefts [active] 123214000449 zinc binding site [ion binding]; other site 123214000450 dimer interface [polypeptide binding]; other site 123214000451 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 123214000452 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 123214000453 trimer interface [polypeptide binding]; other site 123214000454 active site 123214000455 substrate binding site [chemical binding]; other site 123214000456 CoA binding site [chemical binding]; other site 123214000457 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 123214000458 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 123214000459 Deinococcus radiodurans DR1281 and related proteins, metallophosphatase domain; Region: MPP_DR1281; cd07382 123214000460 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 123214000461 putative active site [active] 123214000462 metal binding site [ion binding]; metal-binding site 123214000463 homodimer binding site [polypeptide binding]; other site 123214000464 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 123214000465 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cl00290 123214000466 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 123214000467 4-hydroxythreonine-4-phosphate dehydrogenase; Region: pdxA; TIGR00557 123214000468 DsrE/DsrF-like family; Region: DrsE; cl00672 123214000469 DsrE/DsrF-like family; Region: DrsE; pfam02635 123214000470 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 123214000471 CPxP motif; other site 123214000472 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 123214000473 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 123214000474 ATP binding site [chemical binding]; other site 123214000475 substrate interface [chemical binding]; other site 123214000476 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 123214000477 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 123214000478 FMN binding site [chemical binding]; other site 123214000479 substrate binding site [chemical binding]; other site 123214000480 putative catalytic residue [active] 123214000481 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 123214000482 DHH family; Region: DHH; pfam01368 123214000483 DHHA1 domain; Region: DHHA1; pfam02272 123214000484 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 123214000485 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides; Region: PRX_Typ2cys; cd03015 123214000486 dimer interface [polypeptide binding]; other site 123214000487 decamer (pentamer of dimers) interface [polypeptide binding]; other site 123214000488 catalytic triad [active] 123214000489 peroxidatic and resolving cysteines [active] 123214000490 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 123214000491 Yqey-like protein; Region: YqeY; pfam09424 123214000492 DsrE/DsrF/DrsH-like family; Region: DrsE_2; pfam13686 123214000493 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 123214000494 RIP metalloprotease RseP; Region: TIGR00054 123214000495 active site 123214000496 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 123214000497 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 123214000498 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 123214000499 putative substrate binding region [chemical binding]; other site 123214000500 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 123214000501 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 123214000502 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 123214000503 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 123214000504 Glutaredoxin-like domain protein; Region: GlrX_arch; TIGR02187 123214000505 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 123214000506 Thioredoxin (TRX)-Glutaredoxin (GRX)-like family; composed of archaeal and bacterial proteins that show similarity to both TRX and GRX, including the C-terminal TRX-fold subdomain of Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). All...; Region: TRX_GRX_like; cd02973 123214000507 catalytic residues [active] 123214000508 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 123214000509 4Fe-4S binding domain; Region: Fer4; cl02805 123214000510 NADH:ubiquinone oxidoreductase 27 kD subunit [Energy production and conversion]; Region: NuoC; COG0852 123214000511 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl16917 123214000512 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 123214000513 NADH dehydrogenase subunit D; Validated; Region: PRK06075 123214000514 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 123214000515 tetramer interfaces [polypeptide binding]; other site 123214000516 binuclear metal-binding site [ion binding]; other site 123214000517 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]; Region: COG2957; cl01113 123214000518 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; pfam04371 123214000519 Bacterial SH3 domain; Region: SH3_3; pfam08239 123214000520 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 123214000521 nucleoside/Zn binding site; other site 123214000522 dimer interface [polypeptide binding]; other site 123214000523 catalytic motif [active] 123214000524 cytidylate kinase; Provisional; Region: cmk; PRK00023 123214000525 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 123214000526 CMP-binding site; other site 123214000527 The sites determining sugar specificity; other site 123214000528 Glucoamylase and related glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: SGA1; COG3387 123214000529 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 123214000530 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 123214000531 MoaE interaction surface [polypeptide binding]; other site 123214000532 MoeB interaction surface [polypeptide binding]; other site 123214000533 thiocarboxylated glycine; other site 123214000534 Pyrimidine reductase, riboflavin biosynthesis [Coenzyme metabolism]; Region: RibD; COG1985 123214000535 RibD C-terminal domain; Region: RibD_C; cl17279 123214000536 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 123214000537 ketol-acid reductoisomerase; Provisional; Region: PRK05479 123214000538 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 123214000539 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 123214000540 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 123214000541 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 123214000542 putative valine binding site [chemical binding]; other site 123214000543 dimer interface [polypeptide binding]; other site 123214000544 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 123214000545 acetolactate synthase, large subunit, biosynthetic type; Region: acolac_lg; TIGR00118 123214000546 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 123214000547 PYR/PP interface [polypeptide binding]; other site 123214000548 dimer interface [polypeptide binding]; other site 123214000549 TPP binding site [chemical binding]; other site 123214000550 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 123214000551 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 123214000552 TPP-binding site [chemical binding]; other site 123214000553 dimer interface [polypeptide binding]; other site 123214000554 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 123214000555 Glucose inhibited division protein A; Region: GIDA; pfam01134 123214000556 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 123214000557 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 123214000558 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 123214000559 MoaE homodimer interface [polypeptide binding]; other site 123214000560 MoaD interaction [polypeptide binding]; other site 123214000561 active site residues [active] 123214000562 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 123214000563 aspartate aminotransferase; Provisional; Region: PRK05764 123214000564 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 123214000565 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214000566 homodimer interface [polypeptide binding]; other site 123214000567 catalytic residue [active] 123214000568 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 123214000569 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 123214000570 RNA binding surface [nucleotide binding]; other site 123214000571 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 123214000572 Transcriptional regulator [Transcription]; Region: LysR; COG0583 123214000573 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 123214000574 C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; Region: PBP2_CysL_like; cd08420 123214000575 putative dimerization interface [polypeptide binding]; other site 123214000576 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 123214000577 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 123214000578 putative active site [active] 123214000579 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 123214000580 PSP1 C-terminal conserved region; Region: PSP1; cl00770 123214000581 DNA polymerase III, delta subunit; Region: DNA_pol3_delta2; pfam13177 123214000582 DNA polymerase III subunit delta'; Validated; Region: PRK08485 123214000583 thymidylate kinase; Validated; Region: tmk; PRK00698 123214000584 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 123214000585 TMP-binding site; other site 123214000586 ATP-binding site [chemical binding]; other site 123214000587 NifU-like domain; Region: NifU; pfam01106 123214000588 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 123214000589 metal binding triad; other site 123214000590 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 123214000591 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 123214000592 metal binding triad; other site 123214000593 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 123214000594 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 123214000595 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 123214000596 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 123214000597 protein binding site [polypeptide binding]; other site 123214000598 RNA polymerase sigma factor RpoD, C-terminal domain; Region: RpoD_Cterm; TIGR02393 123214000599 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 123214000600 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 123214000601 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 123214000602 DNA binding residues [nucleotide binding] 123214000603 Predicted membrane protein [Function unknown]; Region: COG1238 123214000604 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 123214000605 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 123214000606 active site 123214000607 HIGH motif; other site 123214000608 dimer interface [polypeptide binding]; other site 123214000609 KMSKS motif; other site 123214000610 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 123214000611 RNA binding surface [nucleotide binding]; other site 123214000612 acetylornithine aminotransferase; Provisional; Region: PRK02627 123214000613 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 123214000614 inhibitor-cofactor binding pocket; inhibition site 123214000615 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214000616 catalytic residue [active] 123214000617 ribonuclease R; Region: RNase_R; TIGR02063 123214000618 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 123214000619 RNB domain; Region: RNB; pfam00773 123214000620 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...; Region: S1_RNase_R; cd04471 123214000621 RNA binding site [nucleotide binding]; other site 123214000622 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 123214000623 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 123214000624 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 123214000625 F0F1-type ATP synthase, delta subunit (mitochondrial oligomycin sensitivity protein) [Energy production and conversion]; Region: AtpH; COG0712 123214000626 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 123214000627 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 123214000628 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 123214000629 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 123214000630 beta subunit interaction interface [polypeptide binding]; other site 123214000631 Walker A motif; other site 123214000632 ATP binding site [chemical binding]; other site 123214000633 Walker B motif; other site 123214000634 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 123214000635 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 123214000636 core domain interface [polypeptide binding]; other site 123214000637 delta subunit interface [polypeptide binding]; other site 123214000638 epsilon subunit interface [polypeptide binding]; other site 123214000639 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 123214000640 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 123214000641 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 123214000642 alpha subunit interaction interface [polypeptide binding]; other site 123214000643 Walker A motif; other site 123214000644 ATP binding site [chemical binding]; other site 123214000645 Walker B motif; other site 123214000646 inhibitor binding site; inhibition site 123214000647 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 123214000648 UGMP family protein; Validated; Region: PRK09604 123214000649 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 123214000650 Carbamoyltransferase; Region: CmcH_NodU; pfam02543 123214000651 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 123214000652 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 123214000653 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 123214000654 protein binding site [polypeptide binding]; other site 123214000655 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 123214000656 Catalytic dyad [active] 123214000657 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 123214000658 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214000659 metal binding site [ion binding]; metal-binding site 123214000660 active site 123214000661 I-site; other site 123214000662 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 123214000663 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 123214000664 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 123214000665 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 123214000666 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 123214000667 Tetramer interface [polypeptide binding]; other site 123214000668 active site 123214000669 FMN-binding site [chemical binding]; other site 123214000670 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 123214000671 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 123214000672 ATP synthase subunit C; Region: ATP-synt_C; cl00466 123214000673 hypothetical protein; Provisional; Region: PRK14382 123214000674 membrane protein insertase; Provisional; Region: PRK01318 123214000675 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 123214000676 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 123214000677 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 123214000678 trmE is a tRNA modification GTPase; Region: trmE; cd04164 123214000679 G1 box; other site 123214000680 GTP/Mg2+ binding site [chemical binding]; other site 123214000681 Switch I region; other site 123214000682 G2 box; other site 123214000683 Switch II region; other site 123214000684 G3 box; other site 123214000685 G4 box; other site 123214000686 G5 box; other site 123214000687 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 123214000688 transcription termination factor Rho; Provisional; Region: rho; PRK09376 123214000689 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 123214000690 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 123214000691 RNA binding site [nucleotide binding]; other site 123214000692 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 123214000693 multimer interface [polypeptide binding]; other site 123214000694 Walker A motif; other site 123214000695 ATP binding site [chemical binding]; other site 123214000696 Walker B motif; other site 123214000697 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00019 123214000698 peptide chain release factor 1; Validated; Region: prfA; PRK00591 123214000699 This domain is found in peptide chain release factors; Region: PCRF; smart00937 123214000700 RF-1 domain; Region: RF-1; pfam00472 123214000701 prolyl-tRNA synthetase; Provisional; Region: PRK09194 123214000702 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...; Region: ProRS_core_prok; cd00779 123214000703 dimer interface [polypeptide binding]; other site 123214000704 motif 1; other site 123214000705 active site 123214000706 motif 2; other site 123214000707 INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and...; Region: ProRS-INS; cd04334 123214000708 putative deacylase active site [active] 123214000709 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 123214000710 active site 123214000711 motif 3; other site 123214000712 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 123214000713 anticodon binding site; other site 123214000714 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 123214000715 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 123214000716 PAS fold; Region: PAS; pfam00989 123214000717 PAS domain; Region: PAS; smart00091 123214000718 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 123214000719 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 123214000720 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 123214000721 Walker A motif; other site 123214000722 ATP binding site [chemical binding]; other site 123214000723 Walker B motif; other site 123214000724 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 123214000725 DNA methylase; Region: N6_N4_Mtase; pfam01555 123214000726 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 123214000727 S-adenosylmethionine binding site [chemical binding]; other site 123214000728 GTP-binding protein YchF; Reviewed; Region: PRK09601 123214000729 YchF GTPase; Region: YchF; cd01900 123214000730 G1 box; other site 123214000731 GTP/Mg2+ binding site [chemical binding]; other site 123214000732 Switch I region; other site 123214000733 G2 box; other site 123214000734 Switch II region; other site 123214000735 G3 box; other site 123214000736 G4 box; other site 123214000737 G5 box; other site 123214000738 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 123214000739 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 123214000740 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 123214000741 Predicted permeases [General function prediction only]; Region: COG0679 123214000742 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 123214000743 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 123214000744 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 123214000745 catalytic residue [active] 123214000746 flagellar biosynthesis anti-sigma factor FlgM; Region: FlgM_jcvi; TIGR03824 123214000747 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 123214000748 Glycoprotease family; Region: Peptidase_M22; pfam00814 123214000749 exopolyphosphatase; Region: exo_poly_only; TIGR03706 123214000750 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 123214000751 nucleotide binding site [chemical binding]; other site 123214000752 NIL domain; Region: NIL; pfam09383 123214000753 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 123214000754 MoaE interaction surface [polypeptide binding]; other site 123214000755 MoeB interaction surface [polypeptide binding]; other site 123214000756 thiocarboxylated glycine; other site 123214000757 threonine synthase; Validated; Region: PRK07591 123214000758 Threonine synthase is a pyridoxal phosphate (PLP) dependent enzyme that catalyses the last reaction in the synthesis of threonine from aspartate. It proceeds by converting O-phospho-L-homoserine (OPH) into threonine and inorganic phosphate. In plants; Region: Thr-synth_1; cd01563 123214000759 homodimer interface [polypeptide binding]; other site 123214000760 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214000761 catalytic residue [active] 123214000762 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 123214000763 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; cl17186 123214000764 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...; Region: CBS_pair_IMPDH; cd04601 123214000765 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...; Region: IMPDH; cd00381 123214000766 active site 123214000767 Phosphoglycerate kinase; Region: PGK; pfam00162 123214000768 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 123214000769 substrate binding site [chemical binding]; other site 123214000770 hinge regions; other site 123214000771 ADP binding site [chemical binding]; other site 123214000772 catalytic site [active] 123214000773 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 123214000774 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 123214000775 active site 123214000776 dimerization interface [polypeptide binding]; other site 123214000777 Chorismate mutase type II; Region: CM_2; smart00830 123214000778 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 123214000779 Prephenate dehydratase; Region: PDT; pfam00800 123214000780 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 123214000781 putative L-Phe binding site [chemical binding]; other site 123214000782 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 123214000783 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 123214000784 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 123214000785 rRNA interaction site [nucleotide binding]; other site 123214000786 S8 interaction site; other site 123214000787 putative laminin-1 binding site; other site 123214000788 elongation factor Ts; Reviewed; Region: tsf; PRK12332 123214000789 UBA/TS-N domain; Region: UBA; pfam00627 123214000790 putative protein-protein interaction site; other site 123214000791 GFP-loop; other site 123214000792 Elongation factor TS; Region: EF_TS; pfam00889 123214000793 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 123214000794 putative nucleotide binding site [chemical binding]; other site 123214000795 uridine monophosphate binding site [chemical binding]; other site 123214000796 homohexameric interface [polypeptide binding]; other site 123214000797 ribosome recycling factor; Reviewed; Region: frr; PRK00083 123214000798 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...; Region: RRF; cd00520 123214000799 hinge region; other site 123214000800 ribosome maturation protein RimP; Reviewed; Region: PRK00092 123214000801 Sm and related proteins; Region: Sm_like; cl00259 123214000802 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 123214000803 putative oligomer interface [polypeptide binding]; other site 123214000804 putative RNA binding site [nucleotide binding]; other site 123214000805 NusA N-terminal domain; Region: NusA_N; pfam08529 123214000806 transcription termination factor NusA; Region: NusA; TIGR01953 123214000807 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 123214000808 RNA binding site [nucleotide binding]; other site 123214000809 homodimer interface [polypeptide binding]; other site 123214000810 NusA-like KH domain; Region: KH_5; pfam13184 123214000811 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 123214000812 G-X-X-G motif; other site 123214000813 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; Region: Ribosomal_L7Ae; cl00600 123214000814 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 123214000815 translation initiation factor IF-2; Region: IF-2; TIGR00487 123214000816 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 123214000817 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 123214000818 G1 box; other site 123214000819 putative GEF interaction site [polypeptide binding]; other site 123214000820 GTP/Mg2+ binding site [chemical binding]; other site 123214000821 Switch I region; other site 123214000822 G2 box; other site 123214000823 G3 box; other site 123214000824 Switch II region; other site 123214000825 G4 box; other site 123214000826 G5 box; other site 123214000827 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 123214000828 Translation-initiation factor 2; Region: IF-2; pfam11987 123214000829 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 123214000830 PilZ domain; Region: PilZ; pfam07238 123214000831 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 123214000832 DNA protecting protein DprA; Region: dprA; TIGR00732 123214000833 Spore germination protein; Region: Spore_permease; cl17796 123214000834 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 123214000835 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 123214000836 RNase E interface [polypeptide binding]; other site 123214000837 trimer interface [polypeptide binding]; other site 123214000838 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 123214000839 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 123214000840 RNase E interface [polypeptide binding]; other site 123214000841 trimer interface [polypeptide binding]; other site 123214000842 active site 123214000843 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 123214000844 putative nucleic acid binding region [nucleotide binding]; other site 123214000845 G-X-X-G motif; other site 123214000846 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 123214000847 RNA binding site [nucleotide binding]; other site 123214000848 domain interface; other site 123214000849 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 123214000850 16S/18S rRNA binding site [nucleotide binding]; other site 123214000851 S13e-L30e interaction site [polypeptide binding]; other site 123214000852 25S rRNA binding site [nucleotide binding]; other site 123214000853 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 123214000854 PLD-like domain; Region: PLDc_2; pfam13091 123214000855 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cd00138 123214000856 putative active site [active] 123214000857 catalytic site [active] 123214000858 Domain of unknown function (DUF1998); Region: DUF1998; pfam09369 123214000859 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 123214000860 nucleotide binding region [chemical binding]; other site 123214000861 ATP-binding site [chemical binding]; other site 123214000862 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 123214000863 endonuclease III; Region: ENDO3c; smart00478 123214000864 minor groove reading motif; other site 123214000865 helix-hairpin-helix signature motif; other site 123214000866 substrate binding pocket [chemical binding]; other site 123214000867 active site 123214000868 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 123214000869 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 123214000870 cofactor binding site; other site 123214000871 DNA binding site [nucleotide binding] 123214000872 substrate interaction site [chemical binding]; other site 123214000873 Uncharacterized conserved protein [Function unknown]; Region: COG3287 123214000874 FIST N domain; Region: FIST; pfam08495 123214000875 FIST C domain; Region: FIST_C; pfam10442 123214000876 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 123214000877 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214000878 metal binding site [ion binding]; metal-binding site 123214000879 active site 123214000880 I-site; other site 123214000881 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 123214000882 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 123214000883 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 123214000884 Walker A/P-loop; other site 123214000885 ATP binding site [chemical binding]; other site 123214000886 Q-loop/lid; other site 123214000887 ABC transporter signature motif; other site 123214000888 Walker B; other site 123214000889 D-loop; other site 123214000890 H-loop/switch region; other site 123214000891 threonine synthase; Reviewed; Region: PRK06721 123214000892 Threonine synthase is a pyridoxal phosphate (PLP) dependent enzyme that catalyses the last reaction in the synthesis of threonine from aspartate. It proceeds by converting O-phospho-L-homoserine (OPH) into threonine and inorganic phosphate. In plants; Region: Thr-synth_1; cd01563 123214000893 homodimer interface [polypeptide binding]; other site 123214000894 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214000895 catalytic residue [active] 123214000896 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 123214000897 2-dehydropantoate 2-reductase; Region: apbA_panE; TIGR00745 123214000898 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 123214000899 ribonuclease PH; Reviewed; Region: rph; PRK00173 123214000900 Ribonuclease PH; Region: RNase_PH_bact; cd11362 123214000901 hexamer interface [polypeptide binding]; other site 123214000902 active site 123214000903 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 123214000904 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 123214000905 GDP-binding site [chemical binding]; other site 123214000906 ACT binding site; other site 123214000907 IMP binding site; other site 123214000908 Uncharacterized conserved protein [Function unknown]; Region: COG0062 123214000909 putative carbohydrate kinase; Provisional; Region: PRK10565 123214000910 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 123214000911 putative substrate binding site [chemical binding]; other site 123214000912 putative ATP binding site [chemical binding]; other site 123214000913 Fructose/tagarose-bisphosphate aldolase class II. This family includes fructose-1,6-bisphosphate (FBP) and tagarose 1,6-bisphosphate (TBP) aldolases. FBP-aldolase is homodimeric and used in gluconeogenesis and glycolysis; the enzyme controls the...; Region: FTBP_aldolase_II; cl17181 123214000914 active site 123214000915 intersubunit interface [polypeptide binding]; other site 123214000916 zinc binding site [ion binding]; other site 123214000917 Na+ binding site [ion binding]; other site 123214000918 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 123214000919 AMP binding site [chemical binding]; other site 123214000920 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 123214000921 metal binding site [ion binding]; metal-binding site 123214000922 active site 123214000923 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 123214000924 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214000925 metal binding site [ion binding]; metal-binding site 123214000926 active site 123214000927 I-site; other site 123214000928 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 123214000929 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 123214000930 NAD(P) binding site [chemical binding]; other site 123214000931 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 123214000932 camphor resistance protein CrcB; Provisional; Region: PRK14227 123214000933 PII-like signaling protein [Signal transduction mechanisms]; Region: COG1993 123214000934 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 123214000935 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 123214000936 putative dimer interface [polypeptide binding]; other site 123214000937 anthranilate synthase component I; Provisional; Region: PRK13565 123214000938 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 123214000939 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 123214000940 succinyl-diaminopimelate desuccinylase; Region: dapE-gram_pos; TIGR01900 123214000941 M20 Peptidase actinobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_actinobac; cd05647 123214000942 metal binding site [ion binding]; metal-binding site 123214000943 putative dimer interface [polypeptide binding]; other site 123214000944 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 123214000945 Transcriptional regulator [Transcription]; Region: IclR; COG1414 123214000946 Bacterial transcriptional regulator; Region: IclR; pfam01614 123214000947 Radical SAM superfamily; Region: Radical_SAM; pfam04055 123214000948 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 123214000949 FeS/SAM binding site; other site 123214000950 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 123214000951 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...; Region: AlaRS_core; cd00673 123214000952 motif 1; other site 123214000953 active site 123214000954 motif 2; other site 123214000955 motif 3; other site 123214000956 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 123214000957 DHHA1 domain; Region: DHHA1; pfam02272 123214000958 Domain of unknown function found in archaea, bacteria, and plants; Region: DUF296; cd11378 123214000959 trimer interface [polypeptide binding]; other site 123214000960 putative Zn binding site [ion binding]; other site 123214000961 Uncharacterized protein family, UPF0114; Region: UPF0114; pfam03350 123214000962 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 123214000963 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 123214000964 active site 123214000965 Predicted amidohydrolase [General function prediction only]; Region: COG0388 123214000966 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 123214000967 active site 123214000968 catalytic triad [active] 123214000969 dimer interface [polypeptide binding]; other site 123214000970 phosphoribosylformylglycinamidine synthase II; Provisional; Region: PRK01213 123214000971 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 123214000972 dimerization interface [polypeptide binding]; other site 123214000973 ATP binding site [chemical binding]; other site 123214000974 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 123214000975 dimerization interface [polypeptide binding]; other site 123214000976 ATP binding site [chemical binding]; other site 123214000977 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 123214000978 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 123214000979 D-pathway; other site 123214000980 Low-spin heme binding site [chemical binding]; other site 123214000981 Putative water exit pathway; other site 123214000982 Binuclear center (active site) [active] 123214000983 K-pathway; other site 123214000984 Putative proton exit pathway; other site 123214000985 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 123214000986 Part of AAA domain; Region: AAA_19; pfam13245 123214000987 Family description; Region: UvrD_C_2; pfam13538 123214000988 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 123214000989 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 123214000990 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 123214000991 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 123214000992 ligand binding site [chemical binding]; other site 123214000993 flexible hinge region; other site 123214000994 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 123214000995 non-specific DNA interactions [nucleotide binding]; other site 123214000996 DNA binding site [nucleotide binding] 123214000997 sequence specific DNA binding site [nucleotide binding]; other site 123214000998 putative cAMP binding site [chemical binding]; other site 123214000999 anaerobic ribonucleoside-triphosphate reductase activating protein; Region: NrdG2; TIGR02495 123214001000 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 123214001001 FeS/SAM binding site; other site 123214001002 Anaerobic ribonucleoside-triphosphate reductase; Region: NRDD; pfam13597 123214001003 Class III ribonucleotide reductase; Region: RNR_III; cd01675 123214001004 effector binding site; other site 123214001005 active site 123214001006 Zn binding site [ion binding]; other site 123214001007 glycine loop; other site 123214001008 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 123214001009 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 123214001010 molybdopterin cofactor binding site; other site 123214001011 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 123214001012 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 123214001013 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 123214001014 molybdopterin cofactor binding site; other site 123214001015 quinol dehydrogenase periplasmic component; Provisional; Region: napG; PRK09476 123214001016 quinol dehydrogenase membrane component; Provisional; Region: napH; PRK09477 123214001017 4Fe-4S binding domain; Region: Fer4_5; pfam12801 123214001018 4Fe-4S binding domain; Region: Fer4_5; pfam12801 123214001019 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 123214001020 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; pfam03892 123214001021 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 123214001022 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 123214001023 4Fe-4S binding domain; Region: Fer4; pfam00037 123214001024 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 123214001025 structural tetrad; other site 123214001026 FOG: WD40 repeat [General function prediction only]; Region: COG2319 123214001027 NapD protein; Region: NapD; pfam03927 123214001028 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 123214001029 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 123214001030 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 123214001031 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 123214001032 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 123214001033 Cytochrome c; Region: Cytochrom_C; pfam00034 123214001034 heme d1 biosynthesis radical SAM protein NirJ; Region: rSAM_NirJ; TIGR04051 123214001035 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 123214001036 FeS/SAM binding site; other site 123214001037 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 123214001038 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 123214001039 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 123214001040 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 123214001041 active site 123214001042 SAM binding site [chemical binding]; other site 123214001043 homodimer interface [polypeptide binding]; other site 123214001044 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 123214001045 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 123214001046 Predicted hydrocarbon binding protein (contains V4R domain) [General function prediction only]; Region: COG1719 123214001047 The V4R (vinyl 4 reductase) domain is a predicted small molecular binding domain, that may bind to hydrocarbons; Region: V4R; smart00989 123214001048 Nitric oxide reductase large subunit [Inorganic ion transport and metabolism]; Region: NorB; COG3256 123214001049 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 123214001050 Binuclear center (active site) [active] 123214001051 K-pathway; other site 123214001052 Putative proton exit pathway; other site 123214001053 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 123214001054 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3399 123214001055 Predicted transcriptional regulator [Transcription]; Region: COG1959 123214001056 Transcriptional regulator; Region: Rrf2; pfam02082 123214001057 Copper resistance protein D; Region: CopD; cl00563 123214001058 3-dehydroquinate dehydratase [Amino acid transport and metabolism]; Region: AroD; COG0710 123214001059 Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase); Region: DHQase_I; cd00502 123214001060 active site 123214001061 catalytic residue [active] 123214001062 dimer interface [polypeptide binding]; other site 123214001063 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 123214001064 Nicotinamidase/pyrazinamidase (PZase). Nicotinamidase, a ubiquitous enzyme in prokaryotes, converts nicotinamide to nicotinic acid (niacin) and ammonia, which in turn can be recycled to make nicotinamide adenine dinucleotide (NAD). The same enzyme is...; Region: nicotinamidase; cd01011 123214001065 Isochorismatase family; Region: Isochorismatase; pfam00857 123214001066 catalytic triad [active] 123214001067 metal binding site [ion binding]; metal-binding site 123214001068 conserved cis-peptide bond; other site 123214001069 Putative heavy-metal-binding; Region: YbjQ_1; cl00426 123214001070 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional; Region: PRK14975 123214001071 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 123214001072 catalytic site [active] 123214001073 putative active site [active] 123214001074 putative substrate binding site [chemical binding]; other site 123214001075 Phylum Aquificae Pol A is different from Escherichia coli Pol A by three signature sequences; Region: DNA_pol_A_Aquificae_like; cd08639 123214001076 active site 123214001077 DNA binding site [nucleotide binding] 123214001078 catalytic site [active] 123214001079 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 123214001080 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 123214001081 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 123214001082 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 123214001083 Recombination protein O N terminal; Region: RecO_N; pfam11967 123214001084 Recombination protein O C terminal; Region: RecO_C; pfam02565 123214001085 Predicted transcriptional regulators [Transcription]; Region: COG1318 123214001086 probable regulatory domain; Region: near_KaiC_dom; TIGR03879 123214001087 KaiC domain protein, AF_0795 family; Region: thermo_KaiC_2; TIGR03878 123214001088 KaiC; Region: KaiC; pfam06745 123214001089 Walker A motif; other site 123214001090 ATP binding site [chemical binding]; other site 123214001091 Walker B motif; other site 123214001092 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 123214001093 active site 123214001094 Selenophosphate synthase [Amino acid transport and metabolism]; Region: SelD; COG0709 123214001095 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK13581 123214001096 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 123214001097 ligand binding site [chemical binding]; other site 123214001098 NAD binding site [chemical binding]; other site 123214001099 dimerization interface [polypeptide binding]; other site 123214001100 catalytic site [active] 123214001101 ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-like; cd04879 123214001102 L-serine binding site [chemical binding]; other site 123214001103 Myo-inositol-1-phosphate synthase [Lipid metabolism]; Region: INO1; COG1260 123214001104 Myo-inositol-1-phosphate synthase; Region: NAD_binding_5; cl00554 123214001105 outer membrane protein; Region: OMP_w_GlyGly; TIGR04219 123214001106 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]; Region: COG1942 123214001107 active site 1 [active] 123214001108 dimer interface [polypeptide binding]; other site 123214001109 hexamer interface [polypeptide binding]; other site 123214001110 active site 2 [active] 123214001111 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 123214001112 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 123214001113 active site 123214001114 phosphorylation site [posttranslational modification] 123214001115 intermolecular recognition site; other site 123214001116 dimerization interface [polypeptide binding]; other site 123214001117 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 123214001118 Walker A motif; other site 123214001119 ATP binding site [chemical binding]; other site 123214001120 Walker B motif; other site 123214001121 arginine finger; other site 123214001122 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 123214001123 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 123214001124 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 123214001125 active site 123214001126 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 123214001127 dimer interface [polypeptide binding]; other site 123214001128 substrate binding site [chemical binding]; other site 123214001129 catalytic residues [active] 123214001130 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 123214001131 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 123214001132 metal-binding site [ion binding] 123214001133 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 123214001134 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 123214001135 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 123214001136 motif II; other