-- dump date 20140619_045439 -- class Genbank::misc_feature -- table misc_feature_note -- id note 1231072000001 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 1231072000002 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 1231072000003 Walker A motif; other site 1231072000004 ATP binding site [chemical binding]; other site 1231072000005 Walker B motif; other site 1231072000006 arginine finger; other site 1231072000007 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 1231072000008 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 1231072000009 Walker A motif; other site 1231072000010 ATP binding site [chemical binding]; other site 1231072000011 Walker B motif; other site 1231072000012 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 1231072000013 cardiolipin synthase; Region: bac_cardiolipin; TIGR04265 1231072000014 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 1231072000015 putative active site [active] 1231072000016 catalytic site [active] 1231072000017 catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_2; cd09112 1231072000018 putative active site [active] 1231072000019 catalytic site [active] 1231072000020 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 1231072000021 active site 1231072000022 Fe-S cluster binding site [ion binding]; other site 1231072000023 Protein of unknown function (DUF4230); Region: DUF4230; pfam14014 1231072000024 flavodoxin; Provisional; Region: PRK06242 1231072000025 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 1231072000026 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 1231072000027 Protein of unknown function (DUF1576); Region: DUF1576; pfam07613 1231072000028 Protein of unknown function (DUF1576); Region: DUF1576; pfam07613 1231072000029 NADH pyrophosphatase, a member of the Nudix hydrolase superfamily, catalyzes the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for...; Region: NADH_pyrophosphatase; cd03429 1231072000030 putative NADH binding site [chemical binding]; other site 1231072000031 putative active site [active] 1231072000032 nudix motif; other site 1231072000033 putative metal binding site [ion binding]; other site 1231072000034 putative DNA-binding transcriptional regulator; Reviewed; Region: PRK00347 1231072000035 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 1231072000036 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cd00640 1231072000037 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1231072000038 catalytic residue [active] 1231072000039 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 1231072000040 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 1231072000041 Walker A motif; other site 1231072000042 ATP binding site [chemical binding]; other site 1231072000043 Walker B motif; other site 1231072000044 arginine finger; other site 1231072000045 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1231072000046 SigmaK-factor processing regulatory protein BofA; Region: BofA; cl06466 1231072000047 recombination protein RecR; Reviewed; Region: recR; PRK00076 1231072000048 RecR protein; Region: RecR; pfam02132 1231072000049 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 1231072000050 putative active site [active] 1231072000051 putative metal-binding site [ion binding]; other site 1231072000052 tetramer interface [polypeptide binding]; other site 1231072000053 hypothetical protein; Validated; Region: PRK00153 1231072000054 DNA polymerase III subunits gamma and tau; Validated; Region: PRK05563 1231072000055 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 1231072000056 Walker A motif; other site 1231072000057 ATP binding site [chemical binding]; other site 1231072000058 Walker B motif; other site 1231072000059 arginine finger; other site 1231072000060 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 1231072000061 Domain of unknown function (DUF4250); Region: DUF4250; pfam14056 1231072000062 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 1231072000063 nucleoside/Zn binding site; other site 1231072000064 dimer interface [polypeptide binding]; other site 1231072000065 catalytic motif [active] 1231072000066 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1231072000067 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1231072000068 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 1231072000069 seryl-tRNA synthetase; Provisional; Region: PRK05431 1231072000070 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 1231072000071 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 1231072000072 dimer interface [polypeptide binding]; other site 1231072000073 active site 1231072000074 motif 1; other site 1231072000075 motif 2; other site 1231072000076 motif 3; other site 1231072000077 Protein of unknown function (DUF1667); Region: DUF1667; pfam07892 1231072000078 Predicted dehydrogenase [General function prediction only]; Region: COG0579 1231072000079 hydroxyglutarate oxidase; Provisional; Region: PRK11728 1231072000080 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 1231072000081 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1231072000082 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 1231072000083 dimer interface [polypeptide binding]; other site 1231072000084 phosphorylation site [posttranslational modification] 1231072000085 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 1231072000086 ATP binding site [chemical binding]; other site 1231072000087 Mg2+ binding site [ion binding]; other site 1231072000088 G-X-G motif; other site 1231072000089 Response regulator receiver domain; Region: Response_reg; pfam00072 1231072000090 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 1231072000091 active site 1231072000092 phosphorylation site [posttranslational modification] 1231072000093 intermolecular recognition site; other site 1231072000094 dimerization interface [polypeptide binding]; other site 1231072000095 Uncharacterized conserved protein [Function unknown]; Region: COG1615 1231072000096 Uncharacterized conserved protein [Function unknown]; Region: COG1615; cl09133 1231072000097 Predicted small molecule binding protein (contains 3H domain) [General function prediction only]; Region: COG1827 1231072000098 HTH domain; Region: HTH_11; pfam08279 1231072000099 3H domain; Region: 3H; pfam02829 1231072000100 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 1231072000101 DNA gyrase subunit A; Validated; Region: PRK05560 1231072000102 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 1231072000103 