site 123214001137 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 123214001138 Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins; Region: GDPD; cd08556 123214001139 active site 123214001140 catalytic site [active] 123214001141 metal binding site [ion binding]; metal-binding site 123214001142 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 123214001143 homodimer interface [polypeptide binding]; other site 123214001144 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214001145 catalytic residue [active] 123214001146 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 123214001147 catalytic core [active] 123214001148 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: hisZ; PRK12292 123214001149 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...; Region: HisRS-like_core; cd00773 123214001150 dimer interface [polypeptide binding]; other site 123214001151 motif 1; other site 123214001152 active site 123214001153 motif 2; other site 123214001154 motif 3; other site 123214001155 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 123214001156 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 123214001157 Lysine 2,3-aminomutase [Amino acid transport and metabolism]; Region: KamA; COG1509 123214001158 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 123214001159 FeS/SAM binding site; other site 123214001160 Lysine-2,3-aminomutase; Region: LAM_C; pfam12544 123214001161 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 123214001162 Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]; Region: HybF; COG0375 123214001163 Hydrogenase expression/synthesis hypA family; Region: HypA; pfam01155 123214001164 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 123214001165 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 123214001166 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 123214001167 N-terminal plug; other site 123214001168 ligand-binding site [chemical binding]; other site 123214001169 Protein of unknown function (DUF1009); Region: DUF1009; pfam06230 123214001170 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 123214001171 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 123214001172 active site 123214001173 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 123214001174 catalytic residues [active] 123214001175 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 123214001176 dimerization interface [polypeptide binding]; other site 123214001177 putative DNA binding site [nucleotide binding]; other site 123214001178 putative Zn2+ binding site [ion binding]; other site 123214001179 Heterodisulfide reductase, subunit B [Energy production and conversion]; Region: HdrB; COG2048 123214001180 Cysteine-rich domain; Region: CCG; pfam02754 123214001181 Cysteine-rich domain; Region: CCG; pfam02754 123214001182 Succinate dehydrogenase/fumarate reductase, Fe-S protein subunit [Energy production and conversion]; Region: FrdB; COG0479 123214001183 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 123214001184 catalytic loop [active] 123214001185 iron binding site [ion binding]; other site 123214001186 7-cyano-7-deazaguanine reductase; Provisional; Region: PRK13258 123214001187 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 123214001188 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 123214001189 substrate binding pocket [chemical binding]; other site 123214001190 chain length determination region; other site 123214001191 substrate-Mg2+ binding site; other site 123214001192 catalytic residues [active] 123214001193 aspartate-rich region 1; other site 123214001194 active site lid residues [active] 123214001195 aspartate-rich region 2; other site 123214001196 hypothetical protein; Reviewed; Region: PRK12497 123214001197 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 123214001198 RNA/DNA hybrid binding site [nucleotide binding]; other site 123214001199 active site 123214001200 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 123214001201 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 123214001202 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 123214001203 catalytic triad [active] 123214001204 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed; Region: PRK02759 123214001205 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 123214001206 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase (HisIE or PRATP-PH) and its homologs; Region: NTP-PPase_HisIE_like; cd11534 123214001207 metal binding site [ion binding]; metal-binding site 123214001208 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 123214001209 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 123214001210 TPP-binding site; other site 123214001211 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 123214001212 PYR/PP interface [polypeptide binding]; other site 123214001213 dimer interface [polypeptide binding]; other site 123214001214 TPP binding site [chemical binding]; other site 123214001215 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 123214001216 Uncharacterized conserved protein (DUF2203); Region: DUF2203; pfam09969 123214001217 Bifunctional nuclease; Region: DNase-RNase; pfam02577 123214001218 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 123214001219 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 123214001220 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 123214001221 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 123214001222 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 123214001223 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 123214001224 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 123214001225 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 123214001226 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 123214001227 Ankyrin repeat; Region: Ank; pfam00023 123214001228 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 123214001229 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 123214001230 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 123214001231 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 123214001232 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 123214001233 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cl02529 123214001234 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 123214001235 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 123214001236 Ankyrin repeats (many copies); Region: Ank_5; pfam13857 123214001237 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 123214001238 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 123214001239 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 123214001240 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 123214001241 binding surface 123214001242 TPR motif; other site 123214001243 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 123214001244 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 123214001245 catalytic residue [active] 123214001246 putative FPP diphosphate binding site; other site 123214001247 putative FPP binding hydrophobic cleft; other site 123214001248 dimer interface [polypeptide binding]; other site 123214001249 putative IPP diphosphate binding site; other site 123214001250 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 123214001251 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 123214001252 menaquinone biosynthesis protein, SCO4550 family; Region: mena_SCO4550; TIGR03699 123214001253 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 123214001254 FeS/SAM binding site; other site 123214001255 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 123214001256 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 123214001257 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 123214001258 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 123214001259 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 123214001260 Predicted Fe-S oxidoreductase [General function prediction only]; Region: COG1242 123214001261 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 123214001262 FeS/SAM binding site; other site 123214001263 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214001264 metal binding site [ion binding]; metal-binding site 123214001265 active site 123214001266 I-site; other site 123214001267 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 123214001268 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 123214001269 tartrate dehydrogenase; Region: TTC; TIGR02089 123214001270 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 123214001271 Nicotinate-nucleotide pyrophosphorylase [Coenzyme metabolism]; Region: NadC; COG0157 123214001272 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 123214001273 dimerization interface [polypeptide binding]; other site 123214001274 active site 123214001275 Uncharacterized protein family (UPF0093); Region: UPF0093; pfam03653 123214001276 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 123214001277 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 123214001278 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 123214001279 tandem repeat interface [polypeptide binding]; other site 123214001280 oligomer interface [polypeptide binding]; other site 123214001281 active site residues [active] 123214001282 Ribosome-binding factor A; Region: RBFA; pfam02033 123214001283 Protein of unknown function (DUF503); Region: DUF503; pfam04456 123214001284 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 123214001285 active site 123214001286 FtsH Extracellular; Region: FtsH_ext; pfam06480 123214001287 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 123214001288 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 123214001289 Walker A motif; other site 123214001290 ATP binding site [chemical binding]; other site 123214001291 Walker B motif; other site 123214001292 arginine finger; other site 123214001293 Peptidase family M41; Region: Peptidase_M41; pfam01434 123214001294 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 123214001295 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 123214001296 Ligand Binding Site [chemical binding]; other site 123214001297 TilS substrate C-terminal domain; Region: TilS_C; smart00977 123214001298 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 123214001299 S-adenosylmethionine synthetase; Provisional; Region: PRK04439 123214001300 Nitrate and nitrite sensing; Region: NIT; pfam08376 123214001301 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 123214001302 HAMP domain; Region: HAMP; pfam00672 123214001303 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 123214001304 dimer interface [polypeptide binding]; other site 123214001305 putative CheW interface [polypeptide binding]; other site 123214001306 reverse gyrase; Reviewed; Region: PRK09401 123214001307 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 123214001308 ATP binding site [chemical binding]; other site 123214001309 nucleotide binding region [chemical binding]; other site 123214001310 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; cl17351 123214001311 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 123214001312 active site 123214001313 metal binding site [ion binding]; metal-binding site 123214001314 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 123214001315 domain I; other site 123214001316 DNA binding groove [nucleotide binding] 123214001317 phosphate binding site [ion binding]; other site 123214001318 domain II; other site 123214001319 domain III; other site 123214001320 nucleotide binding site [chemical binding]; other site 123214001321 catalytic site [active] 123214001322 domain IV; other site 123214001323 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 123214001324 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 123214001325 putative NAD(P) binding site [chemical binding]; other site 123214001326 active site 123214001327 putative substrate binding site [chemical binding]; other site 123214001328 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 123214001329 This family is most closely related to the GT1 family of glycosyltransferases. WabH in Klebsiella pneumoniae has been shown to transfer a GlcNAc residue from UDP-GlcNAc onto the acceptor GalUA residue in the cellular outer core; Region: GT1_WabH_like; cd03811 123214001330 putative ADP-binding pocket [chemical binding]; other site 123214001331 dihydroorotate dehydrogenase (subfamily 1) family protein; Region: pyrD_sub1_fam; TIGR01037 123214001332 Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. 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...; Region: DHOD_1B_like; cd04740 123214001333 heterodimer interface [polypeptide binding]; other site 123214001334 active site 123214001335 FMN binding site [chemical binding]; other site 123214001336 homodimer interface [polypeptide binding]; other site 123214001337 substrate binding site [chemical binding]; other site 123214001338 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 123214001339 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 123214001340 active site 123214001341 Zn binding site [ion binding]; other site 123214001342 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]; Region: COG2329 123214001343 2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Reviewed; Region: mtnW; PRK09549 123214001344 Ribulose bisphosphate carboxylase large chain; Region: RuBisCO_large; cl08232 123214001345 dimer interface [polypeptide binding]; other site 123214001346 catalytic residue [active] 123214001347 metal binding site [ion binding]; metal-binding site 123214001348 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 123214001349 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 123214001350 motif II; other site 123214001351 Cytochrome c; Region: Cytochrom_C; pfam00034 123214001352 Cytochrome c; Region: Cytochrom_C; pfam00034 123214001353 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 123214001354 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 123214001355 Low-spin heme binding site [chemical binding]; other site 123214001356 D-pathway; other site 123214001357 Putative water exit pathway; other site 123214001358 Binuclear center (active site) [active] 123214001359 K-pathway; other site 123214001360 Putative proton exit pathway; other site 123214001361 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 123214001362 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 123214001363 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 123214001364 Interdomain contacts; other site 123214001365 Cytokine receptor motif; other site 123214001366 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 123214001367 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 123214001368 SprA-related family; Region: SprA-related; pfam12118 123214001369 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 123214001370 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 123214001371 Cu(I) binding site [ion binding]; other site 123214001372 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 123214001373 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 123214001374 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 123214001375 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 123214001376 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 123214001377 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 123214001378 RNA/DNA hybrid binding site [nucleotide binding]; other site 123214001379 active site 123214001380 DNA repair protein RadA; Provisional; Region: PRK11823 123214001381 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 123214001382 Walker A motif; other site 123214001383 ATP binding site [chemical binding]; other site 123214001384 Walker B motif; other site 123214001385 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 123214001386 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 123214001387 Fe-S cluster binding site [ion binding]; other site 123214001388 active site 123214001389 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...; Region: OMP_decarboxylase_like; cd04725 123214001390 active site 123214001391 dimer interface [polypeptide binding]; other site 123214001392 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 123214001393 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 123214001394 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 123214001395 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...; Region: RaiA; cd00552 123214001396 30S subunit binding site; other site 123214001397 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 123214001398 23S rRNA interface [nucleotide binding]; other site 123214001399 L3 interface [polypeptide binding]; other site 123214001400 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 123214001401 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 123214001402 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 123214001403 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 123214001404 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 123214001405 putative ribose interaction site [chemical binding]; other site 123214001406 putative ADP binding site [chemical binding]; other site 123214001407 Phosphoribosylformylglycinamidine (FGAM) synthase; Region: PurS; pfam02700 123214001408 phosphoribosylformylglycinamidine synthase I; Provisional; Region: PRK03619 123214001409 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 123214001410 putative active site [active] 123214001411 catalytic triad [active] 123214001412 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 123214001413 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 123214001414 catalytic residues [active] 123214001415 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 123214001416 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 123214001417 Zn2+ binding site [ion binding]; other site 123214001418 Mg2+ binding site [ion binding]; other site 123214001419 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 123214001420 Spore Coat Protein U domain; Region: SCPU; pfam05229 123214001421 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 123214001422 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 123214001423 Sporulation related domain; Region: SPOR; pfam05036 123214001424 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 123214001425 Spore Coat Protein U domain; Region: SCPU; cl02253 123214001426 Spore Coat Protein U domain; Region: SCPU; pfam05229 123214001427 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 123214001428 Putative ATPase subunit of terminase (gpP-like); Region: Terminase_5; pfam06056 123214001429 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 123214001430 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cd00494 123214001431 domain interfaces; other site 123214001432 active site 123214001433 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 123214001434 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 123214001435 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 123214001436 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 123214001437 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 123214001438 Walker A/P-loop; other site 123214001439 ATP binding site [chemical binding]; other site 123214001440 Q-loop/lid; other site 123214001441 ABC transporter signature motif; other site 123214001442 Walker B; other site 123214001443 D-loop; other site 123214001444 H-loop/switch region; other site 123214001445 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; Region: PHP_HisPPase; cd07432 123214001446 active site 123214001447 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 123214001448 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; cd01610 123214001449 active site 123214001450 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...; Region: PNPsynthase; cd00003 123214001451 active site 123214001452 hydrophilic channel; other site 123214001453 dimerization interface [polypeptide binding]; other site 123214001454 catalytic residues [active] 123214001455 active site lid [active] 123214001456 AMIN domain; Region: AMIN; pfam11741 123214001457 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 123214001458 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 123214001459 active site 123214001460 metal binding site [ion binding]; metal-binding site 123214001461 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 123214001462 nucleotide binding site [chemical binding]; other site 123214001463 Type III pantothenate kinase; Region: Pan_kinase; cl17198 123214001464 dihydrodipicolinate reductase; Provisional; Region: PRK00048 123214001465 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 123214001466 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 123214001467 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; pfam09527 123214001468 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 123214001469 DHH family; Region: DHH; pfam01368 123214001470 DHHA1 domain; Region: DHHA1; pfam02272 123214001471 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 123214001472 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 123214001473 minor groove reading motif; other site 123214001474 helix-hairpin-helix signature motif; other site 123214001475 substrate binding pocket [chemical binding]; other site 123214001476 active site 123214001477 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 123214001478 5'-3' exonuclease; Region: 53EXOc; smart00475 123214001479 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 123214001480 active site 123214001481 metal binding site 1 [ion binding]; metal-binding site 123214001482 putative 5' ssDNA interaction site; other site 123214001483 metal binding site 3; metal-binding site 123214001484 metal binding site 2 [ion binding]; metal-binding site 123214001485 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 123214001486 putative DNA binding site [nucleotide binding]; other site 123214001487 putative metal binding site [ion binding]; other site 123214001488 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 123214001489 Peptidase family M23; Region: Peptidase_M23; pfam01551 123214001490 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; cd00384 123214001491 dimer interface [polypeptide binding]; other site 123214001492 active site 123214001493 Schiff base residues; other site 123214001494 RNA methyltransferase, RsmE family; Region: TIGR00046 123214001495 RNA methyltransferase; Region: Methyltrans_RNA; pfam04452 123214001496 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 123214001497 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 123214001498 ABC-ATPase subunit interface; other site 123214001499 dimer interface [polypeptide binding]; other site 123214001500 putative PBP binding regions; other site 123214001501 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 123214001502 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 123214001503 Alcohol dehydrogenases of the MDR family; Region: Zn_ADH_like1; cd08266 123214001504 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 123214001505 putative NAD(P) binding site [chemical binding]; other site 123214001506 structural Zn binding site [ion binding]; other site 123214001507 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 123214001508 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 123214001509 G1 box; other site 123214001510 GTP/Mg2+ binding site [chemical binding]; other site 123214001511 Switch I region; other site 123214001512 G2 box; other site 123214001513 G3 box; other site 123214001514 Switch II region; other site 123214001515 G4 box; other site 123214001516 G5 box; other site 123214001517 Nucleoside recognition; Region: Gate; pfam07670 123214001518 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 123214001519 Nucleoside recognition; Region: Gate; pfam07670 123214001520 FeoA domain; Region: FeoA; pfam04023 123214001521 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 123214001522 Peptidase family M50; Region: Peptidase_M50; pfam02163 123214001523 active site 123214001524 putative substrate binding region [chemical binding]; other site 123214001525 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 123214001526 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 123214001527 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 123214001528 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 123214001529 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 123214001530 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 123214001531 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 123214001532 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 123214001533 homodimer interface [polypeptide binding]; other site 123214001534 putative active site [active] 123214001535 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 123214001536 HIGH motif; other site 123214001537 dimer interface [polypeptide binding]; other site 123214001538 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 123214001539 active site 123214001540 KMSKS motif; other site 123214001541 DEAD-like helicases superfamily; Region: DEXDc; smart00487 123214001542 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 123214001543 ATP binding site [chemical binding]; other site 123214001544 putative Mg++ binding site [ion binding]; other site 123214001545 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 123214001546 nucleotide binding region [chemical binding]; other site 123214001547 ATP-binding site [chemical binding]; other site 123214001548 Domain of unknown function (DUF1998); Region: DUF1998; pfam09369 123214001549 NAD-dependent protein deacetylases, SIR2 family [Transcription]; Region: SIR2; COG0846 123214001550 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cl00195 123214001551 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 123214001552 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 123214001553 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...; Region: LT_GEWL; cd00254 123214001554 N-acetyl-D-glucosamine binding site [chemical binding]; other site 123214001555 catalytic residue [active] 123214001556 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 123214001557 binding surface 123214001558 TPR motif; other site 123214001559 TPR repeat; Region: TPR_11; pfam13414 123214001560 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 123214001561 binding surface 123214001562 TPR repeat; Region: TPR_11; pfam13414 123214001563 TPR motif; other site 123214001564 TPR repeat; Region: TPR_11; pfam13414 123214001565 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 123214001566 binding surface 123214001567 TPR motif; other site 123214001568 TPR repeat; Region: TPR_11; pfam13414 123214001569 CHAT domain; Region: CHAT; cl17868 123214001570 chaperone protein DnaJ; Provisional; Region: PRK14282 123214001571 bifunctional 3-deoxy-7-phosphoheptulonate synthase/chorismate mutase; Reviewed; Region: PRK12595 123214001572 Creatinine amidohydrolase; Region: Creatininase; pfam02633 123214001573 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 123214001574 Helix-hairpin-helix motif; Region: HHH; pfam00633 123214001575 NurA nuclease; Region: NurA; smart00933 123214001576 GTPase CgtA; Reviewed; Region: obgE; PRK12299 123214001577 GTP1/OBG; Region: GTP1_OBG; pfam01018 123214001578 Obg GTPase; Region: Obg; cd01898 123214001579 G1 box; other site 123214001580 GTP/Mg2+ binding site [chemical binding]; other site 123214001581 Switch I region; other site 123214001582 G2 box; other site 123214001583 G3 box; other site 123214001584 Switch II region; other site 123214001585 G4 box; other site 123214001586 G5 box; other site 123214001587 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 123214001588 PLD-like domain; Region: PLDc_2; pfam13091 123214001589 putative active site [active] 123214001590 catalytic site [active] 123214001591 Domain of unknown function DUF87; Region: DUF87; pfam01935 123214001592 AAA-like domain; Region: AAA_10; pfam12846 123214001593 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 123214001594 FOG: CBS domain [General function prediction only]; Region: COG0517 123214001595 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; cd02205 123214001596 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 123214001597 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214001598 metal binding site [ion binding]; metal-binding site 123214001599 active site 123214001600 I-site; other site 123214001601 ribosomal protein S12 methylthiotransferase RimO; Region: TIGR01125 123214001602 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 123214001603 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 123214001604 FeS/SAM binding site; other site 123214001605 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]; Region: COG0182 123214001606 methylthioribose-1-phosphate isomerase; Reviewed; Region: mtnA; PRK05720 123214001607 conserved hypothetical protein, cofD-related; Region: CofD_related; TIGR01826 123214001608 family of mostly uncharacterized proteins similar to B.subtilis YvcK; Region: YvcK_like; cd07187 123214001609 putative substrate binding pocket [chemical binding]; other site 123214001610 dimer interface [polypeptide binding]; other site 123214001611 phosphate binding site [ion binding]; other site 123214001612 L-aspartate oxidase; Provisional; Region: PRK06175 123214001613 Aspartate oxidase [Coenzyme metabolism]; Region: NadB; COG0029 123214001614 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 123214001615 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 123214001616 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 123214001617 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 123214001618 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 123214001619 Phosphatidylglycerophosphate synthase [Lipid metabolism]; Region: PgsA; COG0558 123214001620 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...; Region: PRAI; cd00405 123214001621 active site 123214001622 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 123214001623 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 123214001624 binding surface 123214001625 TPR motif; other site 123214001626 Tetratricopeptide repeat; Region: TPR_12; pfam13424 123214001627 TPR repeat; Region: TPR_11; pfam13414 123214001628 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 123214001629 binding surface 123214001630 TPR motif; other site 123214001631 TPR repeat; Region: TPR_11; pfam13414 123214001632 Tetratricopeptide repeat; Region: TPR_16; pfam13432 123214001633 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 123214001634 Tetratricopeptide repeat; Region: TPR_16; pfam13432 123214001635 TPR motif; other site 123214001636 binding surface 123214001637 Tetratricopeptide repeat; Region: TPR_16; pfam13432 123214001638 TPR repeat; Region: TPR_11; pfam13414 123214001639 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 123214001640 binding surface 123214001641 TPR motif; other site 123214001642 TPR repeat; Region: TPR_11; pfam13414 123214001643 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 123214001644 Ligand Binding Site [chemical binding]; other site 123214001645 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 123214001646 Ligand Binding Site [chemical binding]; other site 123214001647 3-isopropylmalate dehydratase small subunit; Reviewed; Region: leuD; PRK00439 123214001648 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 123214001649 substrate binding site [chemical binding]; other site 123214001650 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 123214001651 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 123214001652 NAD binding site [chemical binding]; other site 123214001653 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 123214001654 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 123214001655 NAD(P) binding site [chemical binding]; other site 123214001656 homotetramer interface [polypeptide binding]; other site 123214001657 homodimer interface [polypeptide binding]; other site 123214001658 active site 123214001659 acyl carrier protein; Provisional; Region: acpP; PRK00982 123214001660 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 123214001661 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 123214001662 dimer interface [polypeptide binding]; other site 123214001663 active site 123214001664 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 123214001665 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 123214001666 dimerization interface [polypeptide binding]; other site 123214001667 active site 123214001668 metal binding site [ion binding]; metal-binding site 123214001669 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 123214001670 dsRNA binding site [nucleotide binding]; other site 123214001671 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 123214001672 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 123214001673 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 123214001674 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 123214001675 Walker A motif; other site 123214001676 ATP binding site [chemical binding]; other site 123214001677 Walker B motif; other site 123214001678 arginine finger; other site 123214001679 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 123214001680 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 123214001681 dimerization interface [polypeptide binding]; other site 123214001682 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 123214001683 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 123214001684 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 123214001685 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 123214001686 CPxP motif; other site 123214001687 Anthranilate phosphoribosyltransferase [Amino acid transport and metabolism]; Region: TrpD; COG0547 123214001688 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 123214001689 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 123214001690 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 123214001691 Active Sites [active] 123214001692 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 123214001693 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 123214001694 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 123214001695 S-adenosylmethionine binding site [chemical binding]; other site 123214001696 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 123214001697 active site 123214001698 tetramer interface; other site 123214001699 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 123214001700 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 123214001701 ATP binding site [chemical binding]; other site 123214001702 active site 123214001703 substrate binding site [chemical binding]; other site 123214001704 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 123214001705 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 123214001706 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 123214001707 putative active site [active] 123214001708 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 123214001709 TPR motif; other site 123214001710 TPR repeat; Region: TPR_11; pfam13414 123214001711 binding surface 123214001712 pyruvate ferredoxin oxidoreductase subunit beta; Provisional; Region: PRK11865 123214001713 Thiamine pyrophosphate (TPP family), PFOR porB-like subfamily, TPP-binding module; composed of proteins similar to the beta subunit (porB) of the Helicobacter pylori four-subunit pyruvate ferredoxin oxidoreductase (PFOR), which are also found in archaea...; Region: TPP_PFOR_porB_like; cd03376 123214001714 TPP-binding site [chemical binding]; other site 123214001715 putative dimer interface [polypeptide binding]; other site 123214001716 pyruvate ferredoxin oxidoreductase subunit alpha; Reviewed; Region: porA; PRK08367 123214001717 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 123214001718 dimer interface [polypeptide binding]; other site 123214001719 PYR/PP interface [polypeptide binding]; other site 123214001720 TPP binding site [chemical binding]; other site 123214001721 substrate binding site [chemical binding]; other site 123214001722 2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate family; Region: PorD_KorD; TIGR02179 123214001723 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 123214001724 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 123214001725 pyruvate/ketoisovalerate ferredoxin oxidoreductase subunit gamma; Provisional; Region: PRK14029 123214001726 recombination protein RecR; Reviewed; Region: recR; PRK00076 123214001727 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 123214001728 putative active site [active] 123214001729 putative metal-binding site [ion binding]; other site 123214001730 tetramer interface [polypeptide binding]; other site 123214001731 hypothetical protein; Provisional; Region: PRK14626 123214001732 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14953 123214001733 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 123214001734 Walker A motif; other site 123214001735 ATP binding site [chemical binding]; other site 123214001736 Walker B motif; other site 123214001737 arginine finger; other site 123214001738 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 123214001739 Circularly permuted YlqF-related GTPases; Region: YlqF_related_GTPase; cl17249 123214001740 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 123214001741 GTP/Mg2+ binding site [chemical binding]; other site 123214001742 G4 box; other site 123214001743 G5 box; other site 123214001744 G1 box; other site 123214001745 Switch I region; other site 123214001746 G2 box; other site 123214001747 G3 box; other site 123214001748 Switch II region; other site 123214001749 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 123214001750 Aralkyl acyl-CoA:amino acid N-acyltransferase, C-terminal region; Region: Gly_acyl_tr_C; pfam08444 123214001751 Organic solvent tolerance protein; Region: OstA_C; pfam04453 123214001752 Transcriptional regulator [Transcription]; Region: IclR; COG1414 123214001753 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 123214001754 Bacterial transcriptional regulator; Region: IclR; pfam01614 123214001755 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 123214001756 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 123214001757 bacterial Hfq-like; Region: Hfq; cd01716 123214001758 hexamer interface [polypeptide binding]; other site 123214001759 Sm1 motif; other site 123214001760 RNA binding site [nucleotide binding]; other site 123214001761 Sm2 motif; other site 123214001762 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 123214001763 HflX GTPase family; Region: HflX; cd01878 123214001764 Elongation factor Tu GTP binding domain; Region: GTP_EFTU; pfam00009 123214001765 G1 box; other site 123214001766 GTP/Mg2+ binding site [chemical binding]; other site 123214001767 Switch I region; other site 123214001768 G2 box; other site 123214001769 G3 box; other site 123214001770 Switch II region; other site 123214001771 G4 box; other site 123214001772 G5 box; other site 123214001773 Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a...; Region: PKCI_related; cd01276 123214001774 nucleotide binding site/active site [active] 123214001775 HIT family signature motif; other site 123214001776 catalytic residue [active] 123214001777 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 123214001778 CPxP motif; other site 123214001779 Protein of unknown function (DUF3343); Region: DUF3343; pfam11823 123214001780 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 123214001781 helix_turn_helix, Deoxyribose operon repressor; Region: HTH_DEOR; smart00420 123214001782 NosL; Region: NosL; cl01769 123214001783 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 123214001784 putative active site pocket [active] 123214001785 4-fold oligomerization interface [polypeptide binding]; other site 123214001786 metal binding residues [ion binding]; metal-binding site 123214001787 3-fold/trimer interface [polypeptide binding]; other site 123214001788 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 123214001789 Walker A motif; other site 123214001790 ATP binding site [chemical binding]; other site 123214001791 Walker B motif; other site 123214001792 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 123214001793 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 123214001794 YsiA-like protein, C-terminal region; Region: TetR_C_4; pfam08359 123214001795 DHH family; Region: DHH; pfam01368 123214001796 Predicted phosphohydrolase (DHH superfamily) [General function prediction only]; Region: COG2404 123214001797 DHHA1 domain; Region: DHHA1; pfam02272 123214001798 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 123214001799 dimer interface [polypeptide binding]; other site 123214001800 putative radical transfer pathway; other site 123214001801 diiron center [ion binding]; other site 123214001802 tyrosyl radical; other site 123214001803 ATP cone domain; Region: ATP-cone; pfam03477 123214001804 ribonucleoside-diphosphate reductase, alpha subunit; Region: NrdE_NrdA; TIGR02506 123214001805 Class I ribonucleotide reductase; Region: RNR_I; cd01679 123214001806 active site 123214001807 dimer interface [polypeptide binding]; other site 123214001808 catalytic residues [active] 123214001809 effector binding site; other site 123214001810 R2 peptide binding site; other site 123214001811 Outer membrane protein family (DUF1597); Region: DUF1597; pfam07642 123214001812 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 123214001813 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 123214001814 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 123214001815 GatB domain; Region: GatB_Yqey; smart00845 123214001816 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 123214001817 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 123214001818 homotetramer interface [polypeptide binding]; other site 123214001819 ligand binding site [chemical binding]; other site 123214001820 catalytic site [active] 123214001821 NAD binding site [chemical binding]; other site 123214001822 dihydroxy-acid dehydratase; Provisional; Region: PRK00911 123214001823 S-adenosylmethionine synthetase; Validated; Region: PRK05250 123214001824 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 123214001825 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 123214001826 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 123214001827 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214001828 I-site; other site 123214001829 metal binding site [ion binding]; metal-binding site 123214001830 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes [Energy production and conversion]; Region: Lpd; COG1249 123214001831 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 123214001832 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 123214001833 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 123214001834 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 123214001835 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 123214001836 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 123214001837 Tfp pilus assembly protein, ATPase PilM [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilM; COG4972 123214001838 phosphoenolpyruvate synthase; Validated; Region: PRK06464 123214001839 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 123214001840 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 123214001841 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 123214001842 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 123214001843 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 123214001844 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 123214001845 dimer interface [polypeptide binding]; other site 123214001846 motif 1; other site 123214001847 active site 123214001848 motif 2; other site 123214001849 motif 3; other site 123214001850 tRNA pseudouridine synthase D; Reviewed; Region: truD; PRK00984 123214001851 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 123214001852 active site 123214001853 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 123214001854 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 123214001855 Transglycosylase; Region: Transgly; pfam00912 123214001856 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 123214001857 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 123214001858 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 123214001859 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214001860 catalytic residue [active] 123214001861 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14467 123214001862 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 123214001863 FeS/SAM binding site; other site 123214001864 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 123214001865 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 123214001866 molybdopterin cofactor binding site; other site 123214001867 Molybdopterin-Binding, C-terminal (MopB_CT) 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-...; Region: MopB_CT; cl09929 123214001868 molybdopterin cofactor binding site; other site 123214001869 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 123214001870 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214001871 metal binding site [ion binding]; metal-binding site 123214001872 active site 123214001873 I-site; other site 123214001874 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 123214001875 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; cl17244 123214001876 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 123214001877 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 123214001878 Ligand binding site; other site 123214001879 oligomer interface; other site 123214001880 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 123214001881 ThiS interaction site; other site 123214001882 putative active site [active] 123214001883 tetramer interface [polypeptide binding]; other site 123214001884 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 123214001885 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 123214001886 Beta-Casp domain; Region: Beta-Casp; smart01027 123214001887 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 123214001888 Family description; Region: DsbD_2; pfam13386 123214001889 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 123214001890 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 123214001891 putative active site [active] 123214001892 substrate binding site [chemical binding]; other site 123214001893 putative cosubstrate binding site; other site 123214001894 catalytic site [active] 123214001895 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 123214001896 substrate binding site [chemical binding]; other site 123214001897 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 123214001898 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 123214001899 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 123214001900 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 123214001901 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 123214001902 [2Fe-2S] cluster binding site [ion binding]; other site 123214001903 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 123214001904 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 123214001905 Qi binding site; other site 123214001906 intrachain domain interface; other site 123214001907 interchain domain interface [polypeptide binding]; other site 123214001908 heme bH binding site [chemical binding]; other site 123214001909 heme bL binding site [chemical binding]; other site 123214001910 Qo binding site; other site 123214001911 intrachain domain interface; other site 123214001912 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 123214001913 Qo binding site; other site 123214001914 Cytochrome c1 [Energy production and conversion]; Region: CYT1; COG2857 123214001915 Cytochrome c; Region: Cytochrom_C; pfam00034 123214001916 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 123214001917 pyrroline-5-carboxylate reductase; Region: PLN02688 123214001918 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 123214001919 active site 123214001920 catalytic site [active] 123214001921 substrate binding site [chemical binding]; other site 123214001922 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 123214001923 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 123214001924 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 123214001925 TrkA-N domain; Region: TrkA_N; pfam02254 123214001926 TrkA-C domain; Region: TrkA_C; pfam02080 123214001927 Glycosyl transferases group 1; Region: Glyco_trans_1_2; pfam13524 123214001928 Sporulation related domain; Region: SPOR; pfam05036 123214001929 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 123214001930 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 123214001931 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 123214001932 active site 123214001933 HIGH motif; other site 123214001934 KMSK motif region; other site 123214001935 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 123214001936 tRNA binding surface [nucleotide binding]; other site 123214001937 anticodon binding site; other site 123214001938 CTP synthetase; Validated; Region: pyrG; PRK05380 123214001939 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 123214001940 Catalytic site [active] 123214001941 active site 123214001942 UTP binding site [chemical binding]; other site 123214001943 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 123214001944 active site 123214001945 putative oxyanion hole; other site 123214001946 catalytic triad [active] 123214001947 acetyl-CoA synthetase; Provisional; Region: PRK00174 123214001948 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 123214001949 active site 123214001950 CoA binding site [chemical binding]; other site 123214001951 acyl-activating enzyme (AAE) consensus motif; other site 123214001952 AMP binding site [chemical binding]; other site 123214001953 acetate binding site [chemical binding]; other site 123214001954 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 123214001955 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 123214001956 Walker A motif; other site 123214001957 ATP binding site [chemical binding]; other site 123214001958 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 123214001959 Walker B motif; other site 123214001960 arginine finger; other site 123214001961 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 123214001962 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...; Region: TOP4c; cl00148 123214001963 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 123214001964 AsnC family; Region: AsnC_trans_reg; pfam01037 123214001965 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 123214001966 SmpB-tmRNA interface; other site 123214001967 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 123214001968 Zn binding site [ion binding]; other site 123214001969 Protein of unknown function, DUF399; Region: DUF399; pfam04187 123214001970 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 123214001971 adenylosuccinate lyase; Provisional; Region: PRK07492 123214001972 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 123214001973 tetramer interface [polypeptide binding]; other site 123214001974 active site 123214001975 Adenylosuccinate lyase C-terminus; Region: ADSL_C; pfam10397 123214001976 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 123214001977 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 123214001978 minor groove reading motif; other site 123214001979 helix-hairpin-helix signature motif; other site 123214001980 substrate binding pocket [chemical binding]; other site 123214001981 active site 123214001982 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 123214001983 NAD synthetase; Provisional; Region: PRK13981 123214001984 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 123214001985 multimer interface [polypeptide binding]; other site 123214001986 active site 123214001987 catalytic triad [active] 123214001988 protein interface 1 [polypeptide binding]; other site 123214001989 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 123214001990 homodimer interface [polypeptide binding]; other site 123214001991 NAD binding pocket [chemical binding]; other site 123214001992 ATP binding pocket [chemical binding]; other site 123214001993 Mg binding site [ion binding]; other site 123214001994 active-site loop [active] 123214001995 EAL domain; Region: EAL; pfam00563 123214001996 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 123214001997 HD domain; Region: HD_4; pfam13328 123214001998 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 123214001999 synthetase active site [active] 123214002000 NTP binding site [chemical binding]; other site 123214002001 metal binding site [ion binding]; metal-binding site 123214002002 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 123214002003 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 123214002004 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 123214002005 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 123214002006 cell division protein FtsZ; Validated; Region: PRK09330 123214002007 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 123214002008 nucleotide binding site [chemical binding]; other site 123214002009 SulA interaction site; other site 123214002010 Cell division ATPase FtsA [Cell division and chromosome partitioning]; Region: ftsA; COG0849 123214002011 Cell division protein FtsA; Region: FtsA; smart00842 123214002012 Cell division protein FtsA; Region: FtsA; pfam14450 123214002013 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 123214002014 Cell division protein FtsQ; Region: FtsQ; pfam03799 123214002015 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 123214002016 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 123214002017 ATP-grasp domain; Region: ATP-grasp_4; cl17255 123214002018 UDP-N-acetylmuramate dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: MurB; COG0812 123214002019 FAD binding domain; Region: FAD_binding_4; pfam01565 123214002020 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 123214002021 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 123214002022 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 123214002023 active site 123214002024 homodimer interface [polypeptide binding]; other site 123214002025 cell division protein FtsW; Region: ftsW; TIGR02614 123214002026 UDP-N-acetylmuramoylalanine--D-glutamate ligase; Region: murD; TIGR01087 123214002027 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 123214002028 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 123214002029 pyruvate carboxylase subunit B; Validated; Region: PRK09282 123214002030 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 123214002031 active site 123214002032 catalytic residues [active] 123214002033 metal binding site [ion binding]; metal-binding site 123214002034 homodimer binding site [polypeptide binding]; other site 123214002035 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 123214002036 carboxyltransferase (CT) interaction site; other site 123214002037 biotinylation site [posttranslational modification]; other site 123214002038 Uncharacterized conserved protein (DUF2173); Region: DUF2173; cl01994 123214002039 dihydropyrimidine dehydrogenase subunit A; Provisional; Region: PRK11749 123214002040 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 123214002041 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 123214002042 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 123214002043 ornithine carbamoyltransferase; Provisional; Region: PRK00779 123214002044 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 123214002045 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 123214002046 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 123214002047 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 123214002048 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 123214002049 PAS domain S-box; Region: sensory_box; TIGR00229 123214002050 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 123214002051 putative active site [active] 123214002052 heme pocket [chemical binding]; other site 123214002053 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 123214002054 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214002055 metal binding site [ion binding]; metal-binding site 123214002056 active site 123214002057 I-site; other site 123214002058 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 123214002059 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK00130 123214002060 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 123214002061 RNA binding site [nucleotide binding]; other site 123214002062 active site 123214002063 Pseudouridine synthase II TruB, C-terminal; Region: TruB-C_2; pfam09157 123214002064 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 123214002065 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 123214002066 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 123214002067 Prolipoprotein diacylglyceryl transferase; Region: LGT; pfam01790 123214002068 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 123214002069 active site 123214002070 catalytic residues [active] 123214002071 metal binding site [ion binding]; metal-binding site 123214002072 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 123214002073 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 123214002074 substrate binding site [chemical binding]; other site 123214002075 hexamer interface [polypeptide binding]; other site 123214002076 metal binding site [ion binding]; metal-binding site 123214002077 Dolichol kinase [Lipid metabolism]; Region: SEC59; COG0170 123214002078 Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]; Region: PaaD; COG2151 123214002079 dihydroorotase; Validated; Region: pyrC; PRK09357 123214002080 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 123214002081 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 123214002082 active site 123214002083 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 123214002084 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 123214002085 Catalytic site [active] 123214002086 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 123214002087 Staphylococcal nuclease homologues; Region: SNc; smart00318 123214002088 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cd00175 123214002089 Catalytic site; other site 123214002090 AIR carboxylase; Region: AIRC; pfam00731 123214002091 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 123214002092 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 123214002093 active site 123214002094 dimer interface [polypeptide binding]; other site 123214002095 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 123214002096 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 123214002097 active site 123214002098 FMN binding site [chemical binding]; other site 123214002099 substrate binding site [chemical binding]; other site 123214002100 3Fe-4S cluster binding site [ion binding]; other site 123214002101 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 123214002102 domain interface; other site 123214002103 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 123214002104 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 123214002105 dimerization interface 3.5A [polypeptide binding]; other site 123214002106 active site 123214002107 GTPase Era; Reviewed; Region: era; PRK00089 123214002108 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 123214002109 G1 box; other site 123214002110 GTP/Mg2+ binding site [chemical binding]; other site 123214002111 Switch I region; other site 123214002112 G2 box; other site 123214002113 Switch II region; other site 123214002114 G3 box; other site 123214002115 G4 box; other site 123214002116 G5 box; other site 123214002117 KH domain; Region: KH_2; pfam07650 123214002118 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 123214002119 MgtE intracellular N domain; Region: MgtE_N; smart00924 123214002120 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 123214002121 Divalent cation transporter; Region: MgtE; pfam01769 123214002122 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 123214002123 dimer interface [polypeptide binding]; other site 123214002124 putative CheW interface [polypeptide binding]; other site 123214002125 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 123214002126 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 123214002127 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 123214002128 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214002129 catalytic residue [active] 123214002130 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 123214002131 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 123214002132 AAA domain; Region: AAA_26; pfam13500 123214002133 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 123214002134 Protein of unknown function DUF72; Region: DUF72; pfam01904 123214002135 MgtC family; Region: MgtC; pfam02308 123214002136 Predicted membrane protein [Function unknown]; Region: COG3174 123214002137 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 123214002138 Endodeoxyribonuclease RusA; Region: RusA; pfam05866 123214002139 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 123214002140 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 123214002141 active site residue [active] 123214002142 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 123214002143 active site residue [active] 123214002144 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 123214002145 active site residue [active] 123214002146 DMSO reductase family type II enzyme, molybdopterin subunit; Region: DMSO_red_II_alp; TIGR03479 123214002147 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 123214002148 molybdopterin cofactor binding site; other site 123214002149 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 123214002150 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 123214002151 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 123214002152 Molybdopterin-Binding, C-terminal (MopB_CT) 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-...; Region: MopB_CT; cl09929 123214002153 molybdopterin cofactor binding site; other site 123214002154 DMSO reductase family type II enzyme, iron-sulfur subunit; Region: DMSO_red_II_bet; TIGR03478 123214002155 4Fe-4S binding domain; Region: Fer4; cl02805 123214002156 Heme-binding domain of bacterial ethylbenzene dehydrogenase; Region: DOMON_EBDH; cd09623 123214002157 heme binding site [chemical binding]; other site 123214002158 beta subunit binding site [polypeptide binding]; other site 123214002159 putative heme-binding domain, Pirellula/Verrucomicrobium type; Region: CxxCH_TIGR02603 123214002160 Cytochrome c; Region: Cytochrom_C; pfam00034 123214002161 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 123214002162 4Fe-4S binding domain; Region: Fer4; pfam00037 123214002163 Formate-dependent nitrite reductase, membrane component [Inorganic ion transport and metabolism]; Region: NrfD; COG3301 123214002164 Predicted membrane protein [Function unknown]; Region: COG4881 123214002165 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 123214002166 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 123214002167 molybdopterin cofactor binding site; other site 123214002168 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 123214002169 Molybdopterin-Binding, C-terminal (MopB_CT) 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-...; Region: MopB_CT; cl09929 123214002170 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 123214002171 Ferredoxin [Energy production and conversion]; Region: COG1146 123214002172 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 123214002173 SCP-2 sterol transfer family; Region: SCP2; cl01225 123214002174 Predicted membrane protein [Function unknown]; Region: COG2855 123214002175 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 123214002176 active site 123214002177 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 123214002178 nucleotide binding site/active site [active] 123214002179 HIT family signature motif; other site 123214002180 catalytic residue [active] 123214002181 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; cd03440 123214002182 active site 2 [active] 123214002183 active site 1 [active] 123214002184 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 123214002185 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 123214002186 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 123214002187 Cell division protein FtsL; Region: FtsL; cl11433 123214002188 MraW methylase family; Region: Methyltransf_5; cl17771 123214002189 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 123214002190 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 123214002191 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 123214002192 SurA N-terminal domain; Region: SurA_N_3; cl07813 123214002193 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 123214002194 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 123214002195 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 123214002196 Walker A/P-loop; other site 123214002197 ATP binding site [chemical binding]; other site 123214002198 Q-loop/lid; other site 123214002199 ABC transporter signature motif; other site 123214002200 Walker B; other site 123214002201 D-loop; other site 123214002202 H-loop/switch region; other site 123214002203 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 123214002204 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 123214002205 HlyD family secretion protein; Region: HlyD_3; pfam13437 123214002206 Outer membrane efflux protein; Region: OEP; pfam02321 123214002207 Outer membrane efflux protein; Region: OEP; pfam02321 123214002208 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 123214002209 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 123214002210 active site 123214002211 HIGH motif; other site 123214002212 nucleotide binding site [chemical binding]; other site 123214002213 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 123214002214 active site 123214002215 KMSKS motif; other site 123214002216 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 123214002217 tRNA binding surface [nucleotide binding]; other site 123214002218 anticodon binding site; other site 123214002219 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 123214002220 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 123214002221 IHF dimer interface [polypeptide binding]; other site 123214002222 IHF - DNA interface [nucleotide binding]; other site 123214002223 Histidinol phosphatase and related phosphatases [Amino acid transport and metabolism]; Region: HisB; COG0241 123214002224 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 123214002225 active site 123214002226 motif I; other site 123214002227 motif II; other site 123214002228 Ferredoxin thioredoxin reductase catalytic beta chain; Region: FeThRed_B; pfam02943 123214002229 Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion]; Region: FrhA; COG3259 123214002230 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 123214002231 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 123214002232 anaerobic sulfite reductase subunit B; Provisional; Region: PRK08221 123214002233 Anaerobic sulfite reductase contains an FAD and NADPH binding module with structural similarity to ferredoxin reductase and sequence similarity to dihydroorotate dehydrogenases. Clostridium pasteurianum inducible dissimilatory type sulfite reductase is...; Region: sulfite_reductase_like; cd06221 123214002234 FAD binding pocket [chemical binding]; other site 123214002235 FAD binding motif [chemical binding]; other site 123214002236 phosphate binding motif [ion binding]; other site 123214002237 beta-alpha-beta structure motif; other site 123214002238 NAD binding pocket [chemical binding]; other site 123214002239 Iron coordination center [ion binding]; other site 123214002240 sulfite reductase, subunit A; Region: sulfite_red_A; TIGR02910 123214002241 Ni,Fe-hydrogenase I small subunit [Energy production and conversion]; Region: HyaA; COG1740 123214002242 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 123214002243 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 123214002244 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 123214002245 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 123214002246 von Willebrand factor type A domain; Region: VWA_2; pfam13519 123214002247 metal ion-dependent adhesion site (MIDAS); other site 123214002248 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 123214002249 metal ion-dependent adhesion site (MIDAS); other site 123214002250 MoxR-like ATPases [General function prediction only]; Region: COG0714 123214002251 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 123214002252 Walker A motif; other site 123214002253 ATP binding site [chemical binding]; other site 123214002254 Walker B motif; other site 123214002255 arginine finger; other site 123214002256 Protein of unknown function DUF58; Region: DUF58; pfam01882 123214002257 Acylphosphatase; Region: Acylphosphatase; pfam00708 123214002258 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 123214002259 HypF finger; Region: zf-HYPF; pfam07503 123214002260 HypF finger; Region: zf-HYPF; pfam07503 123214002261 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 123214002262 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 123214002263 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 123214002264 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 123214002265 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 123214002266 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 123214002267 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 123214002268 Flagellar basal body-associated protein FliL; Region: FliL; pfam03748 123214002269 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 123214002270 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 123214002271 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 123214002272 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 123214002273 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 123214002274 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 123214002275 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 123214002276 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 123214002277 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 123214002278 Walker A motif/ATP binding site; other site 123214002279 Walker B motif; other site 123214002280 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 123214002281 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; pfam01514 123214002282 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 123214002283 Flagellar hook-basal body complex protein FliE; Region: FliE; pfam02049 123214002284 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 123214002285 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 123214002286 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 123214002287 Flagellar basal body protein [Cell motility and secretion]; Region: FlgB; COG1815 123214002288 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 123214002289 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 123214002290 TPR motif; other site 123214002291 binding surface 123214002292 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 123214002293 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 123214002294 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 123214002295 DNA binding residues [nucleotide binding] 123214002296 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 123214002297 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 123214002298 FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by...; Region: FleN-like; cd02038 123214002299 Flagellar GTP-binding protein [Cell motility and secretion]; Region: FlhF; COG1419 123214002300 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 123214002301 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 123214002302 FHIPEP family; Region: FHIPEP; pfam00771 123214002303 Rod binding protein; Region: Rod-binding; cl01626 123214002304 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 123214002305 Flagellar P-ring protein; Region: FlgI; pfam02119 123214002306 Flagellar L-ring protein; Region: FlgH; pfam02107 123214002307 Flagellar basal body L-ring protein [Cell motility and secretion]; Region: FlgH; COG2063 123214002308 SAF-like; Region: SAF_2; pfam13144 123214002309 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 123214002310 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 123214002311 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 123214002312 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 123214002313 Flagellar basal body rod protein [Cell motility and secretion]; Region: FlgG; COG4786 123214002314 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 123214002315 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 123214002316 flagellar motor switch protein FliN; Region: fliN; TIGR02480 123214002317 flagellar motor switch protein FliM; Region: fliM_switch; TIGR01397 123214002318 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 123214002319 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 123214002320 FliG C-terminal domain; Region: FliG_C; pfam01706 123214002321 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 123214002322 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 123214002323 dimerization interface [polypeptide binding]; other site 123214002324 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 123214002325 dimer interface [polypeptide binding]; other site 123214002326 putative CheW interface [polypeptide binding]; other site 123214002327 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 123214002328 dimer interface [polypeptide binding]; other site 123214002329 putative CheW interface [polypeptide binding]; other site 123214002330 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 123214002331 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 123214002332 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 123214002333 active site 123214002334 phosphorylation site [posttranslational modification] 123214002335 intermolecular recognition site; other site 123214002336 dimerization interface [polypeptide binding]; other site 123214002337 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 123214002338 Response regulator receiver domain; Region: Response_reg; pfam00072 123214002339 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 123214002340 active site 123214002341 phosphorylation site [posttranslational modification] 123214002342 intermolecular recognition site; other site 123214002343 dimerization interface [polypeptide binding]; other site 123214002344 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 123214002345 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 123214002346 putative binding surface; other site 123214002347 active site 123214002348 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 123214002349 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 123214002350 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 123214002351 ATP binding site [chemical binding]; other site 123214002352 Mg2+ binding site [ion binding]; other site 123214002353 G-X-G motif; other site 123214002354 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 123214002355 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 123214002356 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 123214002357 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 123214002358 active site 123214002359 phosphorylation site [posttranslational modification] 123214002360 intermolecular recognition site; other site 123214002361 dimerization interface [polypeptide binding]; other site 123214002362 CheB methylesterase; Region: CheB_methylest; pfam01339 123214002363 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 123214002364 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 123214002365 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 123214002366 Permease P (pink-eyed dilution). Mutations in the human melanosomal P gene were responsible for classic phenotype of oculocutaneous albinism type 2 (OCA2). Although the precise function of the P protein is unknown, it was predicted to regulate the...; Region: P_permease; cd01116 123214002367 transmembrane helices; other site 123214002368 histidinol dehydrogenase; Region: hisD; TIGR00069 123214002369 Peptidase family M48; Region: Peptidase_M48; cl12018 123214002370 PAS domain S-box; Region: sensory_box; TIGR00229 123214002371 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 123214002372 putative active site [active] 123214002373 heme pocket [chemical binding]; other site 123214002374 PAS domain; Region: PAS; smart00091 123214002375 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 123214002376 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 123214002377 putative active site [active] 123214002378 heme pocket [chemical binding]; other site 123214002379 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 123214002380 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214002381 metal binding site [ion binding]; metal-binding site 123214002382 active site 123214002383 I-site; other site 123214002384 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 123214002385 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 123214002386 nucleotide binding site [chemical binding]; other site 123214002387 NEF interaction site [polypeptide binding]; other site 123214002388 SBD interface [polypeptide binding]; other site 123214002389 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 123214002390 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 123214002391 ATP binding site [chemical binding]; other site 123214002392 putative Mg++ binding site [ion binding]; other site 123214002393 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 123214002394 nucleotide binding region [chemical binding]; other site 123214002395 ATP-binding site [chemical binding]; other site 123214002396 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 123214002397 PAS domain; Region: PAS_9; pfam13426 123214002398 putative active site [active] 123214002399 heme pocket [chemical binding]; other site 123214002400 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 123214002401 CutA1 divalent ion tolerance protein; Region: CutA1; pfam03091 123214002402 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 123214002403 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 123214002404 Clp amino terminal domain; Region: Clp_N; pfam02861 123214002405 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 123214002406 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 123214002407 Walker A motif; other site 123214002408 ATP binding site [chemical binding]; other site 123214002409 Walker B motif; other site 123214002410 arginine finger; other site 123214002411 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 123214002412 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 123214002413 Walker A motif; other site 123214002414 ATP binding site [chemical binding]; other site 123214002415 Walker B motif; other site 123214002416 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 123214002417 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 123214002418 MutS domain I; Region: MutS_I; pfam01624 123214002419 MutS domain II; Region: MutS_II; pfam05188 123214002420 MutS domain III; Region: MutS_III; pfam05192 123214002421 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 123214002422 Walker A/P-loop; other site 123214002423 ATP binding site [chemical binding]; other site 123214002424 Q-loop/lid; other site 123214002425 ABC transporter signature motif; other site 123214002426 Walker B; other site 123214002427 D-loop; other site 123214002428 H-loop/switch region; other site 123214002429 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 123214002430 Peptidase family M23; Region: Peptidase_M23; pfam01551 123214002431 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14331 123214002432 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 123214002433 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 123214002434 FeS/SAM binding site; other site 123214002435 TRAM domain; Region: TRAM; pfam01938 123214002436 Bifunctional nuclease; Region: DNase-RNase; pfam02577 123214002437 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 123214002438 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 123214002439 dimer interface [polypeptide binding]; other site 123214002440 active site 123214002441 CoA binding pocket [chemical binding]; other site 123214002442 putative phosphate acyltransferase; Provisional; Region: PRK05331 123214002443 50S ribosomal protein L32; Reviewed; Region: rpmF; PRK12286 123214002444 succinyldiaminopimelate transaminase; Region: DapC; TIGR03537 123214002445 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 123214002446 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214002447 homodimer interface [polypeptide binding]; other site 123214002448 catalytic residue [active] 123214002449 AAA domain; Region: AAA_17; pfam13207 123214002450 AAA domain; Region: AAA_33; pfam13671 123214002451 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 123214002452 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 123214002453 NADP binding site [chemical binding]; other site 123214002454 active site 123214002455 steroid binding site; other site 123214002456 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 123214002457 OsmC-like protein; Region: OsmC; pfam02566 123214002458 HflC protein; Region: hflC; TIGR01932 123214002459 SPFH domain / Band 7 family; Region: Band_7; pfam01145 123214002460 excinuclease ABC subunit B; Provisional; Region: PRK05298 123214002461 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 123214002462 ATP binding site [chemical binding]; other site 123214002463 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 123214002464 nucleotide binding region [chemical binding]; other site 123214002465 ATP-binding site [chemical binding]; other site 123214002466 Ultra-violet resistance protein B; Region: UvrB; pfam12344 123214002467 UvrB/uvrC motif; Region: UVR; pfam02151 123214002468 Predicted O-methyltransferase [General function prediction only]; Region: COG4122 123214002469 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 123214002470 S-adenosylmethionine binding site [chemical binding]; other site 123214002471 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 123214002472 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 123214002473 active site 123214002474 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 123214002475 putative metal binding site; other site 123214002476 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 123214002477 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 123214002478 FeS/SAM binding site; other site 123214002479 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 123214002480 Predicted methyltransferases [General function prediction only]; Region: COG0313 123214002481 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 123214002482 putative SAM binding site [chemical binding]; other site 123214002483 putative homodimer interface [polypeptide binding]; other site 123214002484 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 123214002485 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 123214002486 HIGH motif; other site 123214002487 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 123214002488 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 123214002489 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 123214002490 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1672 123214002491 AAA ATPase domain; Region: AAA_16; pfam13191 123214002492 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 123214002493 active site 123214002494 KMSKS motif; other site 123214002495 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 123214002496 tRNA binding surface [nucleotide binding]; other site 123214002497 Anticodon-binding domain of tRNA; Region: Anticodon_1; pfam08264 123214002498 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 123214002499 Ligand Binding Site [chemical binding]; other site 123214002500 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 123214002501 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 123214002502 CAAX protease self-immunity; Region: Abi; pfam02517 123214002503 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 123214002504 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 123214002505 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 123214002506 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 123214002507 Outer membrane protein family (DUF1597); Region: DUF1597; pfam07642 123214002508 Protein of unknown function (DUF501); Region: DUF501; cl00652 123214002509 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 123214002510 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214002511 metal binding site [ion binding]; metal-binding site 123214002512 active site 123214002513 I-site; other site 123214002514 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]; Region: LigT; COG1514 123214002515 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 123214002516 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 123214002517 thiamine biosynthesis protein ThiC; Region: thiC; TIGR00190 123214002518 ThiC family; Region: ThiC; pfam01964 123214002519 PAS domain; Region: PAS; smart00091 123214002520 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 123214002521 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 123214002522 dimer interface [polypeptide binding]; other site 123214002523 phosphorylation site [posttranslational modification] 123214002524 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 123214002525 ATP binding site [chemical binding]; other site 123214002526 Mg2+ binding site [ion binding]; other site 123214002527 G-X-G motif; other site 123214002528 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 123214002529 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 123214002530 active site 123214002531 phosphorylation site [posttranslational modification] 123214002532 intermolecular recognition site; other site 123214002533 dimerization interface [polypeptide binding]; other site 123214002534 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 123214002535 Walker A motif; other site 123214002536 ATP binding site [chemical binding]; other site 123214002537 Walker B motif; other site 123214002538 arginine finger; other site 123214002539 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 123214002540 TPR repeat; Region: TPR_11; pfam13414 123214002541 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 123214002542 binding surface 123214002543 TPR motif; other site 123214002544 Tetratricopeptide repeat; Region: TPR_12; pfam13424 123214002545 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 123214002546 binding surface 123214002547 TPR motif; other site 123214002548 TPR repeat; Region: TPR_11; pfam13414 123214002549 Sporulation related domain; Region: SPOR; pfam05036 123214002550 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 123214002551 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 123214002552 Ligand binding site; other site 123214002553 Putative Catalytic site; other site 123214002554 DXD motif; other site 123214002555 Uncharacterized protein family (UPF0104); Region: UPF0104; pfam03706 123214002556 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 123214002557 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 123214002558 Outer membrane efflux protein; Region: OEP; pfam02321 123214002559 Outer membrane efflux protein; Region: OEP; pfam02321 123214002560 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 123214002561 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 123214002562 HlyD family secretion protein; Region: HlyD_3; pfam13437 123214002563 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 123214002564 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 123214002565 putative substrate translocation pore; other site 123214002566 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 123214002567 HlyD family secretion protein; Region: HlyD_3; pfam13437 123214002568 Mechanosensitive ion channel; Region: MS_channel; pfam00924 123214002569 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 123214002570 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 123214002571 Walker A/P-loop; other site 123214002572 ATP binding site [chemical binding]; other site 123214002573 Q-loop/lid; other site 123214002574 ABC transporter signature motif; other site 123214002575 Walker B; other site 123214002576 D-loop; other site 123214002577 H-loop/switch region; other site 123214002578 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 123214002579 Walker A/P-loop; other site 123214002580 ATP binding site [chemical binding]; other site 123214002581 Q-loop/lid; other site 123214002582 ABC transporter signature motif; other site 123214002583 Walker B; other site 123214002584 D-loop; other site 123214002585 H-loop/switch region; other site 123214002586 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 123214002587 Low molecular weight phosphatase family; Region: LMWPc; cd00115 123214002588 active site 123214002589 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 123214002590 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 123214002591 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 123214002592 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 123214002593 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 123214002594 P-loop; other site 123214002595 Magnesium ion binding site [ion binding]; other site 123214002596 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 123214002597 Magnesium ion binding site [ion binding]; other site 123214002598 ParB-like nuclease domain; Region: ParBc; pfam02195 123214002599 nucleoid occlusion protein; Region: nucleoid_noc; TIGR04285 123214002600 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 123214002601 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 123214002602 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 123214002603 Type II secretory pathway, component PulK [Intracellular trafficking and secretion]; Region: PulK; COG3156 123214002604 Type II secretion system (T2SS), protein M; Region: T2SM; cl01222 123214002605 Peptidase S8 family domain in Subtilisin-like proteins; Region: Peptidases_S8_Subtilisin_like; cd07473 123214002606 catalytic triad [active] 123214002607 putative active site [active] 123214002608 type II secretion system protein C; Region: typeII_sec_gspC; TIGR01713 123214002609 Type IV pilus biogenesis; Region: Pilus_PilP; pfam11356 123214002610 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 123214002611 type II secretion system protein D; Region: type_II_gspD; TIGR02517 123214002612 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 123214002613 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 123214002614 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 123214002615 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 123214002616 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 123214002617 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 123214002618 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 123214002619 Walker A motif; other site 123214002620 ATP binding site [chemical binding]; other site 123214002621 Walker B motif; other site 123214002622 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 123214002623 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 123214002624 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 123214002625 Methyltransferase domain; Region: Methyltransf_31; pfam13847 123214002626 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 123214002627 S-adenosylmethionine binding site [chemical binding]; other site 123214002628 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 123214002629 Rubredoxin [Energy production and conversion]; Region: COG1773 123214002630 iron binding site [ion binding]; other site 123214002631 Predicted enolase-phosphatase [Energy production and conversion]; Region: COG4229 123214002632 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 123214002633 motif II; other site 123214002634 ABC-type Co2+ transport system, permease component [Inorganic ion transport and metabolism]; Region: CbiM; cl00397 123214002635 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; pfam01891 123214002636 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; cl01768 123214002637 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 123214002638 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 123214002639 Transcriptional regulator [Transcription]; Region: IclR; COG1414 123214002640 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 123214002641 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 123214002642 acetyl-CoA synthetase; Provisional; Region: PRK00174 123214002643 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 123214002644 active site 123214002645 CoA binding site [chemical binding]; other site 123214002646 acyl-activating enzyme (AAE) consensus motif; other site 123214002647 AMP binding site [chemical binding]; other site 123214002648 acetate binding site [chemical binding]; other site 123214002649 Protein of unknown function, DUF485; Region: DUF485; pfam04341 123214002650 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 123214002651 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 123214002652 Na binding site [ion binding]; other site 123214002653 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 123214002654 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 123214002655 ligand binding site [chemical binding]; other site 123214002656 flexible hinge region; other site 123214002657 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with either the CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain or the PB1 (Phox and Bem1p) domain; Region: CBS_pair_CAP-ED_DUF294_PBI_assoc2; cd04800 123214002658 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 123214002659 metal binding triad; other site 123214002660 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 123214002661 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 123214002662 active site 123214002663 catalytic site [active] 123214002664 substrate binding site [chemical binding]; other site 123214002665 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1672 123214002666 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 123214002667 Acylphosphatase; Region: Acylphosphatase; pfam00708 123214002668 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 123214002669 HypF finger; Region: zf-HYPF; pfam07503 123214002670 HypF finger; Region: zf-HYPF; pfam07503 123214002671 hypothetical protein; Reviewed; Region: PRK09588 123214002672 Uncharacterized protein family UPF0027; Region: UPF0027; pfam01139 123214002673 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 123214002674 Mechanosensitive ion channel; Region: MS_channel; pfam00924 123214002675 YtkA-like; Region: YtkA; pfam13115 123214002676 Penicillinase repressor; Region: Pencillinase_R; pfam03965 123214002677 Peptidase family M48; Region: Peptidase_M48; cl12018 123214002678 Outer membrane efflux protein; Region: OEP; pfam02321 123214002679 Outer membrane efflux protein; Region: OEP; pfam02321 123214002680 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 123214002681 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 123214002682 HlyD family secretion protein; Region: HlyD_3; pfam13437 123214002683 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 123214002684 AmmeMemoRadiSam system radical SAM enzyme; Region: AmmeMemoSam_rS; TIGR04337 123214002685 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 123214002686 FeS/SAM binding site; other site 123214002687 C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some...; Region: Peptidase_C1; cl00298 123214002688 active site 123214002689 C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some...; Region: Peptidase_C1; cl00298 123214002690 active site 123214002691 polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is...; Region: PKD; cl17457 123214002692 Carbamoylphosphate synthase large subunit (split gene in MJ) [Amino acid transport and metabolism / Nucleotide transport and metabolism]; Region: CarB; COG0458 123214002693 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 123214002694 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 123214002695 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 123214002696 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; smart01096 123214002697 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK06406 123214002698 ATP cone domain; Region: ATP-cone; pfam03477 123214002699 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 123214002700 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 123214002701 active site 123214002702 dimer interface [polypeptide binding]; other site 123214002703 effector binding site; other site 123214002704 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 123214002705 ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; Region: CobA_CobO_BtuR; cl17276 123214002706 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 123214002707 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 123214002708 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214002709 Cytochrome c554 and c-prime; Region: Cytochrome_C554; pfam13435 123214002710 aromatic acid decarboxylase; Validated; Region: PRK05920 123214002711 Flavoprotein; Region: Flavoprotein; pfam02441 123214002712 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 123214002713 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 123214002714 active site 123214002715 DNA binding site [nucleotide binding] 123214002716 Int/Topo IB signature motif; other site 123214002717 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 123214002718 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 123214002719 substrate binding site [chemical binding]; other site 123214002720 glutamase interaction surface [polypeptide binding]; other site 123214002721 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; cd00188 123214002722 active site 123214002723 metal binding site [ion binding]; metal-binding site 123214002724 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 123214002725 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; cl17736 123214002726 active site 123214002727 phosphorylation site [posttranslational modification] 123214002728 intermolecular recognition site; other site 123214002729 dimerization interface [polypeptide binding]; other site 123214002730 Predicted periplasmic solute-binding protein [General function prediction only]; Region: COG2107 123214002731 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 123214002732 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 123214002733 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 123214002734 RNA binding surface [nucleotide binding]; other site 123214002735 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 123214002736 active site 123214002737 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 123214002738 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 123214002739 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 123214002740 putative menaquinone biosynthesis protein, SCO4494 family; Region: mena_SCO4494; TIGR03700 123214002741 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 123214002742 FeS/SAM binding site; other site 123214002743 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 123214002744 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 123214002745 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 123214002746 RNA binding surface [nucleotide binding]; other site 123214002747 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 123214002748 active site 123214002749 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 123214002750 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 123214002751 Walker A/P-loop; other site 123214002752 ATP binding site [chemical binding]; other site 123214002753 Q-loop/lid; other site 123214002754 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 123214002755 ABC transporter signature motif; other site 123214002756 Walker B; other site 123214002757 D-loop; other site 123214002758 H-loop/switch region; other site 123214002759 Outer membrane efflux protein; Region: OEP; pfam02321 123214002760 Outer membrane efflux protein; Region: OEP; pfam02321 123214002761 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 123214002762 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 123214002763 HlyD family secretion protein; Region: HlyD_3; pfam13437 123214002764 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 123214002765 Predicted membrane protein [Function unknown]; Region: COG4244 123214002766 VIT family; Region: VIT1; pfam01988 123214002767 carbamoyl phosphate synthase-like protein; Provisional; Region: PRK12767 123214002768 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 123214002769 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 123214002770 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme MccE; Region: PLPDE_III_MccE_like; cd06841 123214002771 dimer interface [polypeptide binding]; other site 123214002772 active site 123214002773 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 123214002774 catalytic residues [active] 123214002775 substrate binding site [chemical binding]; other site 123214002776 Urea transporter; Region: UT; pfam03253 123214002777 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 123214002778 Peptidase family M23; Region: Peptidase_M23; pfam01551 123214002779 Tetratricopeptide repeat; Region: TPR_16; pfam13432 123214002780 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 123214002781 binding surface 123214002782 TPR motif; other site 123214002783 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 123214002784 binding surface 123214002785 TPR motif; other site 123214002786 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 123214002787 putative active site pocket [active] 123214002788 dimerization interface [polypeptide binding]; other site 123214002789 putative catalytic residue [active] 123214002790 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 123214002791 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_Nitrate-R-NapA-like; cd02754 123214002792 [4Fe-4S] binding site [ion binding]; other site 123214002793 molybdopterin cofactor binding site; other site 123214002794 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 123214002795 molybdopterin cofactor binding site; other site 123214002796 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 123214002797 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 123214002798 putative substrate translocation pore; other site 123214002799 ferredoxin-nitrite reductase; Reviewed; Region: nirA; PRK09566 123214002800 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 123214002801 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 123214002802 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 123214002803 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 123214002804 catalytic triad [active] 123214002805 Siroheme synthase (precorrin-2 oxidase/ferrochelatase domain) [Coenzyme metabolism]; Region: CysG; COG1648 123214002806 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 123214002807 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 123214002808 substrate binding site [chemical binding]; other site 123214002809 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 123214002810 substrate binding site [chemical binding]; other site 123214002811 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 123214002812 intersubunit interface [polypeptide binding]; other site 123214002813 active site 123214002814 Zn2+ binding site [ion binding]; other site 123214002815 Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a...; Region: PRX_Atyp2cys; cd03014 123214002816 dimer interface [polypeptide binding]; other site 123214002817 catalytic triad [active] 123214002818 peroxidatic and resolving cysteines [active] 123214002819 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 123214002820 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 123214002821 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK06916 123214002822 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 123214002823 inhibitor-cofactor binding pocket; inhibition site 123214002824 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214002825 catalytic residue [active] 123214002826 Uncharacterized conserved protein (DUF2267); Region: DUF2267; pfam10025 123214002827 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; Region: PHP_PolIIIA_DnaE3; cd12113 123214002828 PHP domain; Region: PHP; pfam02811 123214002829 active site 123214002830 PHP Thumb interface [polypeptide binding]; other site 123214002831 metal binding site [ion binding]; metal-binding site 123214002832 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 123214002833 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cd00081 123214002834 protein-splicing catalytic site; other site 123214002835 thioester formation/cholesterol transfer; other site 123214002836 Intein/homing endonuclease [DNA replication, recombination, and repair]; Region: COG1372 123214002837 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 123214002838 non-specific DNA binding site [nucleotide binding]; other site 123214002839 salt bridge; other site 123214002840 sequence-specific DNA binding site [nucleotide binding]; other site 123214002841 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cd00081 123214002842 protein-splicing catalytic site; other site 123214002843 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 123214002844 generic binding surface II; other site 123214002845 generic binding surface I; other site 123214002846 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 123214002847 GTP cyclohydrolase I; Provisional; Region: PLN03044 123214002848 active site 123214002849 Predicted CoA-binding protein [General function prediction only]; Region: COG1832 123214002850 lipoyl synthase; Provisional; Region: PRK05481 123214002851 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 123214002852 FeS/SAM binding site; other site 123214002853 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 123214002854 DEAD-like helicases superfamily; Region: DEXDc; smart00487 123214002855 ATP binding site [chemical binding]; other site 123214002856 Mg++ binding site [ion binding]; other site 123214002857 motif III; other site 123214002858 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 123214002859 nucleotide binding region [chemical binding]; other site 123214002860 ATP-binding site [chemical binding]; other site 123214002861 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 123214002862 DnaA N-terminal domain; Region: DnaA_N; pfam11638 123214002863 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 123214002864 Walker A motif; other site 123214002865 ATP binding site [chemical binding]; other site 123214002866 Walker B motif; other site 123214002867 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 123214002868 arginine finger; other site 123214002869 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 123214002870 DnaA box-binding interface [nucleotide binding]; other site 123214002871 Predicted metal-binding protein (DUF2103); Region: DUF2103; cl01651 123214002872 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea; Region: Transaldolase_FSA; cd00956 123214002873 active site 123214002874 intersubunit interactions; other site 123214002875 catalytic residue [active] 123214002876 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 123214002877 Peptidase family M23; Region: Peptidase_M23; pfam01551 123214002878 2-isopropylmalate synthase; Validated; Region: PRK00915 123214002879 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 123214002880 active site 123214002881 catalytic residues [active] 123214002882 metal binding site [ion binding]; metal-binding site 123214002883 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 123214002884 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 123214002885 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 123214002886 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 123214002887 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 123214002888 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 123214002889 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 123214002890 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 123214002891 active site 123214002892 metal binding site [ion binding]; metal-binding site 123214002893 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 123214002894 nickel responsive regulator; Provisional; Region: PRK00630 123214002895 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 123214002896 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 123214002897 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 123214002898 Walker A/P-loop; other site 123214002899 ATP binding site [chemical binding]; other site 123214002900 Q-loop/lid; other site 123214002901 ABC transporter signature motif; other site 123214002902 Walker B; other site 123214002903 D-loop; other site 123214002904 H-loop/switch region; other site 123214002905 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 123214002906 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 123214002907 Cysteine-rich domain; Region: CCG; pfam02754 123214002908 Cysteine-rich domain; Region: CCG; pfam02754 123214002909 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 123214002910 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 123214002911 Walker A motif; other site 123214002912 ATP binding site [chemical binding]; other site 123214002913 Walker B motif; other site 123214002914 arginine finger; other site 123214002915 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 123214002916 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4399 123214002917 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4399 123214002918 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 123214002919 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 123214002920 G1 box; other site 123214002921 putative GEF interaction site [polypeptide binding]; other site 123214002922 GTP/Mg2+ binding site [chemical binding]; other site 123214002923 Switch I region; other site 123214002924 G2 box; other site 123214002925 G3 box; other site 123214002926 Switch II region; other site 123214002927 G4 box; other site 123214002928 G5 box; other site 123214002929 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 123214002930 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 123214002931 excinuclease ABC subunit C; Provisional; Region: uvrC; PRK14667 123214002932 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 123214002933 GIY-YIG motif/motif A; other site 123214002934 active site 123214002935 catalytic site [active] 123214002936 putative DNA binding site [nucleotide binding]; other site 123214002937 metal binding site [ion binding]; metal-binding site 123214002938 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 123214002939 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 123214002940 PAS domain; Region: PAS_9; pfam13426 123214002941 putative active site [active] 123214002942 heme pocket [chemical binding]; other site 123214002943 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 123214002944 putative CheW interface [polypeptide binding]; other site 123214002945 HAD-superfamily subfamily IIA hydrolase, TIGR01458; Region: HAD-SF-IIA-hyp3 123214002946 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 123214002947 active site 123214002948 motif I; other site 123214002949 motif II; other site 123214002950 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 123214002951 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 123214002952 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 123214002953 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214002954 metal binding site [ion binding]; metal-binding site 123214002955 active site 123214002956 I-site; other site 123214002957 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 123214002958 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; cl17186 123214002959 Peptidase family U32; Region: Peptidase_U32; pfam01136 123214002960 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 123214002961 active site 123214002962 ribulose/triose binding site [chemical binding]; other site 123214002963 phosphate binding site [ion binding]; other site 123214002964 substrate (anthranilate) binding pocket [chemical binding]; other site 123214002965 product (indole) binding pocket [chemical binding]; other site 123214002966 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 123214002967 bis(5'-nucleosyl)-tetraphosphatase (symmetrical); Region: apaH; TIGR00668 123214002968 active site 123214002969 metal binding site [ion binding]; metal-binding site 123214002970 Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which...; Region: ZnMc; cl00064 123214002971 active site 123214002972 polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is...; Region: PKD; cl17457 123214002973 polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is...; Region: PKD; cd00146 123214002974 Predicted GTPases [General function prediction only]; Region: COG1162 123214002975 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 123214002976 GTPase/Zn-binding domain interface [polypeptide binding]; other site 123214002977 GTP/Mg2+ binding site [chemical binding]; other site 123214002978 G4 box; other site 123214002979 G5 box; other site 123214002980 G1 box; other site 123214002981 Switch I region; other site 123214002982 G2 box; other site 123214002983 G3 box; other site 123214002984 Switch II region; other site 123214002985 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 123214002986 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 123214002987 intersubunit interface [polypeptide binding]; other site 123214002988 nicotinate phosphoribosyltransferase; Validated; Region: PRK09243 123214002989 Nicotinate phosphoribosyltransferase (NAPRTase), subgroup A. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction...; Region: NAPRTase_A; cd01570 123214002990 active site 123214002991 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 123214002992 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 123214002993 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 123214002994 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 123214002995 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 123214002996 Putative catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases which consist of a 5-stranded beta/alpha barrel; Region: CE4_DAC_u4_5s; cd10973 123214002997 putative active site [active] 123214002998 putative metal binding site [ion binding]; other site 123214002999 Predicted membrane protein [Function unknown]; Region: COG2860 123214003000 UPF0126 domain; Region: UPF0126; pfam03458 123214003001 UPF0126 domain; Region: UPF0126; pfam03458 123214003002 DNA-binding protein, stimulates sugar fermentation [General function prediction only]; Region: SfsA; COG1489 123214003003 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 123214003004 substrate binding site [chemical binding]; other site 123214003005 active site 123214003006 Cytochrome c; Region: Cytochrom_C; cl11414 123214003007 Cytochrome c; Region: Cytochrom_C; cl11414 123214003008 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 123214003009 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 123214003010 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 123214003011 dimer interface [polypeptide binding]; other site 123214003012 phosphorylation site [posttranslational modification] 123214003013 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 123214003014 ATP binding site [chemical binding]; other site 123214003015 Mg2+ binding site [ion binding]; other site 123214003016 G-X-G motif; other site 123214003017 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 123214003018 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 123214003019 active site 123214003020 phosphorylation site [posttranslational modification] 123214003021 intermolecular recognition site; other site 123214003022 dimerization interface [polypeptide binding]; other site 123214003023 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 123214003024 DNA binding site [nucleotide binding] 123214003025 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 123214003026 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 123214003027 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 123214003028 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 123214003029 active site 123214003030 NTP binding site [chemical binding]; other site 123214003031 metal binding triad [ion binding]; metal-binding site 123214003032 tRNA nucleotidyltransferase domain 2 putative; Region: tRNA_NucTran2_2; pfam13735 123214003033 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 123214003034 active site 123214003035 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 123214003036 This PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily and is found in both archaea and bacteria. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible...; Region: PGM_like2; cd05800 123214003037 active site 123214003038 substrate binding site [chemical binding]; other site 123214003039 metal binding site [ion binding]; metal-binding site 123214003040 methionyl-tRNA synthetase; Reviewed; Region: PRK12267 123214003041 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 123214003042 active site 123214003043 HIGH motif; other site 123214003044 KMSKS motif; other site 123214003045 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 123214003046 tRNA binding surface [nucleotide binding]; other site 123214003047 anticodon binding site; other site 123214003048 tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins. This family includes EcMetRS and Aquifex aeolicus Trbp111 (AaTrbp111). This domain has general tRNA binding properties. MetRS aminoacylates methionine...; Region: tRNA_bind_EcMetRS_like; cd02800 123214003049 dimer interface [polypeptide binding]; other site 123214003050 putative tRNA-binding site [nucleotide binding]; other site 123214003051 NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]; Region: NuoE; COG1905 123214003052 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 123214003053 putative dimer interface [polypeptide binding]; other site 123214003054 [2Fe-2S] cluster binding site [ion binding]; other site 123214003055 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 123214003056 SLBB domain; Region: SLBB; pfam10531 123214003057 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 123214003058 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 123214003059 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 123214003060 dimer interface [polypeptide binding]; other site 123214003061 active site 123214003062 heme binding site [chemical binding]; other site 123214003063 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 123214003064 hypothetical protein; Provisional; Region: PRK08960 123214003065 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 123214003066 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214003067 homodimer interface [polypeptide binding]; other site 123214003068 catalytic residue [active] 123214003069 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 123214003070 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl17341 123214003071 Metal-dependent hydrolases of the beta-lactamase superfamily III [General function prediction only]; Region: ElaC; COG1234 123214003072 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 123214003073 pteridine reductase; Provisional; Region: PRK09135 123214003074 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214003075 NAD(P) binding site [chemical binding]; other site 123214003076 active site 123214003077 AAA domain; Region: AAA_22; pfam13401 123214003078 Sporulation related domain; Region: SPOR; pfam05036 123214003079 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 123214003080 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 123214003081 Walker A motif; other site 123214003082 ATP binding site [chemical binding]; other site 123214003083 Walker B motif; other site 123214003084 arginine finger; other site 123214003085 Bacterial SH3 domain; Region: SH3_3; pfam08239 123214003086 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214003087 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 123214003088 metal binding site [ion binding]; metal-binding site 123214003089 active site 123214003090 I-site; other site 123214003091 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 123214003092 Tetratricopeptide repeat; Region: TPR_16; pfam13432 123214003093 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 123214003094 binding surface 123214003095 TPR motif; other site 123214003096 Secretin and TonB N terminus short domain; Region: STN; pfam07660 123214003097 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 123214003098 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 123214003099 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 123214003100 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 123214003101 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 123214003102 Walker A motif; other site 123214003103 ATP binding site [chemical binding]; other site 123214003104 Walker B motif; other site 123214003105 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 123214003106 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 123214003107 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 123214003108 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 123214003109 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 123214003110 active site 123214003111 nucleophile elbow; other site 123214003112 chaperone protein DnaJ; Region: DnaJ_bact; TIGR02349 123214003113 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 123214003114 HSP70 interaction site [polypeptide binding]; other site 123214003115 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 123214003116 Zn binding sites [ion binding]; other site 123214003117 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 123214003118 GrpE; Region: GrpE; pfam01025 123214003119 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 123214003120 dimer interface [polypeptide binding]; other site 123214003121 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 123214003122 Uncharacterized conserved protein [Function unknown]; Region: COG1432 123214003123 LabA_like proteins; Region: LabA; cd10911 123214003124 putative metal binding site [ion binding]; other site 123214003125 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 123214003126 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 123214003127 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 123214003128 active site 123214003129 metal binding site [ion binding]; metal-binding site 123214003130 DNA binding site [nucleotide binding] 123214003131 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 123214003132 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 123214003133 active site 123214003134 catalytic tetrad [active] 123214003135 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 123214003136 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 123214003137 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 123214003138 Zn2+ binding site [ion binding]; other site 123214003139 Mg2+ binding site [ion binding]; other site 123214003140 FecR protein; Region: FecR; pfam04773 123214003141 CHASE2 domain; Region: CHASE2; pfam05226 123214003142 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 123214003143 cyclase homology domain; Region: CHD; cd07302 123214003144 nucleotidyl binding site; other site 123214003145 metal binding site [ion binding]; metal-binding site 123214003146 dimer interface [polypeptide binding]; other site 123214003147 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 123214003148 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 123214003149 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 123214003150 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214003151 metal binding site [ion binding]; metal-binding site 123214003152 active site 123214003153 I-site; other site 123214003154 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 123214003155 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 123214003156 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 123214003157 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 123214003158 Walker A/P-loop; other site 123214003159 ATP binding site [chemical binding]; other site 123214003160 Q-loop/lid; other site 123214003161 ABC transporter signature motif; other site 123214003162 Walker B; other site 123214003163 D-loop; other site 123214003164 H-loop/switch region; other site 123214003165 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 123214003166 Part of AAA domain; Region: AAA_19; pfam13245 123214003167 Family description; Region: UvrD_C_2; pfam13538 123214003168 glutamate racemase; Provisional; Region: PRK00865 123214003169 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 123214003170 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 123214003171 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 123214003172 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 123214003173 homodimer interface [polypeptide binding]; other site 123214003174 oligonucleotide binding site [chemical binding]; other site 123214003175 4Fe-4S binding domain; Region: Fer4_5; pfam12801 123214003176 4Fe-4S binding domain; Region: Fer4_5; pfam12801 123214003177 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 123214003178 PEGA domain; Region: PEGA; pfam08308 123214003179 PEGA domain; Region: PEGA; pfam08308 123214003180 PEGA domain; Region: PEGA; pfam08308 123214003181 FOG: WD40 repeat [General function prediction only]; Region: COG2319 123214003182 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 123214003183 structural tetrad; other site 123214003184 Glutamine phosphoribosylpyrophosphate amidotransferase [Nucleotide transport and metabolism]; Region: PurF; COG0034 123214003185 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 123214003186 active site 123214003187 tetramer interface [polypeptide binding]; other site 123214003188 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 123214003189 active site 123214003190 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 123214003191 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 123214003192 Similar to Prolidase and Aminopeptidase P. The members of this subfamily presumably catalyse hydrolysis of Xaa-Pro dipeptides and/or release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP-like; cd01092 123214003193 active site 123214003194 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 123214003195 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214003196 metal binding site [ion binding]; metal-binding site 123214003197 active site 123214003198 I-site; other site 123214003199 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 123214003200 PilZ domain; Region: PilZ; pfam07238 123214003201 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin...; Region: mcbC-like_oxidoreductase; cd02142 123214003202 putative FMN binding site [chemical binding]; other site 123214003203 NADPH bind site [chemical binding]; other site 123214003204 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 123214003205 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 123214003206 S-adenosylmethionine binding site [chemical binding]; other site 123214003207 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 123214003208 active site 123214003209 catalytic site [active] 123214003210 substrate binding site [chemical binding]; other site 123214003211 HupF/HypC family; Region: HupF_HypC; pfam01455 123214003212 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 123214003213 putative active site [active] 123214003214 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 123214003215 hydrogenase isoenzymes formation protein HypD; Provisional; Region: PRK15062 123214003216 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 123214003217 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; smart00831 123214003218 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 123214003219 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 123214003220 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 123214003221 motif II; other site 123214003222 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 123214003223 Ca2+/Na+ antiporter [Inorganic ion transport and metabolism]; Region: ECM27; COG0530 123214003224 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 123214003225 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 123214003226 HypE (Hydrogenase expression/formation protein). HypE is involved in Ni-Fe hydrogenase biosynthesis. HypE dehydrates its own carbamoyl moiety in an ATP-dependent process to yield the enzyme thiocyanate. The N-terminal domain of HypE is related to the...; Region: HypE; cd02197 123214003227 dimerization interface [polypeptide binding]; other site 123214003228 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 123214003229 ATP binding site [chemical binding]; other site 123214003230 coenzyme F420-reducing hydrogenase delta subunit (putative coenzyme F420 hydrogenase processing subunit); Region: frhD; TIGR00130 123214003231 Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD...; Region: H2MP_MemB-H2up; cd06062 123214003232 putative substrate-binding site; other site 123214003233 nickel binding site [ion binding]; other site 123214003234 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]; Region: COG1579 123214003235 Putative zinc ribbon domain; Region: DUF164; pfam02591 123214003236 diaminopimelate epimerase; Provisional; Region: PRK13577 123214003237 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 123214003238 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 123214003239 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 123214003240 metal binding site 2 [ion binding]; metal-binding site 123214003241 putative DNA binding helix; other site 123214003242 metal binding site 1 [ion binding]; metal-binding site 123214003243 dimer interface [polypeptide binding]; other site 123214003244 structural Zn2+ binding site [ion binding]; other site 123214003245 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 123214003246 Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); Region: MPN_like; cd08070 123214003247 MPN+ (JAMM) motif; other site 123214003248 Zinc-binding site [ion binding]; other site 123214003249 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...; Region: CSP_CDS; cd04458 123214003250 DNA-binding site [nucleotide binding]; DNA binding site 123214003251 RNA-binding motif; other site 123214003252 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 123214003253 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 123214003254 RNA binding surface [nucleotide binding]; other site 123214003255 Pseudouridine synthases, RsuA subfamily; Region: PseudoU_synth_RsuA_like; cd02870 123214003256 active site 123214003257 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; pfam13557 123214003258 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various...; Region: Peptidase_C39G; cd02423 123214003259 putative active site [active] 123214003260 dipeptide transporter; Provisional; Region: PRK10913 123214003261 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 123214003262 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 123214003263 dimer interface [polypeptide binding]; other site 123214003264 conserved gate region; other site 123214003265 ABC-ATPase subunit interface; other site 123214003266 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 123214003267 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 123214003268 dimer interface [polypeptide binding]; other site 123214003269 conserved gate region; other site 123214003270 putative PBP binding loops; other site 123214003271 ABC-ATPase subunit interface; other site 123214003272 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 123214003273 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. CCL cleaves citryl-CoA (CiCoA) to acetyl-CoA (AcCoA) and oxaloacetate (OAA); Region: CCL_ACL-C; cd06100 123214003274 active site 123214003275 oxalacetate binding site [chemical binding]; other site 123214003276 citrylCoA binding site [chemical binding]; other site 123214003277 coenzyme A binding site [chemical binding]; other site 123214003278 catalytic triad [active] 123214003279 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 123214003280 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 123214003281 dimerization interface [polypeptide binding]; other site 123214003282 PAS domain; Region: PAS; smart00091 123214003283 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 123214003284 dimer interface [polypeptide binding]; other site 123214003285 phosphorylation site [posttranslational modification] 123214003286 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 123214003287 ATP binding site [chemical binding]; other site 123214003288 Mg2+ binding site [ion binding]; other site 123214003289 G-X-G motif; other site 123214003290 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 123214003291 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 123214003292 Mg++ binding site [ion binding]; other site 123214003293 putative catalytic motif [active] 123214003294 putative substrate binding site [chemical binding]; other site 123214003295 SAM-dependent RNA methyltransferase; Region: Methyltrn_RNA_4; pfam09936 123214003296 Preprotein translocase SecG subunit; Region: SecG; cl09123 123214003297 triosephosphate isomerase; Provisional; Region: PRK14565 123214003298 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 123214003299 substrate binding site [chemical binding]; other site 123214003300 dimer interface [polypeptide binding]; other site 123214003301 catalytic triad [active] 123214003302 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 123214003303 catalytic core [active] 123214003304 Domain of unknown function (DUF3817); Region: DUF3817; pfam12823 123214003305 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 123214003306 Methyltransferase domain; Region: Methyltransf_26; pfam13659 123214003307 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 123214003308 gamma subunit interface [polypeptide binding]; other site 123214003309 epsilon subunit interface [polypeptide binding]; other site 123214003310 LBP interface [polypeptide binding]; other site 123214003311 isoprenoid biosynthesis protein with amidotransferase-like domain; Provisional; Region: PRK11780 123214003312 Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1; Region: GATase1_ES1; cd03133 123214003313 conserved cys residue [active] 123214003314 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 123214003315 trimer interface [polypeptide binding]; other site 123214003316 active site 123214003317 homoserine dehydrogenase; Provisional; Region: PRK06349 123214003318 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 123214003319 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 123214003320 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 123214003321 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 123214003322 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 123214003323 transmembrane helices; other site 123214003324 Diadenosine hexaphosphate (Ap6A) hydrolase is a member of the Nudix hydrolase superfamily. Ap6A hydrolase specifically hydrolyzes diadenosine polyphosphates, but not ATP or diadenosine triphosphate, and it generates ATP as the product. Ap6A, the most...; Region: Ap6A_hydrolase; cd03673 123214003325 active site 123214003326 Ap6A binding site [chemical binding]; other site 123214003327 nudix motif; other site 123214003328 metal binding site [ion binding]; metal-binding site 123214003329 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 123214003330 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 123214003331 putative acyl-acceptor binding pocket; other site 123214003332 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 123214003333 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 123214003334 inhibitor-cofactor binding pocket; inhibition site 123214003335 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214003336 catalytic residue [active] 123214003337 SnoaL-like domain; Region: SnoaL_2; pfam12680 123214003338 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 123214003339 ATP cone domain; Region: ATP-cone; pfam03477 123214003340 Domain of unknown function (DUF1931); Region: DUF1931; pfam09123 123214003341 cell division ATPase MinD, archaeal; Region: minD_arch; TIGR01969 123214003342 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 123214003343 Walker A motif; other site 123214003344 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 123214003345 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 123214003346 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 123214003347 catalytic residue [active] 123214003348 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 123214003349 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 123214003350 trimerization site [polypeptide binding]; other site 123214003351 active site 123214003352 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 123214003353 ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. It belongs to the Adenosine Nucleotide Hydrolysis suoerfamily and predicted to bind to Adenosine nucleotide; Region: ThiI; cd01712 123214003354 Ligand Binding Site [chemical binding]; other site 123214003355 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 123214003356 CPxP motif; other site 123214003357 Domain of unknown function (DUF1858); Region: DUF1858; cl14817 123214003358 NifU-like domain; Region: NifU; cl00484 123214003359 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 123214003360 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 123214003361 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 123214003362 shikimate binding site; other site 123214003363 NAD(P) binding site [chemical binding]; other site 123214003364 Uncharacterized conserved protein [Function unknown]; Region: COG0432 123214003365 Endonuclease_V, a DNA repair enzyme that initiates repair of nitrosative deaminated purine bases; Region: Endonuclease_V; cd06559 123214003366 Active_site [active] 123214003367 gamma-glutamyl kinase; Provisional; Region: PRK05429 123214003368 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 123214003369 nucleotide binding site [chemical binding]; other site 123214003370 homotetrameric interface [polypeptide binding]; other site 123214003371 putative phosphate binding site [ion binding]; other site 123214003372 putative allosteric binding site; other site 123214003373 PUA domain; Region: PUA; pfam01472 123214003374 tRNA(1-methyladenosine) methyltransferase and related methyltransferases [Translation, ribosomal structure and biogenesis]; Region: GCD14; COG2519 123214003375 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 123214003376 S-adenosylmethionine binding site [chemical binding]; other site 123214003377 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 123214003378 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 123214003379 putative alpha-isopropylmalate/homocitrate synthase family transferase; Provisional; Region: PRK12344 123214003380 Desulfobacterium autotrophicum LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA3; cd07941 123214003381 active site 123214003382 catalytic residues [active] 123214003383 metal binding site [ion binding]; metal-binding site 123214003384 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 123214003385 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 123214003386 thiamine-monophosphate kinase; Region: thiL; TIGR01379 123214003387 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 123214003388 ATP binding site [chemical binding]; other site 123214003389 dimerization interface [polypeptide binding]; other site 123214003390 elongation factor P; Validated; Region: PRK00529 123214003391 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 123214003392 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 123214003393 RNA binding site [nucleotide binding]; other site 123214003394 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 123214003395 RNA binding site [nucleotide binding]; other site 123214003396 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 123214003397 carboxyltransferase (CT) interaction site; other site 123214003398 biotinylation site [posttranslational modification]; other site 123214003399 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214003400 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 123214003401 NAD(P) binding site [chemical binding]; other site 123214003402 active site 123214003403 homoserine kinase; Provisional; Region: PRK01212 123214003404 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 123214003405 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 123214003406 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; pfam02559 123214003407 DEAD-like helicases superfamily; Region: DEXDc; smart00487 123214003408 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 123214003409 ATP binding site [chemical binding]; other site 123214003410 putative Mg++ binding site [ion binding]; other site 123214003411 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 123214003412 nucleotide binding region [chemical binding]; other site 123214003413 ATP-binding site [chemical binding]; other site 123214003414 TRCF domain; Region: TRCF; pfam03461 123214003415 Predicted membrane protein [Function unknown]; Region: COG3431 123214003416 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...; Region: LT_GEWL; cd00254 123214003417 N-acetyl-D-glucosamine binding site [chemical binding]; other site 123214003418 catalytic residue [active] 123214003419 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 123214003420 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 123214003421 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 123214003422 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 123214003423 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 123214003424 Fe-S oxidoreductases [Energy production and conversion]; Region: COG0731 123214003425 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 123214003426 FeS/SAM binding site; other site 123214003427 CRISPR/Cas system-associated RAMP superfamily protein Cas6; Region: Cas6-I-III; cd09652 123214003428 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 123214003429 Flavoprotein; Region: Flavoprotein; pfam02441 123214003430 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 123214003431 Putative regulatory, ligand-binding protein related to C-terminal domains of K+ channels [Inorganic ion transport and metabolism]; Region: COG0490 123214003432 TrkA-C domain; Region: TrkA_C; pfam02080 123214003433 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 123214003434 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 123214003435 poxB regulator PoxA; Provisional; Region: PRK09350 123214003436 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 123214003437 motif 1; other site 123214003438 dimer interface [polypeptide binding]; other site 123214003439 active site 123214003440 motif 2; other site 123214003441 motif 3; other site 123214003442 Ion channel; Region: Ion_trans_2; pfam07885 123214003443 TrkA-N domain; Region: TrkA_N; pfam02254 123214003444 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 123214003445 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 123214003446 active site 123214003447 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 123214003448 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 123214003449 Protein of unknown function DUF86; Region: DUF86; cl01031 123214003450 Protein of unknown function DUF86; Region: DUF86; cl01031 123214003451 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 123214003452 nickel import ATP-binding protein NikD; Region: nickel_nikD; TIGR02770 123214003453 Walker A/P-loop; other site 123214003454 ATP binding site [chemical binding]; other site 123214003455 Q-loop/lid; other site 123214003456 ABC transporter signature motif; other site 123214003457 Walker B; other site 123214003458 D-loop; other site 123214003459 H-loop/switch region; other site 123214003460 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 123214003461 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 123214003462 dimerization domain [polypeptide binding]; other site 123214003463 dimer interface [polypeptide binding]; other site 123214003464 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 123214003465 catalytic residues [active] 123214003466 Ribose/Galactose Isomerase; Region: LacAB_rpiB; pfam02502 123214003467 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 123214003468 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 123214003469 dimer interface [polypeptide binding]; other site 123214003470 active site 123214003471 glycine-pyridoxal phosphate binding site [chemical binding]; other site 123214003472 folate binding site [chemical binding]; other site 123214003473 NAD kinase [Coenzyme metabolism]; Region: nadF; COG0061 123214003474 ATP-NAD kinase; Region: NAD_kinase; pfam01513 123214003475 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 123214003476 homotrimer interaction site [polypeptide binding]; other site 123214003477 zinc binding site [ion binding]; other site 123214003478 CDP-binding sites; other site 123214003479 Domain of unknown function (DUF1858); Region: DUF1858; cl14817 123214003480 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 123214003481 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 123214003482 ssDNA binding site; other site 123214003483 generic binding surface II; other site 123214003484 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 123214003485 ATP binding site [chemical binding]; other site 123214003486 putative Mg++ binding site [ion binding]; other site 123214003487 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 123214003488 nucleotide binding region [chemical binding]; other site 123214003489 ATP-binding site [chemical binding]; other site 123214003490 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 123214003491 PAS fold; Region: PAS_4; pfam08448 123214003492 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 123214003493 putative active site [active] 123214003494 heme pocket [chemical binding]; other site 123214003495 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214003496 metal binding site [ion binding]; metal-binding site 123214003497 active site 123214003498 I-site; other site 123214003499 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 123214003500 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 123214003501 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 123214003502 putative active site [active] 123214003503 heme pocket [chemical binding]; other site 123214003504 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 123214003505 putative active site [active] 123214003506 heme pocket [chemical binding]; other site 123214003507 PAS domain S-box; Region: sensory_box; TIGR00229 123214003508 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 123214003509 putative active site [active] 123214003510 heme pocket [chemical binding]; other site 123214003511 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 123214003512 PAS domain; Region: PAS_9; pfam13426 123214003513 putative active site [active] 123214003514 heme pocket [chemical binding]; other site 123214003515 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 123214003516 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214003517 metal binding site [ion binding]; metal-binding site 123214003518 active site 123214003519 I-site; other site 123214003520 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 123214003521 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 123214003522 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 123214003523 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 123214003524 Protein of unknown function DUF58; Region: DUF58; pfam01882 123214003525 MoxR-like ATPases [General function prediction only]; Region: COG0714 123214003526 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 123214003527 Walker A motif; other site 123214003528 ATP binding site [chemical binding]; other site 123214003529 Walker B motif; other site 123214003530 arginine finger; other site 123214003531 Pantoate-beta-alanine ligase; Region: PanC; cd00560 123214003532 pantoate--beta-alanine ligase; Region: panC; TIGR00018 123214003533 active site 123214003534 ATP-binding site [chemical binding]; other site 123214003535 pantoate-binding site; other site 123214003536 HXXH motif; other site 123214003537 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 123214003538 PAS domain; Region: PAS_9; pfam13426 123214003539 putative active site [active] 123214003540 heme pocket [chemical binding]; other site 123214003541 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214003542 metal binding site [ion binding]; metal-binding site 123214003543 active site 123214003544 I-site; other site 123214003545 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 123214003546 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 123214003547 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 123214003548 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214003549 homodimer interface [polypeptide binding]; other site 123214003550 catalytic residue [active] 123214003551 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 123214003552 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 123214003553 dimer interface [polypeptide binding]; other site 123214003554 putative functional site; other site 123214003555 putative MPT binding site; other site 123214003556 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 123214003557 Carbamoylphosphate synthase large subunit (split gene in MJ) [Amino acid transport and metabolism / Nucleotide transport and metabolism]; Region: CarB; COG0458 123214003558 ATP-grasp domain; Region: ATP-grasp_4; cl17255 123214003559 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 123214003560 IMP binding site; other site 123214003561 dimer interface [polypeptide binding]; other site 123214003562 interdomain contacts; other site 123214003563 partial ornithine binding site; other site 123214003564 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 123214003565 thiamine phosphate binding site [chemical binding]; other site 123214003566 active site 123214003567 pyrophosphate binding site [ion binding]; other site 123214003568 Trm112p-like protein; Region: Trm112p; cl01066 123214003569 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 123214003570 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_4; cd08500 123214003571 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 123214003572 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214003573 metal binding site [ion binding]; metal-binding site 123214003574 active site 123214003575 I-site; other site 123214003576 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 123214003577 alkylhydroperoxidase AhpD family core domain; Region: ahpD_dom; TIGR00778 123214003578 malate dehydrogenase; Reviewed; Region: PRK06223 123214003579 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 123214003580 NAD(P) binding site [chemical binding]; other site 123214003581 dimer interface [polypeptide binding]; other site 123214003582 tetramer (dimer of dimers) interface [polypeptide binding]; other site 123214003583 substrate binding site [chemical binding]; other site 123214003584 fumarate hydratase; Provisional; Region: PRK06246 123214003585 Fumarase C-terminus; Region: Fumerase_C; cl00795 123214003586 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 123214003587 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 123214003588 CoA-ligase; Region: Ligase_CoA; pfam00549 123214003589 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 123214003590 CoA binding domain; Region: CoA_binding; smart00881 123214003591 CoA-ligase; Region: Ligase_CoA; pfam00549 123214003592 2-oxoacid:acceptor oxidoreductase, alpha subunit; Region: OAFO_sf; TIGR03710 123214003593 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 123214003594 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 123214003595 dimer interface [polypeptide binding]; other site 123214003596 PYR/PP interface [polypeptide binding]; other site 123214003597 TPP binding site [chemical binding]; other site 123214003598 substrate binding site [chemical binding]; other site 123214003599 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Reviewed; Region: PRK11867 123214003600 Thiamine pyrophosphate (TPP family), 2-oxoglutarate ferredoxin oxidoreductase (OGFOR) subfamily, TPP-binding module; OGFOR catalyzes the oxidative decarboxylation of 2-oxo-acids, with ferredoxin acting as an electron acceptor. In the TCA cycle, OGFOR...; Region: TPP_OGFOR; cd03375 123214003601 TPP-binding site [chemical binding]; other site 123214003602 Pyruvate ferredoxin oxidoreductase beta subunit C terminal; Region: PFO_beta_C; pfam12367 123214003603 Domain of unknown function (DUF4323); Region: DUF4323; pfam14211 123214003604 Domain of unknown function (DUF4324); Region: DUF4324; pfam14212 123214003605 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 123214003606 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Thermotoga marina NorM; Region: MATE_NorM_like; cd13137 123214003607 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 123214003608 heavy metal translocating P-type ATPase; Region: ATPase-IB_hvy; TIGR01525 123214003609 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 123214003610 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 123214003611 motif II; other site 123214003612 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 123214003613 active site residue [active] 123214003614 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 123214003615 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 123214003616 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 123214003617 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 123214003618 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 123214003619 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 123214003620 Type II secretory pathway, component PulJ [Intracellular trafficking and secretion]; Region: PulJ; COG4795 123214003621 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 123214003622 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 123214003623 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 123214003624 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 123214003625 active site 123214003626 phosphorylation site [posttranslational modification] 123214003627 intermolecular recognition site; other site 123214003628 dimerization interface [polypeptide binding]; other site 123214003629 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 123214003630 DNA binding site [nucleotide binding] 123214003631 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 123214003632 substrate binding site; other site 123214003633 dimer interface; other site 123214003634 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 123214003635 catalytic core [active] 123214003636 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 123214003637 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 123214003638 Coenzyme A binding pocket [chemical binding]; other site 123214003639 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 123214003640 Found in ATP-dependent protease La (LON); Region: LON; smart00464 123214003641 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 123214003642 Walker A motif; other site 123214003643 ATP binding site [chemical binding]; other site 123214003644 Walker B motif; other site 123214003645 arginine finger; other site 123214003646 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 123214003647 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 123214003648 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 123214003649 putative dimer interface [polypeptide binding]; other site 123214003650 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 123214003651 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 123214003652 S-adenosyl-l-methionine hydroxide adenosyltransferase; Region: SAM_adeno_trans; pfam01887 123214003653 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 123214003654 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 123214003655 acyl-activating enzyme (AAE) consensus motif; other site 123214003656 putative AMP binding site [chemical binding]; other site 123214003657 putative active site [active] 123214003658 putative CoA binding site [chemical binding]; other site 123214003659 Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcpP; COG0236 123214003660 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 123214003661 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 123214003662 putative acyl-acceptor binding pocket; other site 123214003663 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 123214003664 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 123214003665 catalytic triad [active] 123214003666 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 123214003667 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 123214003668 elongation factor Tu; Reviewed; Region: PRK00049 123214003669 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 123214003670 G1 box; other site 123214003671 GEF interaction site [polypeptide binding]; other site 123214003672 GTP/Mg2+ binding site [chemical binding]; other site 123214003673 Switch I region; other site 123214003674 G2 box; other site 123214003675 G3 box; other site 123214003676 Switch II region; other site 123214003677 G4 box; other site 123214003678 G5 box; other site 123214003679 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 123214003680 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 123214003681 Antibiotic Binding Site [chemical binding]; other site 123214003682 50S ribosomal protein L33; Validated; Region: rpmG; PRK00504 123214003683 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; pfam00584 123214003684 N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; Region: NGN; cl02766 123214003685 NGN-insert domain found between N-terminal domain (D1) and C-terminal KOW domain (DIII) repeats of some N-Utilization Substance G (NusG) N-terminal (NGN); Region: NGN-insert_like; cd09910 123214003686 transcriptional activator RfaH; Region: RfaH; TIGR01955 123214003687 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 123214003688 putative homodimer interface [polypeptide binding]; other site 123214003689 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 123214003690 heterodimer interface [polypeptide binding]; other site 123214003691 homodimer interface [polypeptide binding]; other site 123214003692 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 123214003693 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 123214003694 23S rRNA interface [nucleotide binding]; other site 123214003695 L7/L12 interface [polypeptide binding]; other site 123214003696 putative thiostrepton binding site; other site 123214003697 L25 interface [polypeptide binding]; other site 123214003698 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 123214003699 mRNA/rRNA interface [nucleotide binding]; other site 123214003700 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 123214003701 23S rRNA interface [nucleotide binding]; other site 123214003702 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 123214003703 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 123214003704 core dimer interface [polypeptide binding]; other site 123214003705 peripheral dimer interface [polypeptide binding]; other site 123214003706 L10 interface [polypeptide binding]; other site 123214003707 L11 interface [polypeptide binding]; other site 123214003708 putative EF-Tu interaction site [polypeptide binding]; other site 123214003709 putative EF-G interaction site [polypeptide binding]; other site 123214003710 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 123214003711 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; cl17585 123214003712 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 123214003713 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 123214003714 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 123214003715 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; cl17585 123214003716 RPB1 interaction site [polypeptide binding]; other site 123214003717 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 123214003718 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 123214003719 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 123214003720 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 123214003721 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 123214003722 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 123214003723 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 123214003724 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 123214003725 DNA binding site [nucleotide binding] 123214003726 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 123214003727 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 123214003728 S17 interaction site [polypeptide binding]; other site 123214003729 S8 interaction site; other site 123214003730 16S rRNA interaction site [nucleotide binding]; other site 123214003731 streptomycin interaction site [chemical binding]; other site 123214003732 23S rRNA interaction site [nucleotide binding]; other site 123214003733 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 123214003734 30S ribosomal protein S7; Validated; Region: PRK05302 123214003735 elongation factor G; Reviewed; Region: PRK00007 123214003736 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 123214003737 G1 box; other site 123214003738 putative GEF interaction site [polypeptide binding]; other site 123214003739 GTP/Mg2+ binding site [chemical binding]; other site 123214003740 Switch I region; other site 123214003741 G2 box; other site 123214003742 G3 box; other site 123214003743 Switch II region; other site 123214003744 G4 box; other site 123214003745 G5 box; other site 123214003746 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 123214003747 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 123214003748 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 123214003749 elongation factor Tu; Reviewed; Region: PRK00049 123214003750 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 123214003751 G1 box; other site 123214003752 GEF interaction site [polypeptide binding]; other site 123214003753 GTP/Mg2+ binding site [chemical binding]; other site 123214003754 Switch I region; other site 123214003755 G2 box; other site 123214003756 G3 box; other site 123214003757 Switch II region; other site 123214003758 G4 box; other site 123214003759 G5 box; other site 123214003760 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 123214003761 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 123214003762 Antibiotic Binding Site [chemical binding]; other site 123214003763 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 123214003764 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 123214003765 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 123214003766 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 123214003767 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 123214003768 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 123214003769 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 123214003770 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 123214003771 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 123214003772 putative translocon binding site; other site 123214003773 protein-rRNA interface [nucleotide binding]; other site 123214003774 ribosomal protein S3, bacterial type; Region: rpsC_bact; TIGR01009 123214003775 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 123214003776 G-X-X-G motif; other site 123214003777 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 123214003778 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 123214003779 23S rRNA interface [nucleotide binding]; other site 123214003780 5S rRNA interface [nucleotide binding]; other site 123214003781 putative antibiotic binding site [chemical binding]; other site 123214003782 L25 interface [polypeptide binding]; other site 123214003783 L27 interface [polypeptide binding]; other site 123214003784 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 123214003785 L23 interface [polypeptide binding]; other site 123214003786 signal recognition particle (SRP54) interaction site; other site 123214003787 trigger factor interaction site; other site 123214003788 23S rRNA interface [nucleotide binding]; other site 123214003789 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 123214003790 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 123214003791 KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); Region: KOW; cl00354 123214003792 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 123214003793 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 123214003794 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 123214003795 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 123214003796 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08061 123214003797 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 123214003798 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 123214003799 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 123214003800 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 123214003801 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 123214003802 23S rRNA interface [nucleotide binding]; other site 123214003803 5S rRNA interface [nucleotide binding]; other site 123214003804 L27 interface [polypeptide binding]; other site 123214003805 L5 interface [polypeptide binding]; other site 123214003806 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 123214003807 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 123214003808 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 123214003809 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 123214003810 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 123214003811 23S rRNA binding site [nucleotide binding]; other site 123214003812 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 123214003813 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 123214003814 SecY translocase; Region: SecY; pfam00344 123214003815 adenylate kinase; Reviewed; Region: adk; PRK00279 123214003816 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 123214003817 AMP-binding site [chemical binding]; other site 123214003818 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 123214003819 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 123214003820 active site 123214003821 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 123214003822 rRNA binding site [nucleotide binding]; other site 123214003823 predicted 30S ribosome binding site; other site 123214003824 50S ribosomal protein L36; Reviewed; Region: rpmJ; PRK00465 123214003825 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 123214003826 30S ribosomal protein S13; Region: bact_S13; TIGR03631 123214003827 30S ribosomal protein S11; Validated; Region: PRK05309 123214003828 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 123214003829 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 123214003830 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 123214003831 RNA binding surface [nucleotide binding]; other site 123214003832 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 123214003833 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 123214003834 alphaNTD homodimer interface [polypeptide binding]; other site 123214003835 alphaNTD - beta interaction site [polypeptide binding]; other site 123214003836 alphaNTD - beta' interaction site [polypeptide binding]; other site 123214003837 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 123214003838 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 123214003839 YGGT family; Region: YGGT; pfam02325 123214003840 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 123214003841 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 123214003842 homodimer interface [polypeptide binding]; other site 123214003843 substrate-cofactor binding pocket; other site 123214003844 catalytic residue [active] 123214003845 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 123214003846 Aminotransferase class I and II; Region: Aminotran_1_2; pfam00155 123214003847 substrate-cofactor binding pocket; other site 123214003848 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214003849 catalytic residue [active] 123214003850 2-hydroxyacid dehydrogenase; Provisional; Region: PRK08410 123214003851 Putative D-isomer specific 2-hydroxyacid dehydrogenases; Region: 2-Hacid_dh_4; cd12162 123214003852 putative ligand binding site [chemical binding]; other site 123214003853 putative NAD binding site [chemical binding]; other site 123214003854 catalytic site [active] 123214003855 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 123214003856 active site 123214003857 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 123214003858 dimerization interface [polypeptide binding]; other site 123214003859 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 123214003860 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214003861 metal binding site [ion binding]; metal-binding site 123214003862 active site 123214003863 I-site; other site 123214003864 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 123214003865 ABC transporter periplasmic binding protein, urea carboxylase region; Region: ABC_peri_uca; TIGR03427 123214003866 NMT1/THI5 like; Region: NMT1; pfam09084 123214003867 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cl00528 123214003868 HTH domain; Region: HTH_11; cl17392 123214003869 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 123214003870 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 123214003871 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 123214003872 Anthranilate phosphoribosyltransferase [Amino acid transport and metabolism]; Region: TrpD; COG0547 123214003873 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 123214003874 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 123214003875 GTP-binding protein LepA; Provisional; Region: PRK05433 123214003876 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 123214003877 G1 box; other site 123214003878 putative GEF interaction site [polypeptide binding]; other site 123214003879 GTP/Mg2+ binding site [chemical binding]; other site 123214003880 Switch I region; other site 123214003881 G2 box; other site 123214003882 G3 box; other site 123214003883 Switch II region; other site 123214003884 G4 box; other site 123214003885 G5 box; other site 123214003886 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 123214003887 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 123214003888 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 123214003889 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 123214003890 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 123214003891 catalytic residues [active] 123214003892 Cupin domain; Region: Cupin_2; pfam07883 123214003893 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl17548 123214003894 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 123214003895 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 123214003896 catalytic residues [active] 123214003897 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 123214003898 binding surface 123214003899 TPR motif; other site 123214003900 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 123214003901 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily; Region: Alpha_ANH_like_II; cd01993 123214003902 Ligand Binding Site [chemical binding]; other site 123214003903 TIGR00269 family protein; Region: TIGR00269 123214003904 Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ThiS; COG2104 123214003905 charged pocket; other site 123214003906 hydrophobic patch; other site 123214003907 N-formylglutamate amidohydrolase; Region: FGase; pfam05013 123214003908 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 123214003909 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 123214003910 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 123214003911 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 123214003912 ATP-grasp domain; Region: ATP-grasp_4; cl17255 123214003913 ADP-ribose pyrophosphatase [Nucleotide transport and metabolism]; Region: COG1051 123214003914 nudix motif; other site 123214003915 Cytochrome c; Region: Cytochrom_C; cl11414 123214003916 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 123214003917 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 123214003918 ligand binding site [chemical binding]; other site 123214003919 flexible hinge region; other site 123214003920 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 123214003921 non-specific DNA interactions [nucleotide binding]; other site 123214003922 DNA binding site [nucleotide binding] 123214003923 sequence specific DNA binding site [nucleotide binding]; other site 123214003924 putative cAMP binding site [chemical binding]; other site 123214003925 Cytochrome c; Region: Cytochrom_C; cl11414 123214003926 nitrous-oxide reductase, Sec-dependent; Region: nitrous_NosZ_Gp; TIGR04246 123214003927 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 123214003928 NosL; Region: NosL; cl01769 123214003929 nitrous oxide reductase family maturation protein NosD; Region: NosD_copper_fam; TIGR04247 123214003930 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 123214003931 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 123214003932 Walker A/P-loop; other site 123214003933 ATP binding site [chemical binding]; other site 123214003934 Q-loop/lid; other site 123214003935 ABC transporter signature motif; other site 123214003936 Walker B; other site 123214003937 D-loop; other site 123214003938 H-loop/switch region; other site 123214003939 ABC-2 family transporter protein; Region: ABC2_membrane_2; cl17866 123214003940 Cytochrome c; Region: Cytochrom_C; cl11414 123214003941 Protein of unknown function (DUF461); Region: DUF461; pfam04314 123214003942 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 123214003943 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 123214003944 Cu(I) binding site [ion binding]; other site 123214003945 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 123214003946 N-terminal plug; other site 123214003947 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 123214003948 ligand-binding site [chemical binding]; other site 123214003949 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 123214003950 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214003951 metal binding site [ion binding]; metal-binding site 123214003952 active site 123214003953 I-site; other site 123214003954 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; pfam02606 123214003955 tetraacyldisaccharide 4'-kinase; Region: lpxK; TIGR00682 123214003956 ScpA/B protein; Region: ScpA_ScpB; cl00598 123214003957 ScpA/B protein; Region: ScpA_ScpB; cl00598 123214003958 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 123214003959 CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This...; Region: Voltage_gated_ClC; cd00400 123214003960 Cl- selectivity filter; other site 123214003961 Cl- binding residues [ion binding]; other site 123214003962 pore gating glutamate residue; other site 123214003963 dimer interface [polypeptide binding]; other site 123214003964 FOG: CBS domain [General function prediction only]; Region: COG0517 123214003965 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; cd02205 123214003966 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 123214003967 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 123214003968 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 123214003969 TrkA-N domain; Region: TrkA_N; pfam02254 123214003970 TrkA-C domain; Region: TrkA_C; pfam02080 123214003971 TrkA-N domain; Region: TrkA_N; pfam02254 123214003972 TrkA-C domain; Region: TrkA_C; pfam02080 123214003973 Radical SAM superfamily; Region: Radical_SAM; pfam04055 123214003974 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 123214003975 FeS/SAM binding site; other site 123214003976 FMN-binding domain; Region: FMN_bind; pfam04205 123214003977 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 123214003978 ApbE family; Region: ApbE; pfam02424 123214003979 Outer membrane protein family (DUF1597); Region: DUF1597; pfam07642 123214003980 prephenate dehydrogenase; Validated; Region: PRK08507 123214003981 Prephenate dehydrogenase; Region: PDH; pfam02153 123214003982 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 123214003983 Ligand Binding Site [chemical binding]; other site 123214003984 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 123214003985 Ligand Binding Site [chemical binding]; other site 123214003986 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 123214003987 Cation efflux family; Region: Cation_efflux; cl00316 123214003988 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 123214003989 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 123214003990 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 123214003991 catalytic site [active] 123214003992 subunit interface [polypeptide binding]; other site 123214003993 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK14611 123214003994 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 123214003995 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 123214003996 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 123214003997 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 123214003998 active site 123214003999 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 123214004000 ribosomal protein L25, Ctc-form; Region: ctc_TL5; TIGR00731 123214004001 5S rRNA interface [nucleotide binding]; other site 123214004002 CTC domain interface [polypeptide binding]; other site 123214004003 L16 interface [polypeptide binding]; other site 123214004004 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 123214004005 putative active site [active] 123214004006 catalytic residue [active] 123214004007 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 123214004008 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 123214004009 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 123214004010 dimer interface [polypeptide binding]; other site 123214004011 ssDNA binding site [nucleotide binding]; other site 123214004012 tetramer (dimer of dimers) interface [polypeptide binding]; other site 123214004013 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 123214004014 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 123214004015 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 123214004016 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 123214004017 replicative DNA helicase; Region: DnaB; TIGR00665 123214004018 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 123214004019 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 123214004020 Walker A motif; other site 123214004021 ATP binding site [chemical binding]; other site 123214004022 Walker B motif; other site 123214004023 DNA binding loops [nucleotide binding] 123214004024 Permease; Region: Permease; cl00510 123214004025 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 123214004026 6-phosphofructokinase; Provisional; Region: PRK03202 123214004027 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 123214004028 active site 123214004029 ADP/pyrophosphate binding site [chemical binding]; other site 123214004030 dimerization interface [polypeptide binding]; other site 123214004031 allosteric effector site; other site 123214004032 fructose-1,6-bisphosphate binding site; other site 123214004033 SpoVG; Region: SpoVG; cl00915 123214004034 Protein of unknown function, DUF481; Region: DUF481; pfam04338 123214004035 4Fe-4S single cluster domain; Region: Fer4_15; pfam13459 123214004036 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 123214004037 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 123214004038 putative active site [active] 123214004039 catalytic triad [active] 123214004040 putative dimer interface [polypeptide binding]; other site 123214004041 Protein of unknown function DUF45; Region: DUF45; pfam01863 123214004042 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 123214004043 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 123214004044 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 123214004045 ATP binding site [chemical binding]; other site 123214004046 putative Mg++ binding site [ion binding]; other site 123214004047 AAA domain; Region: AAA_13; pfam13166 123214004048 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 123214004049 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 123214004050 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 123214004051 Protein of unknown function (DUF3644); Region: DUF3644; pfam12358 123214004052 TIGR02391 family protein; Region: hypoth_ymh 123214004053 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 123214004054 HsdM N-terminal domain; Region: HsdM_N; pfam12161 123214004055 Methyltransferase domain; Region: Methyltransf_26; pfam13659 123214004056 TniQ; Region: TniQ; pfam06527 123214004057 FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1; Region: FYVE; cl17764 123214004058 Bacterial TniB protein; Region: TniB; pfam05621 123214004059 AAA domain; Region: AAA_22; pfam13401 123214004060 Helix-turn-helix domain; Region: HTH_28; pfam13518 123214004061 Homeodomain-like domain; Region: HTH_32; pfam13565 123214004062 Integrase core domain; Region: rve; pfam00665 123214004063 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 123214004064 TnsA endonuclease N terminal; Region: Tn7_Tnp_TnsA_N; pfam08722 123214004065 Archaeal ATPase; Region: Arch_ATPase; pfam01637 123214004066 AAA domain; Region: AAA_14; pfam13173 123214004067 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 123214004068 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 123214004069 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 123214004070 FeS/SAM binding site; other site 123214004071 trigger factor; Provisional; Region: tig; PRK01490 123214004072 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 123214004073 Clp protease; Region: CLP_protease; pfam00574 123214004074 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 123214004075 oligomer interface [polypeptide binding]; other site 123214004076 active site residues [active] 123214004077 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 123214004078 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 123214004079 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 123214004080 Walker A motif; other site 123214004081 ATP binding site [chemical binding]; other site 123214004082 Walker B motif; other site 123214004083 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 123214004084 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 123214004085 Elongation factor Tu GTP binding domain; Region: GTP_EFTU; pfam00009 123214004086 G1 box; other site 123214004087 GTP/Mg2+ binding site [chemical binding]; other site 123214004088 Switch I region; other site 123214004089 G2 box; other site 123214004090 G3 box; other site 123214004091 Switch II region; other site 123214004092 G4 box; other site 123214004093 G5 box; other site 123214004094 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 123214004095 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 123214004096 substrate binding site [chemical binding]; other site 123214004097 active site 123214004098 catalytic residues [active] 123214004099 heterodimer interface [polypeptide binding]; other site 123214004100 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13141 123214004101 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 123214004102 putative active site [active] 123214004103 oxyanion strand; other site 123214004104 catalytic triad [active] 123214004105 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 123214004106 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 123214004107 FeS/SAM binding site; other site 123214004108 HemN C-terminal domain; Region: HemN_C; pfam06969 123214004109 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 123214004110 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 123214004111 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 123214004112 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 123214004113 CRISPR/Cas system-associated RAMP superfamily protein Cas6; Region: Cas6-I-III; cd09652 123214004114 CRISPR/Cas system-associated protein Cas8a1; Region: Cas8a1_I-A; cd09665 123214004115 CRISPR/Cas system-associated RAMP superfamily protein Cas7; Region: Cas7_I-C; cd09687 123214004116 CRISPR-associated autoregulator DevR family; Region: cas_MJ0381; TIGR01875 123214004117 CRISPR-associated protein Cas5, subtype I-B/TNEAP; Region: cas_Cas5t; TIGR01895 123214004118 CRISPR/Cas system-associated RAMP superfamily protein Cas5; Region: Cas5_I-B; cd09658 123214004119 CRISPR/Cas system-associated protein Cas3'' Region: Cas3''_I; cd09641 123214004120 CRISPR-associated helicase Cas3 [Defense mechanisms]; Region: COG1203 123214004121 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; cl17251 123214004122 Predicted nucleotidyltransferase; Region: Nuc-transf; pfam10127 123214004123 Domain of unknown function DUF83; Region: Cas_Cas4; pfam01930 123214004124 GTPase subunit of restriction endonuclease [Defense mechanisms]; Region: McrB; COG1401 123214004125 Domain of unknown function (DUF2357); Region: DUF2357; pfam09823 123214004126 Protein of unknown function (DUF524); Region: DUF524; pfam04411 123214004127 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-B; cd09722 123214004128 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cd09725 123214004129 Methyltransferase domain; Region: Methyltransf_23; pfam13489 123214004130 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 123214004131 S-adenosylmethionine binding site [chemical binding]; other site 123214004132 hypothetical protein; Provisional; Region: PRK11820 123214004133 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 123214004134 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 123214004135 Ferritin-CCC1, N-terminal ferritin-like diiron-binding domain; Region: Ferritin_CCC1_N; cd01044 123214004136 diiron binding motif [ion binding]; other site 123214004137 CCC1-related domain of ferritin; Region: Ferritin_CCC1_C; cd02431 123214004138 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]; Region: KdtA; COG1519 123214004139 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 123214004140 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG0390 123214004141 Lipid A disaccharide synthetase [Cell envelope biogenesis, outer membrane]; Region: LpxB; COG0763 123214004142 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 123214004143 biotin synthase; Region: bioB; TIGR00433 123214004144 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 123214004145 FeS/SAM binding site; other site 123214004146 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 123214004147 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214004148 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 123214004149 NAD(P) binding site [chemical binding]; other site 123214004150 active site 123214004151 Tetratricopeptide repeat; Region: TPR_15; pfam13429 123214004152 TM1410 hypothetical-related protein; Region: DUF297; pfam03537 123214004153 C-terminal Putative NodB-like catalytic domain of PelA-like uncharacterized hypothetical proteins found in bacteria; Region: CE4_PelA_like_C; cd10922 123214004154 putative active site [active] 123214004155 Predicted membrane protein [Function unknown]; Region: COG4267 123214004156 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_3; cd03813 123214004157 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 123214004158 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 123214004159 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 123214004160 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 123214004161 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 123214004162 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) N-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs; Region: NTP-PPase_MazG_Nterm; cd11528 123214004163 homodimer interface [polypeptide binding]; other site 123214004164 metal binding site [ion binding]; metal-binding site 123214004165 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs' Region: NTP-PPase_MazG_Cterm; cd11529 123214004166 homodimer interface [polypeptide binding]; other site 123214004167 active site 123214004168 putative chemical substrate binding site [chemical binding]; other site 123214004169 metal binding site [ion binding]; metal-binding site 123214004170 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 123214004171 active site 123214004172 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 123214004173 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 123214004174 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 123214004175 putative NAD(P) binding site [chemical binding]; other site 123214004176 active site 123214004177 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 123214004178 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 123214004179 Walker A motif; other site 123214004180 ATP binding site [chemical binding]; other site 123214004181 Walker B motif; other site 123214004182 arginine finger; other site 123214004183 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3034 123214004184 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 123214004185 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cd00596 123214004186 active site 123214004187 Zn binding site [ion binding]; other site 123214004188 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 123214004189 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 123214004190 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 123214004191 IHF dimer interface [polypeptide binding]; other site 123214004192 IHF - DNA interface [nucleotide binding]; other site 123214004193 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 123214004194 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 123214004195 trimer interface [polypeptide binding]; other site 123214004196 putative metal binding site [ion binding]; other site 123214004197 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 123214004198 active site 123214004199 dihydroorotate dehydrogenase electron transfer subunit; Reviewed; Region: PRK00054 123214004200 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to...; Region: DHOD_e_trans; cd06218 123214004201 FAD binding pocket [chemical binding]; other site 123214004202 FAD binding motif [chemical binding]; other site 123214004203 phosphate binding motif [ion binding]; other site 123214004204 beta-alpha-beta structure motif; other site 123214004205 NAD binding pocket [chemical binding]; other site 123214004206 Iron coordination center [ion binding]; other site 123214004207 L-aspartate oxidase; Provisional; Region: PRK06175 123214004208 succinate dehydrogenase or fumarate reductase, flavoprotein subunitGram-negative/mitochondrial subgroup; Region: sdhA_frdA_Gneg; TIGR01812 123214004209 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 123214004210 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 123214004211 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 123214004212 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 123214004213 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 123214004214 diaminopimelate decarboxylase; Region: lysA; TIGR01048 123214004215 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 123214004216 active site 123214004217 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 123214004218 substrate binding site [chemical binding]; other site 123214004219 catalytic residues [active] 123214004220 dimer interface [polypeptide binding]; other site 123214004221 septum site-determining protein MinC; Region: minC; TIGR01222 123214004222 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 123214004223 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 123214004224 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal...; Region: MinD; cd02036 123214004225 Switch I; other site 123214004226 Switch II; other site 123214004227 Septum formation topological specificity factor MinE; Region: MinE; cl00538 123214004228 ATP phosphoribosyltransferase catalytic subunit; Reviewed; Region: hisG; PRK01686 123214004229 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 123214004230 N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]; Region: GlmU; COG1207 123214004231 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 123214004232 Substrate binding site; other site 123214004233 Mg++ binding site; other site 123214004234 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 123214004235 active site 123214004236 substrate binding site [chemical binding]; other site 123214004237 CoA binding site [chemical binding]; other site 123214004238 SurA N-terminal domain; Region: SurA_N; pfam09312 123214004239 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 123214004240 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 123214004241 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 123214004242 7-alpha-hydroxysteroid dehydrogenase; Provisional; Region: PRK08416 123214004243 1-cyclohexenylcarbonyl_coenzyme A_reductase (ChcA)_like, classical (c) SDRs; Region: ChcA_like_SDR_c; cd05359 123214004244 putative NAD(P) binding site [chemical binding]; other site 123214004245 active site 123214004246 RNA polymerase sigma factor, FliA/WhiG family; Region: FliA_WhiG; TIGR02479 123214004247 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 123214004248 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 123214004249 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 123214004250 DNA binding residues [nucleotide binding] 123214004251 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 123214004252 FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by...; Region: FleN-like; cd02038 123214004253 P-loop; other site 123214004254 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 123214004255 flagellar biosynthetic protein FlhF; Region: FlhF; TIGR03499 123214004256 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 123214004257 Phosphopantetheinyl transferase (holo-ACP synthase) [Lipid metabolism]; Region: AcpS; COG0736 123214004258 shikimate kinase; Reviewed; Region: aroK; PRK00131 123214004259 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 123214004260 ADP binding site [chemical binding]; other site 123214004261 magnesium binding site [ion binding]; other site 123214004262 putative shikimate binding site; other site 123214004263 Uncharacterized ACR, YggU family COG1872; Region: DUF167; pfam02594 123214004264 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 123214004265 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 123214004266 Protein of unknown function (DUF2905); Region: DUF2905; pfam11146 123214004267 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 123214004268 thiamine phosphate binding site [chemical binding]; other site 123214004269 active site 123214004270 pyrophosphate binding site [ion binding]; other site 123214004271 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 123214004272 NADH dehydrogenase subunit B; Validated; Region: PRK06411 123214004273 NADH:ubiquinone oxidoreductase 27 kD subunit [Energy production and conversion]; Region: NuoC; COG0852 123214004274 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl16917 123214004275 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 123214004276 NADH dehydrogenase subunit D; Validated; Region: PRK06075 123214004277 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 123214004278 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 123214004279 Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Energy production and conversion]; Region: NuoI; COG1143 123214004280 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 123214004281 NADH:ubiquinone oxidoreductase subunit 6 (chain J) [Energy production and conversion]; Region: NuoJ; COG0839 123214004282 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 123214004283 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 123214004284 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 123214004285 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 123214004286 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 123214004287 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 123214004288 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 123214004289 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 123214004290 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 123214004291 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 123214004292 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 123214004293 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 123214004294 catalytic site [active] 123214004295 G-X2-G-X-G-K; other site 123214004296 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 123214004297 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 123214004298 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 123214004299 dimer interface [polypeptide binding]; other site 123214004300 phosphorylation site [posttranslational modification] 123214004301 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 123214004302 ATP binding site [chemical binding]; other site 123214004303 Mg2+ binding site [ion binding]; other site 123214004304 G-X-G motif; other site 123214004305 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 123214004306 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 123214004307 active site 123214004308 phosphorylation site [posttranslational modification] 123214004309 intermolecular recognition site; other site 123214004310 dimerization interface [polypeptide binding]; other site 123214004311 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 123214004312 Walker A motif; other site 123214004313 ATP binding site [chemical binding]; other site 123214004314 Walker B motif; other site 123214004315 arginine finger; other site 123214004316 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 123214004317 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 123214004318 LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop; Region: LysRS_N; cd04322 123214004319 dimer interface [polypeptide binding]; other site 123214004320 putative anticodon binding site; other site 123214004321 Lys_tRNA synthetase (LysRS) class II core domain. Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three...; Region: LysRS_core; cd00775 123214004322 motif 1; other site 123214004323 active site 123214004324 motif 2; other site 123214004325 motif 3; other site 123214004326 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; cl00614 123214004327 bacterial Hfq-like; Region: Hfq; cd01716 123214004328 hexamer interface [polypeptide binding]; other site 123214004329 Sm1 motif; other site 123214004330 RNA binding site [nucleotide binding]; other site 123214004331 Sm2 motif; other site 123214004332 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 123214004333 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 123214004334 Predicted RNA-binding protein (contains KH domain) [General function prediction only]; Region: COG1837 123214004335 KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional...; Region: KH-II; cl00098 123214004336 Ribosomal protein S16 [Translation, ribosomal structure and biogenesis]; Region: RpsP; COG0228 123214004337 signal recognition particle protein; Provisional; Region: PRK10867 123214004338 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 123214004339 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 123214004340 Signal peptide binding domain; Region: SRP_SPB; pfam02978 123214004341 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 123214004342 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 123214004343 Surface antigen; Region: Bac_surface_Ag; pfam01103 123214004344 SapC; Region: SapC; pfam07277 123214004345 haemagglutination activity domain; Region: Haemagg_act; smart00912 123214004346 Large exoproteins involved in heme utilization or adhesion [Intracellular trafficking and secretion]; Region: FhaB; COG3210 123214004347 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 123214004348 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 123214004349 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 123214004350 spermidine synthase; Provisional; Region: PRK00811 123214004351 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 123214004352 S-adenosylmethionine binding site [chemical binding]; other site 123214004353 Predicted methyltransferases [General function prediction only]; Region: COG1568 123214004354 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 123214004355 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 123214004356 AAA domain; Region: AAA_14; pfam13173 123214004357 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 123214004358 Aconitase B swivel domain. Aconitate hydratase B is involved in energy metabolism as part of the TCA cycle. It catalyses the formation of cis-aconitate from citrate. This is the aconitase swivel domain, which undergoes swivelling conformational change in...; Region: AcnB_Swivel; cd01576 123214004359 substrate binding site [chemical binding]; other site 123214004360 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 123214004361 substrate binding site [chemical binding]; other site 123214004362 ligand binding site [chemical binding]; other site 123214004363 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 123214004364 Carbonic anhydrase [Inorganic ion transport and metabolism]; Region: Cah; COG3338 123214004365 Carbonic anhydrase alpha, prokaryotic-like subfamily. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon...; Region: alpha_CA_prokaryotic_like; cd03124 123214004366 active site 123214004367 zinc binding site [ion binding]; other site 123214004368 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 123214004369 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 123214004370 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 123214004371 Cytochrome c; Region: Cytochrom_C; cl11414 123214004372 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214004373 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 123214004374 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214004375 Uncharacterized conserved protein [Function unknown]; Region: COG3391 123214004376 NHL repeat; Region: NHL; pfam01436 123214004377 NHL repeat; Region: NHL; pfam01436 123214004378 NHL repeat; Region: NHL; pfam01436 123214004379 NHL repeat; Region: NHL; pfam01436 123214004380 Sporulation related domain; Region: SPOR; pfam05036 123214004381 SurA N-terminal domain; Region: SurA_N_3; cl07813 123214004382 nitrogen fixation protein NifM; Region: nifM_nitrog; TIGR02933 123214004383 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 123214004384 Uncharacterized conserved protein [Function unknown]; Region: COG3391 123214004385 NHL repeat; Region: NHL; pfam01436 123214004386 NHL repeat; Region: NHL; pfam01436 123214004387 NHL repeat; Region: NHL; pfam01436 123214004388 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214004389 Uncharacterized conserved protein [Function unknown]; Region: COG3391 123214004390 NHL repeat; Region: NHL; pfam01436 123214004391 NHL repeat; Region: NHL; pfam01436 123214004392 NHL repeat; Region: NHL; pfam01436 123214004393 NHL repeat; Region: NHL; pfam01436 123214004394 NHL repeat; Region: NHL; pfam01436 123214004395 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 123214004396 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214004397 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 123214004398 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 123214004399 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 123214004400 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 123214004401 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 123214004402 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 123214004403 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 123214004404 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 123214004405 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 123214004406 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 123214004407 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 123214004408 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 123214004409 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214004410 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 123214004411 doubled CXXCH domain; Region: paired_CXXCH_1; TIGR01905 123214004412 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214004413 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 123214004414 ATP-dependent Clp protease adaptor protein ClpS; Region: ClpS; pfam02617 123214004415 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 123214004416 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 123214004417 active site 123214004418 (T/H)XGH motif; other site 123214004419 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 123214004420 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 123214004421 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 123214004422 protein binding site [polypeptide binding]; other site 123214004423 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 123214004424 protein binding site [polypeptide binding]; other site 123214004425 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 123214004426 HAD-superfamily subfamily IIA hydrolase, TIGR01457; Region: HAD-SF-IIA-hyp2 123214004427 motif II; other site 123214004428 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 123214004429 4-hydroxybenzoate polyprenyltransferase and related prenyltransferases [Coenzyme metabolism]; Region: UbiA; cl00337 123214004430 UbiA prenyltransferase family; Region: UbiA; pfam01040 123214004431 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 123214004432 hypothetical protein; Reviewed; Region: PRK00024 123214004433 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 123214004434 MPN+ (JAMM) motif; other site 123214004435 Zinc-binding site [ion binding]; other site 123214004436 peptidyl-prolyl cis-trans isomerase A (rotamase A); Provisional; Region: PRK10903 123214004437 cyclophilin_EcCYP_like: cyclophilin-type A-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to the cytosolic E. coli cyclophilin A and Streptomyces antibioticus SanCyp18. Compared to the archetypal cyclophilin Human cyclophilin A, these...; Region: cyclophilin_EcCYP_like; cd01920 123214004438 substrate binding site [chemical binding]; other site 123214004439 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 123214004440 Hydantoinase B/oxoprolinase; Region: Hydantoinase_B; pfam02538 123214004441 N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuA; COG0145 123214004442 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 123214004443 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 123214004444 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 123214004445 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 123214004446 active site 123214004447 HIGH motif; other site 123214004448 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 123214004449 KMSKS motif; other site 123214004450 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 123214004451 tRNA binding surface [nucleotide binding]; other site 123214004452 anticodon binding site; other site 123214004453 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 123214004454 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 123214004455 S-adenosylmethionine binding site [chemical binding]; other site 123214004456 Predicted alternative 3-dehydroquinate synthase [Amino acid transport and metabolism]; Region: COG1465 123214004457 3-dehydroquinate synthase; Provisional; Region: PRK02290 123214004458 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 123214004459 mce related protein; Region: MCE; pfam02470 123214004460 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 123214004461 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 123214004462 ligand binding site [chemical binding]; other site 123214004463 flexible hinge region; other site 123214004464 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 123214004465 putative switch regulator; other site 123214004466 non-specific DNA interactions [nucleotide binding]; other site 123214004467 DNA binding site [nucleotide binding] 123214004468 sequence specific DNA binding site [nucleotide binding]; other site 123214004469 putative cAMP binding site [chemical binding]; other site 123214004470 Outer membrane efflux protein; Region: OEP; pfam02321 123214004471 Outer membrane efflux protein; Region: OEP; pfam02321 123214004472 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 123214004473 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 123214004474 HlyD family secretion protein; Region: HlyD_3; pfam13437 123214004475 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 123214004476 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 123214004477 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 123214004478 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 123214004479 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 123214004480 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 123214004481 FtsX-like permease family; Region: FtsX; pfam02687 123214004482 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 123214004483 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 123214004484 FtsX-like permease family; Region: FtsX; pfam02687 123214004485 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 123214004486 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 123214004487 dimerization interface [polypeptide binding]; other site 123214004488 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 123214004489 dimer interface [polypeptide binding]; other site 123214004490 putative CheW interface [polypeptide binding]; other site 123214004491 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 123214004492 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 123214004493 DnaK suppressor protein [Signal transduction mechanisms]; Region: DksA; COG1734 123214004494 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 123214004495 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214004496 ATP-grasp domain; Region: ATP-grasp; pfam02222 123214004497 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 123214004498 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 123214004499 active site 123214004500 phosphorylation site [posttranslational modification] 123214004501 intermolecular recognition site; other site 123214004502 dimerization interface [polypeptide binding]; other site 123214004503 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 123214004504 Walker A motif; other site 123214004505 ATP binding site [chemical binding]; other site 123214004506 Walker B motif; other site 123214004507 arginine finger; other site 123214004508 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 123214004509 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 123214004510 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 123214004511 active site 123214004512 phosphorylation site [posttranslational modification] 123214004513 intermolecular recognition site; other site 123214004514 dimerization interface [polypeptide binding]; other site 123214004515 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 123214004516 Zn2+ binding site [ion binding]; other site 123214004517 Mg2+ binding site [ion binding]; other site 123214004518 Response regulator receiver domain; Region: Response_reg; pfam00072 123214004519 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 123214004520 active site 123214004521 phosphorylation site [posttranslational modification] 123214004522 intermolecular recognition site; other site 123214004523 dimerization interface [polypeptide binding]; other site 123214004524 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: VicK; COG5002 123214004525 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 123214004526 dimerization interface [polypeptide binding]; other site 123214004527 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 123214004528 dimer interface [polypeptide binding]; other site 123214004529 phosphorylation site [posttranslational modification] 123214004530 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 123214004531 ATP binding site [chemical binding]; other site 123214004532 Mg2+ binding site [ion binding]; other site 123214004533 G-X-G motif; other site 123214004534 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 123214004535 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 123214004536 purine monophosphate binding site [chemical binding]; other site 123214004537 dimer interface [polypeptide binding]; other site 123214004538 putative catalytic residues [active] 123214004539 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 123214004540 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 123214004541 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 123214004542 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 123214004543 metal binding triad [ion binding]; metal-binding site 123214004544 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 123214004545 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 123214004546 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 123214004547 Ligand Binding Site [chemical binding]; other site 123214004548 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 123214004549 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 123214004550 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 123214004551 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 123214004552 Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism...; Region: PilT; cd01131 123214004553 Walker A motif; other site 123214004554 ATP binding site [chemical binding]; other site 123214004555 Walker B motif; other site 123214004556 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 123214004557 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 123214004558 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 123214004559 Walker A motif; other site 123214004560 ATP binding site [chemical binding]; other site 123214004561 Walker B motif; other site 123214004562 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 123214004563 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 123214004564 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 123214004565 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 123214004566 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 123214004567 AP endonuclease family 2; Region: AP2Ec; smart00518 123214004568 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of...; Region: AP2Ec; cd00019 123214004569 AP (apurinic/apyrimidinic) site pocket; other site 123214004570 DNA interaction; other site 123214004571 Metal-binding active site; metal-binding site 123214004572 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 123214004573 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 123214004574 substrate binding pocket [chemical binding]; other site 123214004575 chain length determination region; other site 123214004576 substrate-Mg2+ binding site; other site 123214004577 catalytic residues [active] 123214004578 aspartate-rich region 1; other site 123214004579 active site lid residues [active] 123214004580 aspartate-rich region 2; other site 123214004581 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 123214004582 tetramerization interface [polypeptide binding]; other site 123214004583 active site 123214004584 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...; Region: LT_GEWL; cd00254 123214004585 N-acetyl-D-glucosamine binding site [chemical binding]; other site 123214004586 catalytic residue [active] 123214004587 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 123214004588 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 123214004589 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 123214004590 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 123214004591 Plant protein of unknown function (DUF946); Region: DUF946; pfam06101 123214004592 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 123214004593 feedback inhibition sensing region; other site 123214004594 homohexameric interface [polypeptide binding]; other site 123214004595 nucleotide binding site [chemical binding]; other site 123214004596 N-acetyl-L-glutamate binding site [chemical binding]; other site 123214004597 DNA helicase, putative; Region: TIGR00376 123214004598 AAA domain; Region: AAA_12; pfam13087 123214004599 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 123214004600 heme-binding site [chemical binding]; other site 123214004601 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 123214004602 SecA preprotein cross-linking domain; Region: SecA_PP_bind; pfam01043 123214004603 lipoprotein signal peptidase; Provisional; Region: PRK14779 123214004604 DnaK suppressor protein [Signal transduction mechanisms]; Region: DksA; COG1734 123214004605 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 123214004606 metabolite-proton symporter; Region: 2A0106; TIGR00883 123214004607 putative substrate translocation pore; other site 123214004608 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate...; Region: citrate_synt_like_1; cd06118 123214004609 dimer interface [polypeptide binding]; other site 123214004610 Citrate synthase; Region: Citrate_synt; pfam00285 123214004611 active site 123214004612 coenzyme A binding site [chemical binding]; other site 123214004613 citrylCoA binding site [chemical binding]; other site 123214004614 oxalacetate/citrate binding site [chemical binding]; other site 123214004615 catalytic triad [active] 123214004616 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 123214004617 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 123214004618 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 123214004619 motif II; other site 123214004620 Menaquinone biosynthesis; Region: VitK2_biosynth; pfam02621 123214004621 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 123214004622 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 123214004623 S-adenosyl-L-methionine-dependent methyltransferase; Region: Methyltransf_30; cl17711 123214004624 DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both...; Region: POLBc; cl10023 123214004625 active site 123214004626 metal-binding site 123214004627 LexA repressor; Validated; Region: PRK00215 123214004628 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 123214004629 non-specific DNA interactions [nucleotide binding]; other site 123214004630 DNA binding site [nucleotide binding] 123214004631 sequence specific DNA binding site [nucleotide binding]; other site 123214004632 putative cAMP binding site [chemical binding]; other site 123214004633 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 123214004634 Catalytic site [active] 123214004635 DNA polymerase III subunit beta; Validated; Region: PRK05643 123214004636 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 123214004637 putative DNA binding surface [nucleotide binding]; other site 123214004638 dimer interface [polypeptide binding]; other site 123214004639 beta-clamp/clamp loader binding surface; other site 123214004640 beta-clamp/translesion DNA polymerase binding surface; other site 123214004641 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 123214004642 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 123214004643 ATP binding site [chemical binding]; other site 123214004644 Mg2+ binding site [ion binding]; other site 123214004645 G-X-G motif; other site 123214004646 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 123214004647 anchoring element; other site 123214004648 dimer interface [polypeptide binding]; other site 123214004649 ATP binding site [chemical binding]; other site 123214004650 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 123214004651 active site 123214004652 putative metal-binding site [ion binding]; other site 123214004653 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 123214004654 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 123214004655 Cytochrome c; Region: Cytochrom_C; cl11414 123214004656 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 123214004657 PAS fold; Region: PAS_3; pfam08447 123214004658 putative active site [active] 123214004659 heme pocket [chemical binding]; other site 123214004660 PAS domain S-box; Region: sensory_box; TIGR00229 123214004661 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 123214004662 putative active site [active] 123214004663 heme pocket [chemical binding]; other site 123214004664 GAF domain; Region: GAF_2; pfam13185 123214004665 GAF domain; Region: GAF_3; pfam13492 123214004666 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 123214004667 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214004668 metal binding site [ion binding]; metal-binding site 123214004669 active site 123214004670 I-site; other site 123214004671 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 123214004672 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 123214004673 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 123214004674 putative membrane fusion protein; Region: TIGR02828 123214004675 Outer membrane efflux protein; Region: OEP; pfam02321 123214004676 Outer membrane efflux protein; Region: OEP; pfam02321 123214004677 anthranilate synthase component I; Provisional; Region: PRK13570 123214004678 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 123214004679 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 123214004680 GAF domain; Region: GAF_3; pfam13492 123214004681 GAF domain; Region: GAF_2; pfam13185 123214004682 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 123214004683 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 123214004684 dimer interface [polypeptide binding]; other site 123214004685 phosphorylation site [posttranslational modification] 123214004686 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 123214004687 ATP binding site [chemical binding]; other site 123214004688 Mg2+ binding site [ion binding]; other site 123214004689 G-X-G motif; other site 123214004690 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 123214004691 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 123214004692 active site 123214004693 phosphorylation site [posttranslational modification] 123214004694 intermolecular recognition site; other site 123214004695 dimerization interface [polypeptide binding]; other site 123214004696 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 123214004697 Walker A motif; other site 123214004698 ATP binding site [chemical binding]; other site 123214004699 Walker B motif; other site 123214004700 arginine finger; other site 123214004701 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 123214004702 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 123214004703 MutS domain III; Region: MutS_III; pfam05192 123214004704 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 123214004705 Walker A/P-loop; other site 123214004706 ATP binding site [chemical binding]; other site 123214004707 Q-loop/lid; other site 123214004708 ABC transporter signature motif; other site 123214004709 Walker B; other site 123214004710 D-loop; other site 123214004711 H-loop/switch region; other site 123214004712 Smr domain; Region: Smr; pfam01713 123214004713 A type 1 glutamine amidotransferase (GATase1)-like domain found in PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_like; cd03134 123214004714 intracellular protease, PfpI family; Region: PfpI; TIGR01382 123214004715 proposed catalytic triad [active] 123214004716 conserved cys residue [active] 123214004717 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 123214004718 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 123214004719 nucleotide binding site [chemical binding]; other site 123214004720 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 123214004721 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 123214004722 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 123214004723 Protein export membrane protein; Region: SecD_SecF; pfam02355 123214004724 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 123214004725 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 123214004726 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 123214004727 glucose-6-phosphate isomerase; Provisional; Region: PRK00973 123214004728 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 123214004729 active site 123214004730 dimer interface [polypeptide binding]; other site 123214004731 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the second SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of...; Region: SIS_PGI_2; cd05016 123214004732 dimer interface [polypeptide binding]; other site 123214004733 active site 123214004734 seryl-tRNA synthetase; Provisional; Region: PRK05431 123214004735 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 123214004736 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme...; Region: SerRS_core; cd00770 123214004737 dimer interface [polypeptide binding]; other site 123214004738 active site 123214004739 motif 1; other site 123214004740 motif 2; other site 123214004741 motif 3; other site 123214004742 TPR repeat; Region: TPR_11; pfam13414 123214004743 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 123214004744 TPR repeat; Region: TPR_11; pfam13414 123214004745 TPR motif; other site 123214004746 binding surface 123214004747 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 123214004748 TPR repeat; Region: TPR_11; pfam13414 123214004749 binding surface 123214004750 TPR motif; other site 123214004751 Family of unknown function (DUF490); Region: DUF490; pfam04357 123214004752 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 123214004753 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 123214004754 glutamine binding [chemical binding]; other site 123214004755 catalytic triad [active] 123214004756 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...; Region: TOP4c; cl00148 123214004757 CAP-like domain; other site 123214004758 active site 123214004759 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cd00081 123214004760 protein-splicing catalytic site; other site 123214004761 thioester formation/cholesterol transfer; other site 123214004762 Intein/homing endonuclease [DNA replication, recombination, and repair]; Region: COG1372 123214004763 Hint (Hedgehog/Intein) domain C-terminal region; Region: HintC; smart00305 123214004764 Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair]; Region: GyrA; COG0188 123214004765 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...; Region: TOP4c; cd00187 123214004766 primary dimer interface [polypeptide binding]; other site 123214004767 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 123214004768 Domain of unknown function (DUF4416); Region: DUF4416; pfam14385 123214004769 bifunctional molybdenum cofactor biosynthesis protein MoaC/MogA; Provisional; Region: moaC; PRK03604 123214004770 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 123214004771 trimer interface [polypeptide binding]; other site 123214004772 dimer interface [polypeptide binding]; other site 123214004773 putative active site [active] 123214004774 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 123214004775 MPT binding site; other site 123214004776 trimer interface [polypeptide binding]; other site 123214004777 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 123214004778 active site 123214004779 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 123214004780 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 123214004781 Coenzyme A binding pocket [chemical binding]; other site 123214004782 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09311 123214004783 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 123214004784 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cd00641 123214004785 dimerization interface [polypeptide binding]; other site 123214004786 active site 123214004787 PBP superfamily domain; Region: PBP_like_2; cl17296 123214004788 phosphate transporter permease subunit PstC; Provisional; Region: pstC; PRK11275 123214004789 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 123214004790 dimer interface [polypeptide binding]; other site 123214004791 conserved gate region; other site 123214004792 putative PBP binding loops; other site 123214004793 ABC-ATPase subunit interface; other site 123214004794 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstA; COG0581 123214004795 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 123214004796 dimer interface [polypeptide binding]; other site 123214004797 conserved gate region; other site 123214004798 putative PBP binding loops; other site 123214004799 ABC-ATPase subunit interface; other site 123214004800 ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: PstB; COG1117 123214004801 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 123214004802 Walker A/P-loop; other site 123214004803 ATP binding site [chemical binding]; other site 123214004804 Q-loop/lid; other site 123214004805 ABC transporter signature motif; other site 123214004806 Walker B; other site 123214004807 D-loop; other site 123214004808 H-loop/switch region; other site 123214004809 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 123214004810 PhoU domain; Region: PhoU; pfam01895 123214004811 PhoU domain; Region: PhoU; pfam01895 123214004812 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 123214004813 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 123214004814 dimer interface [polypeptide binding]; other site 123214004815 phosphorylation site [posttranslational modification] 123214004816 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 123214004817 ATP binding site [chemical binding]; other site 123214004818 Mg2+ binding site [ion binding]; other site 123214004819 G-X-G motif; other site 123214004820 mannosyl-3-phosphoglycerate phosphatase; Reviewed; Region: PRK00192 123214004821 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 123214004822 active site 123214004823 motif I; other site 123214004824 motif II; other site 123214004825 Putative glycerate kinase [Carbohydrate transport and metabolism]; Region: GckA; COG2379 123214004826 Domain of unknown function (DUF4147); Region: DUF4147; pfam13660 123214004827 MOFRL family; Region: MOFRL; pfam05161 123214004828 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 123214004829 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 123214004830 active site 123214004831 putative glucosyl-3-phosphoglycerate synthase; Provisional; Region: PRK13915 123214004832 cysteine synthase B; Region: cysM; TIGR01138 123214004833 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 123214004834 dimer interface [polypeptide binding]; other site 123214004835 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214004836 catalytic residue [active] 123214004837 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 123214004838 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 123214004839 Uncharacterized ALDH (y4uC) with similarity to Tortula ruralis aldehyde dehydrogenase ALDH21A1; Region: ALDH_y4uC; cd07149 123214004840 NAD(P) binding site [chemical binding]; other site 123214004841 catalytic residues [active] 123214004842 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 123214004843 Nitrogen regulatory protein P-II; Region: P-II; smart00938 123214004844 glutamine synthetase, type I; Region: GlnA; TIGR00653 123214004845 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 123214004846 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 123214004847 PilZ domain; Region: PilZ; pfam07238 123214004848 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 123214004849 binding surface 123214004850 TPR motif; other site 123214004851 Anaphase-promoting complex, cyclosome, subunit 3; Region: Apc3; pfam12895 123214004852 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 123214004853 TPR motif; other site 123214004854 binding surface 123214004855 TPR repeat; Region: TPR_11; pfam13414 123214004856 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 123214004857 TPR motif; other site 123214004858 Tetratricopeptide repeat; Region: TPR_12; pfam13424 123214004859 binding surface 123214004860 TPR repeat; Region: TPR_11; pfam13414 123214004861 Tetratricopeptide repeat; Region: TPR_12; pfam13424 123214004862 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 123214004863 binding surface 123214004864 TPR motif; other site 123214004865 Tetratricopeptide repeat; Region: TPR_16; pfam13432 123214004866 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 123214004867 binding surface 123214004868 Tetratricopeptide repeat; Region: TPR_16; pfam13432 123214004869 TPR motif; other site 123214004870 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 123214004871 binding surface 123214004872 TPR repeat; Region: TPR_11; pfam13414 123214004873 TPR motif; other site 123214004874 TPR repeat; Region: TPR_11; pfam13414 123214004875 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 123214004876 Predicted Ser/Thr protein kinase [Signal transduction mechanisms]; Region: COG2112 123214004877 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 123214004878 active site 123214004879 substrate binding site [chemical binding]; other site 123214004880 ATP binding site [chemical binding]; other site 123214004881 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 123214004882 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 123214004883 CoA-binding site [chemical binding]; other site 123214004884 ATP-binding [chemical binding]; other site 123214004885 Cupredoxin-like domain; Region: Cupredoxin_1; cl17234 123214004886 Permeases of the major facilitator superfamily [General function prediction only]; Region: COG2270 123214004887 Permeases of the major facilitator superfamily [General function prediction only]; Region: COG2270 123214004888 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 123214004889 pseudouridine synthase; Region: TIGR00093 123214004890 active site 123214004891 uracil binding [chemical binding]; other site 123214004892 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 123214004893 IHF - DNA interface [nucleotide binding]; other site 123214004894 IHF dimer interface [polypeptide binding]; other site 123214004895 Ferredoxin [Energy production and conversion]; Region: Fer; COG1141 123214004896 chromosome segregation protein; Provisional; Region: PRK01156 123214004897 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 123214004898 Walker A/P-loop; other site 123214004899 ATP binding site [chemical binding]; other site 123214004900 ATP-binding cassette domain of Rad50; Region: ABC_Rad50; cd03240 123214004901 ABC transporter signature motif; other site 123214004902 Walker B; other site 123214004903 D-loop; other site 123214004904 H-loop/switch region; other site 123214004905 Domain of unknown function DUF77; Region: DUF77; pfam01910 123214004906 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 123214004907 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 123214004908 S-adenosylmethionine binding site [chemical binding]; other site 123214004909 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 123214004910 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 123214004911 Walker A/P-loop; other site 123214004912 ATP binding site [chemical binding]; other site 123214004913 Q-loop/lid; other site 123214004914 ABC transporter signature motif; other site 123214004915 Walker B; other site 123214004916 D-loop; other site 123214004917 H-loop/switch region; other site 123214004918 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 123214004919 Domain of unknown function DUF21; Region: DUF21; pfam01595 123214004920 gliding motility-associated protein GldE; Region: GldE; TIGR03520 123214004921 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 123214004922 Transporter associated domain; Region: CorC_HlyC; smart01091 123214004923 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 123214004924 Domain of unknown function DUF21; Region: DUF21; pfam01595 123214004925 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 123214004926 Transporter associated domain; Region: CorC_HlyC; smart01091 123214004927 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 123214004928 Major Facilitator Superfamily; Region: MFS_1; pfam07690 123214004929 putative substrate translocation pore; other site 123214004930 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 123214004931 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 123214004932 N-glycosylase/DNA lyase; Provisional; Region: PRK01229 123214004933 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 123214004934 minor groove reading motif; other site 123214004935 helix-hairpin-helix signature motif; other site 123214004936 substrate binding pocket [chemical binding]; other site 123214004937 active site 123214004938 Helix-turn-helix domain; Region: HTH_25; pfam13413 123214004939 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 123214004940 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases and ATP sulphurylases. The domain forms a apha/beta/apha fold which binds to Adenosine group; Region: Alpha_ANH_like; cd01986 123214004941 Ligand Binding Site [chemical binding]; other site 123214004942 HNH endonuclease; Region: HNH_3; pfam13392 123214004943 Homeodomain-like domain; Region: HTH_23; pfam13384 123214004944 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 123214004945 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 123214004946 Mg2+ transporter Helicobacter pylori CorA-like subgroup; Region: HpCorA-like; cd12836 123214004947 Cl binding site [ion binding]; other site 123214004948 oligomer interface [polypeptide binding]; other site 123214004949 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK07739 123214004950 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 123214004951 flagellar hook-associated protein 3; Region: flagell_flgL; TIGR02550 123214004952 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 123214004953 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 123214004954 Flagellar protein FliS; Region: FliS; cl00654 123214004955 Flagellar capping protein [Cell motility and secretion]; Region: FliD; COG1345 123214004956 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 123214004957 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 123214004958 FlaG protein; Region: FlaG; pfam03646 123214004959 flagellin; Provisional; Region: PRK12804 123214004960 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 123214004961 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 123214004962 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2604 123214004963 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 123214004964 ligand binding site; other site 123214004965 tetramer interface; other site 123214004966 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 123214004967 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 123214004968 NTP_trnasferase_like_2 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_2; cd06426 123214004969 Substrate binding site; other site 123214004970 metal-binding site 123214004971 UDP-N-acetyl-D-glucosamine 2-epimerase, UDP-hydrolysing; Region: NeuC_NnaA; TIGR03568 123214004972 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 123214004973 active site 123214004974 homodimer interface [polypeptide binding]; other site 123214004975 PIN domains of VapC and Smg6 ribonucleases, ribosome assembly factor NOB1, Archaeoglobus fulgidus AF0591 protein and homologs; Region: PIN_VapC-Smg6-like; cd09855 123214004976 putative active site [active] 123214004977 N-acetylneuraminate synthase; Region: NeuB_NnaB; TIGR03569 123214004978 NeuB family; Region: NeuB; pfam03102 123214004979 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 123214004980 NeuB binding interface [polypeptide binding]; other site 123214004981 putative substrate binding site [chemical binding]; other site 123214004982 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 123214004983 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 123214004984 putative trimer interface [polypeptide binding]; other site 123214004985 putative CoA binding site [chemical binding]; other site 123214004986 aminotransferase, LLPSF_NHT_00031 family; Region: NHT_00031; TIGR04181 123214004987 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 123214004988 inhibitor-cofactor binding pocket; inhibition site 123214004989 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214004990 catalytic residue [active] 123214004991 Arna decarboxylase_like, extended (e) SDRs; Region: Arna_like_SDR_e; cd05257 123214004992 NAD dependent epimerase/dehydratase, LLPSF_EDH_00030 family; Region: EDH_00030; TIGR04180 123214004993 NAD binding site [chemical binding]; other site 123214004994 substrate binding site [chemical binding]; other site 123214004995 active site 123214004996 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 123214004997 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 123214004998 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 123214004999 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 123214005000 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and...; Region: PLPDE_IV; cd00449 123214005001 homodimer interface [polypeptide binding]; other site 123214005002 substrate-cofactor binding pocket; other site 123214005003 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214005004 catalytic residue [active] 123214005005 aspartate kinase; Reviewed; Region: PRK06635 123214005006 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 123214005007 putative nucleotide binding site [chemical binding]; other site 123214005008 putative catalytic residues [active] 123214005009 putative Mg ion binding site [ion binding]; other site 123214005010 putative aspartate binding site [chemical binding]; other site 123214005011 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 123214005012 putative allosteric regulatory site; other site 123214005013 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 123214005014 putative allosteric regulatory residue; other site 123214005015 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 123214005016 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 123214005017 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 123214005018 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 123214005019 enolase; Provisional; Region: eno; PRK00077 123214005020 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 123214005021 dimer interface [polypeptide binding]; other site 123214005022 metal binding site [ion binding]; metal-binding site 123214005023 substrate binding pocket [chemical binding]; other site 123214005024 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 123214005025 Septum formation initiator; Region: DivIC; pfam04977 123214005026 phosphoglycolate phosphatase; Provisional; Region: PRK13222 123214005027 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 123214005028 motif II; other site 123214005029 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 123214005030 heterotetramer interface [polypeptide binding]; other site 123214005031 active site pocket [active] 123214005032 cleavage site 123214005033 SH3 domain protein; Region: SH3_and_anchor; TIGR04211 123214005034 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 123214005035 catalytic loop [active] 123214005036 iron binding site [ion binding]; other site 123214005037 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 123214005038 4Fe-4S binding domain; Region: Fer4; pfam00037 123214005039 4Fe-4S double cluster binding domain; Region: Fer4_16; pfam13484 123214005040 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; cd00368 123214005041 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 123214005042 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 123214005043 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 123214005044 trimer interface [polypeptide binding]; other site 123214005045 active site 123214005046 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 123214005047 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 123214005048 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 123214005049 homotrimer interaction site [polypeptide binding]; other site 123214005050 putative active site [active] 123214005051 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 123214005052 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; Region: TIGR00007 123214005053 catalytic residues [active] 123214005054 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 123214005055 ABC1 family; Region: ABC1; cl17513 123214005056 Thymidylate synthase complementing protein; Region: Thy1; cl03630 123214005057 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 123214005058 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 123214005059 Macro domain, Appr-1"-pase_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...; Region: Macro_Appr_pase_like; cd02908 123214005060 putative ADP-ribose binding site [chemical binding]; other site 123214005061 putative active site [active] 123214005062 Restriction endonuclease; Region: Mrr_cat; pfam04471 123214005063 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 123214005064 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 123214005065 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 123214005066 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 123214005067 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214005068 metal binding site [ion binding]; metal-binding site 123214005069 active site 123214005070 I-site; other site 123214005071 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 123214005072 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK12879 123214005073 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; cl17244 123214005074 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 123214005075 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 123214005076 GTP binding site; other site 123214005077 Outer membrane efflux protein; Region: OEP; pfam02321 123214005078 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 123214005079 metal binding site 2 [ion binding]; metal-binding site 123214005080 putative DNA binding helix; other site 123214005081 metal binding site 1 [ion binding]; metal-binding site 123214005082 dimer interface [polypeptide binding]; other site 123214005083 structural Zn2+ binding site [ion binding]; other site 123214005084 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 123214005085 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 123214005086 Sec-independent protein secretion pathway components [Intracellular trafficking and secretion]; Region: TatA; COG1826 123214005087 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 123214005088 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 123214005089 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 123214005090 Surface antigen; Region: Bac_surface_Ag; pfam01103 123214005091 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 123214005092 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 123214005093 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 123214005094 dimer interface [polypeptide binding]; other site 123214005095 substrate binding site [chemical binding]; other site 123214005096 ATP binding site [chemical binding]; other site 123214005097 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 123214005098 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 123214005099 active site 123214005100 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 123214005101 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 123214005102 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 123214005103 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 123214005104 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; cl00465 123214005105 Domain of unknown function DUF20; Region: UPF0118; pfam01594 123214005106 S-adenosylmethionine decarboxylase proenzyme; Provisional; Region: PRK01236 123214005107 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 123214005108 5-methyltetrahydrofolate--homocysteine methyltransferase; Region: metH; TIGR02082 123214005109 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 123214005110 substrate binding pocket [chemical binding]; other site 123214005111 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 123214005112 B12 binding site [chemical binding]; other site 123214005113 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 123214005114 Protein of unknown function (DUF523); Region: DUF523; pfam04463 123214005115 Ferrochelatase; Region: Ferrochelatase; pfam00762 123214005116 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 123214005117 C-terminal domain interface [polypeptide binding]; other site 123214005118 active site 123214005119 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 123214005120 active site 123214005121 N-terminal domain interface [polypeptide binding]; other site 123214005122 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 123214005123 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 123214005124 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 123214005125 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 123214005126 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 123214005127 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 123214005128 DNA binding residues [nucleotide binding] 123214005129 DNA primase, catalytic core; Region: dnaG; TIGR01391 123214005130 CHC2 zinc finger; Region: zf-CHC2; pfam01807 123214005131 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 123214005132 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 123214005133 active site 123214005134 metal binding site [ion binding]; metal-binding site 123214005135 interdomain interaction site; other site 123214005136 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 123214005137 dihydropteroate synthase; Region: DHPS; TIGR01496 123214005138 substrate binding pocket [chemical binding]; other site 123214005139 dimer interface [polypeptide binding]; other site 123214005140 inhibitor binding site; inhibition site 123214005141 TIGR00159 family protein; Region: TIGR00159 123214005142 DisA bacterial checkpoint controller nucleotide-binding; Region: DisA_N; pfam02457 123214005143 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 123214005144 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 123214005145 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 123214005146 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 123214005147 active site 123214005148 dimer interface [polypeptide binding]; other site 123214005149 motif 1; other site 123214005150 motif 2; other site 123214005151 motif 3; other site 123214005152 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 123214005153 anticodon binding site; other site 123214005154 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 123214005155 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 123214005156 active site 123214005157 phosphorylation site [posttranslational modification] 123214005158 intermolecular recognition site; other site 123214005159 dimerization interface [polypeptide binding]; other site 123214005160 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 123214005161 DNA binding site [nucleotide binding] 123214005162 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 123214005163 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 123214005164 putative catalytic cysteine [active] 123214005165 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 123214005166 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 123214005167 ligand binding site [chemical binding]; other site 123214005168 flexible hinge region; other site 123214005169 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 123214005170 putative switch regulator; other site 123214005171 non-specific DNA interactions [nucleotide binding]; other site 123214005172 DNA binding site [nucleotide binding] 123214005173 sequence specific DNA binding site [nucleotide binding]; other site 123214005174 putative cAMP binding site [chemical binding]; other site 123214005175 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 123214005176 oligomerization interface [polypeptide binding]; other site 123214005177 active site 123214005178 metal binding site [ion binding]; metal-binding site 123214005179 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 123214005180 Malic enzyme [Energy production and conversion]; Region: SfcA; COG0281 123214005181 Malic enzyme, N-terminal domain; Region: malic; pfam00390 123214005182 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 123214005183 putative NAD(P) binding site [chemical binding]; other site 123214005184 S-adenosylmethionine decarboxylase; Region: AdoMet_dc; pfam02675 123214005185 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 123214005186 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 123214005187 THF binding site; other site 123214005188 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 123214005189 substrate binding site [chemical binding]; other site 123214005190 THF binding site; other site 123214005191 zinc-binding site [ion binding]; other site 123214005192 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 123214005193 metal binding site 2 [ion binding]; metal-binding site 123214005194 putative DNA binding helix; other site 123214005195 metal binding site 1 [ion binding]; metal-binding site 123214005196 dimer interface [polypeptide binding]; other site 123214005197 structural Zn2+ binding site [ion binding]; other site 123214005198 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 123214005199 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; cl17244 123214005200 Protein of unknown function, DUF481; Region: DUF481; pfam04338 123214005201 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; pfam09527 123214005202 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 123214005203 alternate F1F0 ATPase, F1 subunit epsilon; Region: alt_F1F0_F1_eps; TIGR03166 123214005204 gamma subunit interface [polypeptide binding]; other site 123214005205 epsilon subunit interface [polypeptide binding]; other site 123214005206 LBP interface [polypeptide binding]; other site 123214005207 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 123214005208 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 123214005209 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 123214005210 alpha subunit interaction interface [polypeptide binding]; other site 123214005211 Walker A motif; other site 123214005212 ATP binding site [chemical binding]; other site 123214005213 Walker B motif; other site 123214005214 inhibitor binding site; inhibition site 123214005215 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 123214005216 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 123214005217 core domain interface [polypeptide binding]; other site 123214005218 delta subunit interface [polypeptide binding]; other site 123214005219 epsilon subunit interface [polypeptide binding]; other site 123214005220 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 123214005221 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 123214005222 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 123214005223 Walker A motif; other site 123214005224 ATP binding site [chemical binding]; other site 123214005225 Walker B motif; other site 123214005226 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 123214005227 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 123214005228 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 123214005229 F0F1-type ATP synthase, delta subunit (mitochondrial oligomycin sensitivity protein) [Energy production and conversion]; Region: AtpH; cl17210 123214005230 F0F1 ATP synthase subunit C; Provisional; Region: PRK13468 123214005231 ATP synthase A chain; Region: ATP-synt_A; cl00413 123214005232 N-ATPase, AtpR subunit; Region: AtpR; pfam12966 123214005233 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 123214005234 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 123214005235 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 123214005236 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 123214005237 TPP-binding site [chemical binding]; other site 123214005238 dimer interface [polypeptide binding]; other site 123214005239 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 123214005240 PYR/PP interface [polypeptide binding]; other site 123214005241 dimer interface [polypeptide binding]; other site 123214005242 TPP binding site [chemical binding]; other site 123214005243 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 123214005244 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 123214005245 Uncharacterized conserved protein [Function unknown]; Region: COG0585 123214005246 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 123214005247 active site 123214005248 Protein of unknown function (DUF507); Region: DUF507; cl01112 123214005249 ADP-glucose phosphorylase; Region: PLN02643 123214005250 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 123214005251 nucleotide binding site/active site [active] 123214005252 HIT family signature motif; other site 123214005253 catalytic residue [active] 123214005254 dUTPase; Region: dUTPase_2; pfam08761 123214005255 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in dimeric 2-Deoxyuridine 5'-triphosphate nucleotidohydrolase and similar proteins; Region: NTP-PPase_dUTPase; cd11527 123214005256 active site 123214005257 homodimer interface [polypeptide binding]; other site 123214005258 metal binding site [ion binding]; metal-binding site 123214005259 Serine dehydrogenase proteinase; Region: SDH_sah; pfam01972 123214005260 Caseinolytic protease (ClpP) is an ATP-dependent protease; Region: Clp_protease_like; cl15763 123214005261 active site 123214005262 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 123214005263 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 123214005264 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 123214005265 homodimer interface [polypeptide binding]; other site 123214005266 NADP binding site [chemical binding]; other site 123214005267 substrate binding site [chemical binding]; other site 123214005268 ATP citrate (pro-S)-lyase; Region: PLN02522 123214005269 CoA-ligase; Region: Ligase_CoA; pfam00549 123214005270 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. CCL cleaves citryl-CoA (CiCoA) to acetyl-CoA (AcCoA) and oxaloacetate (OAA); Region: CCL_ACL-C; cd06100 123214005271 active site 123214005272 oxalacetate binding site [chemical binding]; other site 123214005273 citrylCoA binding site [chemical binding]; other site 123214005274 coenzyme A binding site [chemical binding]; other site 123214005275 catalytic triad [active] 123214005276 ATP citrate (pro-S)-lyase; Region: PLN02235 123214005277 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 123214005278 Monomeric isocitrate dehydrogenase [Energy production and conversion]; Region: Icd; COG2838 123214005279 Monomeric isocitrate dehydrogenase; Region: IDH; cl15383 123214005280 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 123214005281 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 123214005282 substrate binding site [chemical binding]; other site 123214005283 ligand binding site [chemical binding]; other site 123214005284 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 123214005285 Uncharacterized protein family (UPF0081); Region: UPF0081; pfam03652 123214005286 YceG-like family; Region: YceG; pfam02618 123214005287 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 123214005288 dimerization interface [polypeptide binding]; other site 123214005289 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 123214005290 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 123214005291 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 123214005292 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 123214005293 hinge; other site 123214005294 active site 123214005295 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 123214005296 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 123214005297 Walker A motif; other site 123214005298 ATP binding site [chemical binding]; other site 123214005299 Walker B motif; other site 123214005300 arginine finger; other site 123214005301 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1934 123214005302 OstA-like protein; Region: OstA; pfam03968 123214005303 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 123214005304 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 123214005305 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 123214005306 tRNA; other site 123214005307 putative tRNA binding site [nucleotide binding]; other site 123214005308 putative NADP binding site [chemical binding]; other site 123214005309 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 123214005310 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 123214005311 Na binding site [ion binding]; other site 123214005312 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 123214005313 active site 123214005314 multimer interface [polypeptide binding]; other site 123214005315 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 123214005316 Vitamin K epoxide reductase (VKOR) family; Region: VKOR; cl01729 123214005317 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 123214005318 dimerization interface [polypeptide binding]; other site 123214005319 Uncharacterized distant relative of homeotic protein bithoraxoid [General function prediction only]; Region: COG2018 123214005320 Domain of unknown function (DUF4388); Region: DUF4388; pfam14332 123214005321 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 123214005322 Conserved hypothetical ATP binding protein; Region: ATP_bind_1; pfam03029 123214005323 G1 box; other site 123214005324 GTP/Mg2+ binding site [chemical binding]; other site 123214005325 G2 box; other site 123214005326 Switch I region; other site 123214005327 G3 box; other site 123214005328 Switch II region; other site 123214005329 G4 box; other site 123214005330 G5 box; other site 123214005331 N-ethylammeline chlorohydrolase; Provisional; Region: PRK06038 123214005332 TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are...; Region: ATZ_TRZ_like; cd01298 123214005333 active site 123214005334 putative substrate binding pocket [chemical binding]; other site 123214005335 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 123214005336 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 123214005337 FtsX-like permease family; Region: FtsX; pfam02687 123214005338 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 123214005339 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 123214005340 Walker A/P-loop; other site 123214005341 ATP binding site [chemical binding]; other site 123214005342 Q-loop/lid; other site 123214005343 ABC transporter signature motif; other site 123214005344 Walker B; other site 123214005345 D-loop; other site 123214005346 H-loop/switch region; other site 123214005347 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 123214005348 Clp amino terminal domain; Region: Clp_N; pfam02861 123214005349 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 123214005350 Walker A motif; other site 123214005351 ATP binding site [chemical binding]; other site 123214005352 Walker B motif; other site 123214005353 arginine finger; other site 123214005354 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 123214005355 Walker A motif; other site 123214005356 ATP binding site [chemical binding]; other site 123214005357 Walker B motif; other site 123214005358 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 123214005359 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 123214005360 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 123214005361 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 123214005362 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 123214005363 Surface antigen; Region: Bac_surface_Ag; pfam01103 123214005364 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 123214005365 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 123214005366 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 123214005367 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 123214005368 trimer interface [polypeptide binding]; other site 123214005369 active site 123214005370 UDP-GlcNAc binding site [chemical binding]; other site 123214005371 lipid binding site [chemical binding]; lipid-binding site 123214005372 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 123214005373 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; pfam02683 123214005374 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 123214005375 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 123214005376 catalytic residues [active] 123214005377 Succinate dehydrogenase/fumarate reductase, Fe-S protein subunit [Energy production and conversion]; Region: FrdB; COG0479 123214005378 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 123214005379 catalytic loop [active] 123214005380 iron binding site [ion binding]; other site 123214005381 Domain of unknown function DUF20; Region: UPF0118; pfam01594 123214005382 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 123214005383 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 123214005384 UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs; Region: UGD_SDR_e; cd05230 123214005385 NAD binding site [chemical binding]; other site 123214005386 putative substrate binding site 2 [chemical binding]; other site 123214005387 putative substrate binding site 1 [chemical binding]; other site 123214005388 active site 123214005389 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 123214005390 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 123214005391 DhnA-type fructose-1,6-bisphosphate aldolase and related enzymes [Carbohydrate transport and metabolism]; Region: FbaB; COG1830 123214005392 Class I fructose-1,6-bisphosphate (FBP) aldolases of the archaeal type (DhnA homologs); Region: DhnA; cd00958 123214005393 putative active site; other site 123214005394 catalytic residue [active] 123214005395 Protein of unknown function (DUF1049); Region: DUF1049; cl01539 123214005396 FHIT (fragile histidine family): FHIT proteins, related to the HIT family carry a motif HxHxH/Qxx (x, is a hydrophobic amino acid), On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified into...; Region: FHIT; cd01275 123214005397 nucleotide binding site/active site [active] 123214005398 HIT family signature motif; other site 123214005399 catalytic residue [active] 123214005400 Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]; Region: PriA; COG1198 123214005401 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 123214005402 active site 123214005403 HslU subunit interaction site [polypeptide binding]; other site 123214005404 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 123214005405 NlpC/P60 family; Region: NLPC_P60; pfam00877 123214005406 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 123214005407 S-adenosylmethionine binding site [chemical binding]; other site 123214005408 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 123214005409 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 123214005410 active site 123214005411 (T/H)XGH motif; other site 123214005412 Lipopolysaccharide-assembly; Region: LptE; pfam04390 123214005413 DNA polymerase III, delta subunit [DNA replication, recombination, and repair]; Region: HolA; COG1466 123214005414 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 123214005415 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 123214005416 Walker A motif; other site 123214005417 ATP binding site [chemical binding]; other site 123214005418 Walker B motif; other site 123214005419 arginine finger; other site 123214005420 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 123214005421 quinolinate synthetase; Provisional; Region: PRK09375 123214005422 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 123214005423 active site residue [active] 123214005424 FAD binding domain; Region: FAD_binding_4; pfam01565 123214005425 glycolate oxidase, subunit GlcD; Region: glcD; TIGR00387 123214005426 CRISPR/Cas system-associated RAMP superfamily protein Cas6; Region: Cas6-I-III; cd09652 123214005427 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 123214005428 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 123214005429 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214005430 metal binding site [ion binding]; metal-binding site 123214005431 active site 123214005432 I-site; other site 123214005433 M28 Zn-Peptidases; Region: M28_like_1; cd05640 123214005434 Peptidase family M28; Region: Peptidase_M28; pfam04389 123214005435 metal binding site [ion binding]; metal-binding site 123214005436 Hemerythrin; Region: Hemerythrin; cd12107 123214005437 Fe binding site [ion binding]; other site 123214005438 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 123214005439 S-adenosylmethionine binding site [chemical binding]; other site 123214005440 ATP-dependent nuclease, subunit B [DNA replication, recombination, and repair]; Region: AddB; COG3857 123214005441 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 123214005442 phage tail tape measure protein, TP901 family, core region; Region: tape_meas_TP901; TIGR01760 123214005443 Phage-related protein [Function unknown]; Region: COG5412 123214005444 Phage virion morphogenesis family; Region: Phage_tail_S; cl02089 123214005445 Phage portal protein, SPP1 Gp6-like; Region: Phage_prot_Gp6; pfam05133 123214005446 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 123214005447 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 123214005448 Uncharacterized conserved protein (DUF2190); Region: DUF2190; pfam09956 123214005449 RecT family; Region: RecT; cl04285 123214005450 YopX protein; Region: YopX; pfam09643 123214005451 Bacterial DNA-binding protein; Region: Bac_DNA_binding; pfam00216 123214005452 IHF - DNA interface [nucleotide binding]; other site 123214005453 IHF dimer interface [polypeptide binding]; other site 123214005454 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 123214005455 AAA domain; Region: AAA_22; pfam13401 123214005456 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 123214005457 DNA-binding interface [nucleotide binding]; DNA binding site 123214005458 Winged helix-turn helix; Region: HTH_29; pfam13551 123214005459 Integrase core domain; Region: rve; pfam00665 123214005460 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 123214005461 ParB-like nuclease domain; Region: ParBc; cl02129 123214005462 Helix-turn-helix domain; Region: HTH_38; pfam13936 123214005463 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 123214005464 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 123214005465 non-specific DNA binding site [nucleotide binding]; other site 123214005466 salt bridge; other site 123214005467 sequence-specific DNA binding site [nucleotide binding]; other site 123214005468 Chalcone-flavanone isomerase; Region: Chalcone; cl03589 123214005469 Baseplate J-like protein; Region: Baseplate_J; pfam04865 123214005470 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 123214005471 putative active site [active] 123214005472 flagellar capping protein; Provisional; Region: PRK12765 123214005473 Terminase-like family; Region: Terminase_6; pfam03237 123214005474 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5410 123214005475 Phage-related terminase [General function prediction only]; Region: COG5362; cl02216 123214005476 Protein of unknown function (DUF2586); Region: DUF2586; pfam10758 123214005477 Protein of unknown function (DUF2597); Region: DUF2597; pfam10772 123214005478 Phage tail protein (Tail_P2_I); Region: Tail_P2_I; cl01817 123214005479 Phage tail-collar fibre protein; Region: DUF3751; pfam12571 123214005480 Protein of unknown function (DUF3380); Region: DUF3380; pfam11860 123214005481 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 123214005482 dimer interface [polypeptide binding]; other site 123214005483 active site 123214005484 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 123214005485 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 123214005486 Walker A motif; other site 123214005487 ATP binding site [chemical binding]; other site 123214005488 Walker B motif; other site 123214005489 arginine finger; other site 123214005490 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 123214005491 TPR repeat; Region: TPR_11; pfam13414 123214005492 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 123214005493 binding surface 123214005494 TPR motif; other site 123214005495 Major Facilitator Superfamily; Region: MFS_1; pfam07690 123214005496 Domain of unknown function DUF87; Region: DUF87; pfam01935 123214005497 AAA-like domain; Region: AAA_10; pfam12846 123214005498 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 123214005499 active site 123214005500 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 123214005501 Protein of unknown function (DUF1271); Region: DUF1271; cl01443 123214005502 Ferredoxin [Energy production and conversion]; Region: Fer; COG1141 123214005503 Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]; Region: HemN; COG0635 123214005504 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 123214005505 FeS/SAM binding site; other site 123214005506 HemN C-terminal domain; Region: HemN_C; pfam06969 123214005507 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 123214005508 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 123214005509 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 123214005510 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 123214005511 nucleotide binding pocket [chemical binding]; other site 123214005512 K-X-D-G motif; other site 123214005513 catalytic site [active] 123214005514 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 123214005515 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 123214005516 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 123214005517 Dimer interface [polypeptide binding]; other site 123214005518 BRCT sequence motif; other site 123214005519 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 123214005520 intersubunit interface [polypeptide binding]; other site 123214005521 active site 123214005522 catalytic residue [active] 123214005523 Methyltransferase domain; Region: Methyltransf_31; pfam13847 123214005524 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 123214005525 S-adenosylmethionine binding site [chemical binding]; other site 123214005526 Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Region: HTH_HspR; cd04766 123214005527 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 123214005528 DNA binding residues [nucleotide binding] 123214005529 chaperone protein DnaJ; Provisional; Region: PRK14291 123214005530 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 123214005531 HSP70 interaction site [polypeptide binding]; other site 123214005532 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 123214005533 substrate binding site [polypeptide binding]; other site 123214005534 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 123214005535 Zn binding sites [ion binding]; other site 123214005536 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 123214005537 dimer interface [polypeptide binding]; other site 123214005538 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 123214005539 histidinol dehydrogenase; Region: hisD; TIGR00069 123214005540 NAD binding site [chemical binding]; other site 123214005541 dimerization interface [polypeptide binding]; other site 123214005542 product binding site; other site 123214005543 substrate binding site [chemical binding]; other site 123214005544 zinc binding site [ion binding]; other site 123214005545 catalytic residues [active] 123214005546 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; pfam02578 123214005547 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 123214005548 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 123214005549 Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa; Region: MobB; cd03116 123214005550 Walker A motif; other site 123214005551 Acylphosphatase; Region: Acylphosphatase; pfam00708 123214005552 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 123214005553 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 123214005554 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 123214005555 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 123214005556 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 123214005557 Peptidase family M23; Region: Peptidase_M23; pfam01551 123214005558 aminotransferase; Validated; Region: PRK08175 123214005559 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 123214005560 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214005561 homodimer interface [polypeptide binding]; other site 123214005562 catalytic residue [active] 123214005563 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 123214005564 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 123214005565 Walker A/P-loop; other site 123214005566 ATP binding site [chemical binding]; other site 123214005567 Q-loop/lid; other site 123214005568 ABC transporter signature motif; other site 123214005569 Walker B; other site 123214005570 D-loop; other site 123214005571 H-loop/switch region; other site 123214005572 6-carboxyhexanoate--CoA ligase; Provisional; Region: PRK01322 123214005573 pimelyl-[acyl-carrier protein] methyl ester esterase; Region: bioH; TIGR01738 123214005574 Methyltransferase domain; Region: Methyltransf_23; pfam13489 123214005575 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 123214005576 S-adenosylmethionine binding site [chemical binding]; other site 123214005577 Protein of unknown function (DUF433); Region: DUF433; pfam04255 123214005578 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 123214005579 oligomeric interface; other site 123214005580 putative active site [active] 123214005581 homodimer interface [polypeptide binding]; other site 123214005582 Uncharacterized protein family (UPF0175); Region: UPF0175; pfam03683 123214005583 Domain of unknown function (DUF3368); Region: DUF3368; pfam11848 123214005584 PIN domain; Region: PIN_3; pfam13470 123214005585 Virulence-associated protein and related proteins [Function unknown]; Region: VagC; COG4456 123214005586 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 123214005587 oligomeric interface; other site 123214005588 putative active site [active] 123214005589 homodimer interface [polypeptide binding]; other site 123214005590 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 123214005591 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 123214005592 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214005593 metal binding site [ion binding]; metal-binding site 123214005594 active site 123214005595 I-site; other site 123214005596 methylthioribulose-1-phosphate dehydratase; Reviewed; Region: mtnB; PRK06754 123214005597 intersubunit interface [polypeptide binding]; other site 123214005598 active site 123214005599 Zn2+ binding site [ion binding]; other site 123214005600 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1791 123214005601 Cupin domain; Region: Cupin_2; cl17218 123214005602 Enoyl-[acyl-carrier-protein]; Region: FabI; COG0623 123214005603 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 123214005604 NAD binding site [chemical binding]; other site 123214005605 homotetramer interface [polypeptide binding]; other site 123214005606 homodimer interface [polypeptide binding]; other site 123214005607 substrate binding site [chemical binding]; other site 123214005608 active site 123214005609 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 123214005610 thiS-thiF/thiG interaction site; other site 123214005611 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 123214005612 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...; Region: HisRS-like_core; cd00773 123214005613 dimer interface [polypeptide binding]; other site 123214005614 motif 1; other site 123214005615 active site 123214005616 motif 2; other site 123214005617 motif 3; other site 123214005618 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 123214005619 anticodon binding site; other site 123214005620 Hemerythrin; Region: Hemerythrin; cd12107 123214005621 Fe binding site [ion binding]; other site 123214005622 tRNA-guanine family transglycosylase; Region: tgt_general; TIGR00449 123214005623 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 123214005624 Uncharacterized conserved protein [Function unknown]; Region: COG1432 123214005625 LabA_like proteins; Region: LabA_like/DUF88; cl10034 123214005626 putative metal binding site [ion binding]; other site 123214005627 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 123214005628 Histone deacetylases and histone-like deacetylases, classII; Region: HDAC_classII; cd09992 123214005629 active site 123214005630 Zn binding site [ion binding]; other site 123214005631 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 123214005632 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 123214005633 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 123214005634 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 123214005635 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 123214005636 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214005637 metal binding site [ion binding]; metal-binding site 123214005638 active site 123214005639 I-site; other site 123214005640 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 123214005641 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 123214005642 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; cl17244 123214005643 Domain of unknown function DUF302; Region: DUF302; cl01364 123214005644 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 123214005645 Thermus thermophilus SoxB and related proteins, N-terminal metallophosphatase domain; Region: MPP_SoxB_N; cd07411 123214005646 active site 123214005647 metal binding site [ion binding]; metal-binding site 123214005648 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 123214005649 Cytochrome c [Energy production and conversion]; Region: COG3258 123214005650 Cytochrome c [Energy production and conversion]; Region: COG3258 123214005651 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 123214005652 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 123214005653 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 123214005654 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 123214005655 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 123214005656 active site 123214005657 phosphorylation site [posttranslational modification] 123214005658 intermolecular recognition site; other site 123214005659 dimerization interface [polypeptide binding]; other site 123214005660 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 123214005661 Walker A motif; other site 123214005662 ATP binding site [chemical binding]; other site 123214005663 Walker B motif; other site 123214005664 arginine finger; other site 123214005665 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 123214005666 DsrE/DsrF-like family; Region: DrsE; cl00672 123214005667 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 123214005668 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 123214005669 TPR repeat; Region: TPR_11; pfam13414 123214005670 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 123214005671 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...; Region: LT_GEWL; cd00254 123214005672 N-acetyl-D-glucosamine binding site [chemical binding]; other site 123214005673 catalytic residue [active] 123214005674 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 123214005675 Lumazine binding domain; Region: Lum_binding; pfam00677 123214005676 Lumazine binding domain; Region: Lum_binding; pfam00677 123214005677 Ion channel; Region: Ion_trans_2; pfam07885 123214005678 TrkA-N domain; Region: TrkA_N; pfam02254 123214005679 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 123214005680 TrkA-C domain; Region: TrkA_C; pfam02080 123214005681 ATP-dependent DNA ligase; Provisional; Region: PRK01109 123214005682 Adenylation domain of archaeal and bacterial LigB-like DNA ligases; Region: Adenylation_DNA_ligase_Arch_LigB; cd07901 123214005683 active site 123214005684 DNA binding site [nucleotide binding] 123214005685 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit; Region: OBF_DNA_ligase_I; cd07969 123214005686 DNA binding site [nucleotide binding] 123214005687 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 123214005688 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 123214005689 multifunctional aminopeptidase A; Provisional; Region: PRK00913 123214005690 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 123214005691 interface (dimer of trimers) [polypeptide binding]; other site 123214005692 Substrate-binding/catalytic site; other site 123214005693 Zn-binding sites [ion binding]; other site 123214005694 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 123214005695 active site 123214005696 Superoxide reductase-like (SORL) domain; present in a family of mononuclear non-heme iron proteins that includes superoxide reductase and desulfoferrodoxin. Superoxide reductase-like proteins scavenge superoxide anion radicals as a defense mechanism...; Region: SORL; cl00014 123214005697 non-heme iron binding site [ion binding]; other site 123214005698 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 123214005699 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 123214005700 catalytic motif [active] 123214005701 Zn binding site [ion binding]; other site 123214005702 RibD C-terminal domain; Region: RibD_C; cl17279 123214005703 Nucleotidyltransferase (NT) domain of family X DNA Polymerases; Region: NT_POLXc; cd00141 123214005704 hypothetical protein; Provisional; Region: PRK08609 123214005705 active site 123214005706 primer binding site [nucleotide binding]; other site 123214005707 NTP binding site [chemical binding]; other site 123214005708 metal binding triad [ion binding]; metal-binding site 123214005709 Polymerase and Histidinol Phosphatase domain of bacterial polymerase X; Region: PHP_PolX; cd07436 123214005710 active site 123214005711 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 123214005712 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 123214005713 HIGH motif; other site 123214005714 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 123214005715 active site 123214005716 KMSKS motif; other site 123214005717 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 123214005718 active site 123214005719 catalytic residues [active] 123214005720 Domain of unknown function (DUF4142); Region: DUF4142; cl17876 123214005721 CRISPR/Cas system-associated RAMP superfamily protein Cas6; Region: Cas6-I-III; cl11443 123214005722 CRISPR/Cas system-associated RAMP superfamily protein Cas6; Region: Cas6-I-III; cl11443 123214005723 ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]; Region: OpuBA; COG1125 123214005724 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 123214005725 Walker A/P-loop; other site 123214005726 ATP binding site [chemical binding]; other site 123214005727 Q-loop/lid; other site 123214005728 ABC transporter signature motif; other site 123214005729 Walker B; other site 123214005730 D-loop; other site 123214005731 H-loop/switch region; other site 123214005732 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 123214005733 dimer interface [polypeptide binding]; other site 123214005734 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 123214005735 conserved gate region; other site 123214005736 putative PBP binding loops; other site 123214005737 ABC-ATPase subunit interface; other site 123214005738 TOBE domain; Region: TOBE; cl01440 123214005739 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 123214005740 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 123214005741 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; COG2005 123214005742 DNA-binding transcriptional regulator ModE; Provisional; Region: PRK10676 123214005743 molybdenum-pterin binding domain; Region: Mop; TIGR00638 123214005744 Molybdopterin-binding protein [Coenzyme metabolism]; Region: MopI; COG3585 123214005745 Myo-inositol-1-phosphate synthase; Region: NAD_binding_5; pfam07994 123214005746 Myo-inositol-1-phosphate synthase [Lipid metabolism]; Region: INO1; COG1260 123214005747 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 123214005748 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 123214005749 active site 123214005750 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 123214005751 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 123214005752 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 123214005753 Walker A/P-loop; other site 123214005754 ATP binding site [chemical binding]; other site 123214005755 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; smart00968 123214005756 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 123214005757 ABC transporter signature motif; other site 123214005758 Walker B; other site 123214005759 D-loop; other site 123214005760 H-loop/switch region; other site 123214005761 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 123214005762 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 123214005763 acyl-activating enzyme (AAE) consensus motif; other site 123214005764 putative AMP binding site [chemical binding]; other site 123214005765 putative active site [active] 123214005766 putative CoA binding site [chemical binding]; other site 123214005767 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 123214005768 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 123214005769 histidinol-phosphate aminotransferase; Region: hisC; TIGR01141 123214005770 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214005771 homodimer interface [polypeptide binding]; other site 123214005772 catalytic residue [active] 123214005773 Protein of unknown function (DUF1461); Region: DUF1461; cl01862 123214005774 Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones]; Region: COG1331 123214005775 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 123214005776 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 123214005777 Phosphatidylglycerophosphate synthase [Lipid metabolism]; Region: PgsA; COG0558 123214005778 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 123214005779 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 123214005780 active site 123214005781 nucleotide binding site [chemical binding]; other site 123214005782 HIGH motif; other site 123214005783 KMSKS motif; other site 123214005784 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; COG2005 123214005785 Type II secretory pathway, prepilin signal peptidase PulO and related peptidases [Cell motility and secretion / Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: PulO; COG1989 123214005786 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 123214005787 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 123214005788 N-ATPase, AtpR subunit; Region: AtpR; pfam12966 123214005789 Domain of unknown function (DUF4324); Region: DUF4324; pfam14212 123214005790 Domain of unknown function (DUF4323); Region: DUF4323; pfam14211 123214005791 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 123214005792 dimer interface [polypeptide binding]; other site 123214005793 substrate binding site [chemical binding]; other site 123214005794 metal binding sites [ion binding]; metal-binding site 123214005795 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 123214005796 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 123214005797 active site 123214005798 HIGH motif; other site 123214005799 nucleotide binding site [chemical binding]; other site 123214005800 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 123214005801 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 123214005802 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 123214005803 active site 123214005804 KMSKS motif; other site 123214005805 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 123214005806 tRNA binding surface [nucleotide binding]; other site 123214005807 anticodon binding site; other site 123214005808 Anticodon-binding domain of tRNA; Region: Anticodon_1; pfam08264 123214005809 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 123214005810 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 123214005811 argininosuccinate synthase; Provisional; Region: PRK13820 123214005812 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 123214005813 ANP binding site [chemical binding]; other site 123214005814 Substrate Binding Site II [chemical binding]; other site 123214005815 Substrate Binding Site I [chemical binding]; other site 123214005816 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 123214005817 binding surface 123214005818 TPR motif; other site 123214005819 TPR repeat; Region: TPR_11; pfam13414 123214005820 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 123214005821 binding surface 123214005822 TPR motif; other site 123214005823 Tetratricopeptide repeat; Region: TPR_12; pfam13424 123214005824 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 123214005825 TPR repeat; Region: TPR_11; pfam13414 123214005826 binding surface 123214005827 TPR motif; other site 123214005828 Tetratricopeptide repeat; Region: TPR_12; pfam13424 123214005829 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 123214005830 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 123214005831 active site 123214005832 catalytic tetrad [active] 123214005833 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 123214005834 MiaB-like tRNA modifying enzyme; Region: MiaB-like-C; TIGR01579 123214005835 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 123214005836 FeS/SAM binding site; other site 123214005837 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 123214005838 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 123214005839 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 123214005840 active site residue [active] 123214005841 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 123214005842 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...; Region: LT_GEWL; cd00254 123214005843 N-acetyl-D-glucosamine binding site [chemical binding]; other site 123214005844 catalytic residue [active] 123214005845 Domain of unknown function (DUF3393); Region: DUF3393; pfam11873 123214005846 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...; Region: LT_GEWL; cd00254 123214005847 N-acetyl-D-glucosamine binding site [chemical binding]; other site 123214005848 catalytic residue [active] 123214005849 LPP20 lipoprotein; Region: LPP20; pfam02169 123214005850 Curli production assembly/transport component CsgG; Region: CsgG; cl17434 123214005851 LPP20 lipoprotein; Region: LPP20; pfam02169 123214005852 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG0319 123214005853 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 123214005854 PhoH-like protein; Region: PhoH; pfam02562 123214005855 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 123214005856 RimM N-terminal domain; Region: RimM; pfam01782 123214005857 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 123214005858 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 123214005859 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 123214005860 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 123214005861 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 123214005862 binding surface 123214005863 Tetratricopeptide repeat; Region: TPR_16; pfam13432 123214005864 TPR motif; other site 123214005865 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 123214005866 binding surface 123214005867 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 123214005868 TPR motif; other site 123214005869 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 123214005870 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 123214005871 active site 123214005872 Riboflavin kinase; Region: Flavokinase; pfam01687 123214005873 recombination regulator RecX; Reviewed; Region: recX; PRK00117 123214005874 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 123214005875 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 123214005876 Walker A motif; other site 123214005877 ATP binding site [chemical binding]; other site 123214005878 Walker B motif; other site 123214005879 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 123214005880 recombinase A; Provisional; Region: recA; PRK09354 123214005881 hexamer interface [polypeptide binding]; other site 123214005882 Walker A motif; other site 123214005883 ATP binding site [chemical binding]; other site 123214005884 Walker B motif; other site 123214005885 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 123214005886 Topoisomerase IA [DNA replication, recombination, and repair]; Region: TopA; COG0550 123214005887 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 123214005888 active site 123214005889 metal binding site [ion binding]; metal-binding site 123214005890 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 123214005891 domain I; other site 123214005892 DNA binding groove [nucleotide binding] 123214005893 phosphate binding site [ion binding]; other site 123214005894 domain II; other site 123214005895 domain III; other site 123214005896 nucleotide binding site [chemical binding]; other site 123214005897 catalytic site [active] 123214005898 domain IV; other site 123214005899 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 123214005900 Ligand Binding Site [chemical binding]; other site 123214005901 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 123214005902 Peptidase family M23; Region: Peptidase_M23; pfam01551 123214005903 peptide chain release factor 2; Validated; Region: prfB; PRK00578 123214005904 PCRF domain; Region: PCRF; pfam03462 123214005905 RF-1 domain; Region: RF-1; pfam00472 123214005906 Uncharacterized conserved protein [Function unknown]; Region: COG1565 123214005907 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 123214005908 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 123214005909 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 123214005910 glutaminase active site [active] 123214005911 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 123214005912 dimer interface [polypeptide binding]; other site 123214005913 active site 123214005914 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 123214005915 dimer interface [polypeptide binding]; other site 123214005916 active site 123214005917 sulfate adenylyltransferase; Reviewed; Region: sat; PRK04149 123214005918 ATP-sulfurylase; Region: ATPS; cd00517 123214005919 active site 123214005920 HXXH motif; other site 123214005921 flexible loop; other site 123214005922 Domain of unknown function (DUF820). This family consists of hypothetical proteins that are greatly expanded in cyanobacteria. The proteins are found sporadically in other bacteria. They have been predicted to belong to the PD-(D/E)xK superfamily of...; Region: DUF820; cl01898 123214005923 putative active site [active] 123214005924 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 123214005925 metal binding triad [ion binding]; metal-binding site 123214005926 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 123214005927 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...; Region: CysQ; cd01638 123214005928 active site 123214005929 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 123214005930 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; cl17221 123214005931 transmembrane helices; other site 123214005932 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 123214005933 TrkA-C domain; Region: TrkA_C; pfam02080 123214005934 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; cl17221 123214005935 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...; Region: APSK; cd02027 123214005936 Predicted kinase [General function prediction only]; Region: COG0645 123214005937 ligand-binding site [chemical binding]; other site 123214005938 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 123214005939 active site 123214005940 NTP binding site [chemical binding]; other site 123214005941 metal binding triad [ion binding]; metal-binding site 123214005942 antibiotic binding site [chemical binding]; other site 123214005943 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; cl17552 123214005944 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 123214005945 G1P_cytidylyltransferase catalyzes the production of CDP-D-Glucose; Region: G1P_cytidylyltransferase; cd02524 123214005946 substrate binding site; other site 123214005947 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214005948 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 123214005949 NAD(P) binding site [chemical binding]; other site 123214005950 active site 123214005951 CDP-glucose 4,6-dehydratase; Region: CDP_4_6_dhtase; TIGR02622 123214005952 CDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: CDP_GD_SDR_e; cd05252 123214005953 NAD binding site [chemical binding]; other site 123214005954 homotetramer interface [polypeptide binding]; other site 123214005955 homodimer interface [polypeptide binding]; other site 123214005956 substrate binding site [chemical binding]; other site 123214005957 active site 123214005958 lipopolysaccharide biosynthesis protein RfbH; Provisional; Region: PRK15407 123214005959 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 123214005960 inhibitor-cofactor binding pocket; inhibition site 123214005961 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214005962 catalytic residue [active] 123214005963 CDP-tyvelose 2-epimerase, extended (e) SDRs; Region: CDP_TE_SDR_e; cd05258 123214005964 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 123214005965 NAD binding site [chemical binding]; other site 123214005966 homotetramer interface [polypeptide binding]; other site 123214005967 homodimer interface [polypeptide binding]; other site 123214005968 active site 123214005969 substrate binding site [chemical binding]; other site 123214005970 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 123214005971 Glycosyl transferase family 2; Region: Glycos_transf_2; pfam00535 123214005972 active site 123214005973 Wzx, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_Wzx_like; cd13128 123214005974 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 123214005975 O-Antigen ligase; Region: Wzy_C; cl04850 123214005976 Sulfotransferase domain; Region: Sulfotransfer_1; pfam00685 123214005977 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 123214005978 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 123214005979 NADP-binding site; other site 123214005980 homotetramer interface [polypeptide binding]; other site 123214005981 substrate binding site [chemical binding]; other site 123214005982 homodimer interface [polypeptide binding]; other site 123214005983 active site 123214005984 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 123214005985 This family is most closely related to the GT1 family of glycosyltransferases. wbaZ in Salmonella enterica has been shown to possess the mannosyl transferase activity. The members of this family are found in certain bacteria and Archaea; Region: GT1_wbaZ_like; cd03804 123214005986 putative ADP-binding pocket [chemical binding]; other site 123214005987 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 123214005988 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 123214005989 Substrate binding site; other site 123214005990 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 123214005991 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 123214005992 putative active site [active] 123214005993 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 123214005994 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 123214005995 NAD binding site [chemical binding]; other site 123214005996 homodimer interface [polypeptide binding]; other site 123214005997 active site 123214005998 substrate binding site [chemical binding]; other site 123214005999 exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase; Region: EPS_sugtrans; TIGR03025 123214006000 Bacterial sugar transferase; Region: Bac_transf; pfam02397 123214006001 Predicted integral membrane protein [Function unknown]; Region: COG5652 123214006002 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 123214006003 Domain of unknown function (DUF820). This family consists of hypothetical proteins that are greatly expanded in cyanobacteria. The proteins are found sporadically in other bacteria. They have been predicted to belong to the PD-(D/E)xK superfamily of...; Region: DUF820; cd06260 123214006004 putative active site [active] 123214006005 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; cl17552 123214006006 Domain of unknown function (DUF820). This family consists of hypothetical proteins that are greatly expanded in cyanobacteria. The proteins are found sporadically in other bacteria. They have been predicted to belong to the PD-(D/E)xK superfamily of...; Region: DUF820; cd06260 123214006007 putative active site [active] 123214006008 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 123214006009 catalytic center binding site [active] 123214006010 ATP binding site [chemical binding]; other site 123214006011 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 123214006012 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 123214006013 alanine--tRNA ligase; Region: alaS; TIGR00344 123214006014 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 123214006015 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 123214006016 active site 123214006017 motif I; other site 123214006018 motif II; other site 123214006019 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 123214006020 S-adenosylmethionine binding site [chemical binding]; other site 123214006021 Competence protein; Region: Competence; pfam03772 123214006022 Outer membrane protein family (DUF1597); Region: DUF1597; pfam07642 123214006023 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 123214006024 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 123214006025 Nitrogen regulatory protein P-II; Region: P-II; smart00938 123214006026 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 123214006027 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 123214006028 ring oligomerisation interface [polypeptide binding]; other site 123214006029 ATP/Mg binding site [chemical binding]; other site 123214006030 stacking interactions; other site 123214006031 hinge regions; other site 123214006032 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 123214006033 roof hairpin; other site 123214006034 oligomerisation interface [polypeptide binding]; other site