CAP-like domain; other site 1231072000104 active site 1231072000105 primary dimer interface [polypeptide binding]; other site 1231072000106 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1231072000107 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1231072000108 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1231072000109 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1231072000110 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1231072000111 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1231072000112 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 1231072000113 anchoring element; other site 1231072000114 dimer interface [polypeptide binding]; other site 1231072000115 ATP binding site [chemical binding]; other site 1231072000116 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 1231072000117 active site 1231072000118 putative metal-binding site [ion binding]; other site 1231072000119 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1231072000120 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 1231072000121 Mg2+ binding site [ion binding]; other site 1231072000122 G-X-G motif; other site 1231072000123 Glycosyl transferase family 41; Region: Glyco_transf_41; pfam13844 1231072000124 recombination protein F; Reviewed; Region: recF; PRK00064 1231072000125 ATP-binding cassette domain of RecF; Region: ABC_RecF; cd03242 1231072000126 Walker A/P-loop; other site 1231072000127 ATP binding site [chemical binding]; other site 1231072000128 Q-loop/lid; other site 1231072000129 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1231072000130 ABC transporter signature motif; other site 1231072000131 Walker B; other site 1231072000132 D-loop; other site 1231072000133 H-loop/switch region; other site 1231072000134 S4 domain; Region: S4_2; pfam13275 1231072000135 DNA polymerase III subunit beta; Validated; Region: PRK05643 1231072000136 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 1231072000137 putative DNA binding surface [nucleotide binding]; other site 1231072000138 dimer interface [polypeptide binding]; other site 1231072000139 beta-clamp/clamp loader binding surface; other site 1231072000140 beta-clamp/translesion DNA polymerase binding surface; other site 1231072000141 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 1231072000142 DnaA N-terminal domain; Region: DnaA_N; pfam11638 1231072000143 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 1231072000144 Walker A motif; other site 1231072000145 ATP binding site [chemical binding]; other site 1231072000146 Walker B motif; other site 1231072000147 arginine finger; other site 1231072000148 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 1231072000149 DnaA box-binding interface [nucleotide binding]; other site 1231072000150 Ribosomal protein L34; Region: Ribosomal_L34; cl00370 1231072000151 ribonuclease P; Reviewed; Region: rnpA; PRK00499 1231072000152 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 1231072000153 Predicted RNA-binding protein [General function prediction only]; Region: Jag; COG1847 1231072000154 jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta...; Region: jag_KH; cd02414 1231072000155 G-X-X-G motif; other site 1231072000156 R3H domain found in proteins homologous to Bacillus subtilus Jag, which is associated with SpoIIIJ. SpoIIIJ is necessary for the third stage of sporulation. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine...; Region: R3H_jag; cd02644 1231072000157 RxxxH motif; other site 1231072000158 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 1231072000159 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 1231072000160 trmE is a tRNA modification GTPase; Region: trmE; cd04164 1231072000161 G1 box; other site 1231072000162 GTP/Mg2+ binding site [chemical binding]; other site 1231072000163 Switch I region; other site 1231072000164 G2 box; other site 1231072000165 Switch II region; other site 1231072000166 G3 box; other site 1231072000167 G4 box; other site 1231072000168 G5 box; other site 1231072000169 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 1231072000170 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 1231072000171 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 1231072000172 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 1231072000173 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 1231072000174 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 1231072000175 S-adenosylmethionine binding site [chemical binding]; other site 1231072000176 nucleoid occlusion protein; Region: nucleoid_noc; TIGR04285 1231072000177 ParB-like nuclease domain; Region: ParBc; pfam02195 1231072000178 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 1231072000179 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 1231072000180 P-loop; other site 1231072000181 Magnesium ion binding site [ion binding]; other site 1231072000182 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 1231072000183 Magnesium ion binding site [ion binding]; other site 1231072000184 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 1231072000185 ParB-like nuclease domain; Region: ParB; smart00470 1231072000186 putative sporulation protein YyaC; Region: spore_YyaC; TIGR02841 1231072000187 sporulation integral membrane protein YtvI; Region: spore_ytvI; TIGR02872 1231072000188 Domain of unknown function DUF20; Region: UPF0118; pfam01594 1231072000189 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 1231072000190 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1231072000191 Bacterial protein of unknown function (DUF951); Region: DUF951; pfam06107 1231072000192 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 1231072000193 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 1231072000194 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 1231072000195 dimer interface [polypeptide binding]; other site 1231072000196 ssDNA binding site [nucleotide binding]; other site 1231072000197 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1231072000198 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 1231072000199 MazG-like family; Region: MazG-like; pfam12643 1231072000200 Predicted membrane protein (DUF2232); Region: DUF2232; cl01728 1231072000201 Predicted membrane protein (DUF2232); Region: DUF2232; pfam09991 1231072000202 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]; Region: COG3887 1231072000203 DHH family; Region: DHH; pfam01368 1231072000204 DHHA1 domain; Region: DHHA1; pfam02272 1231072000205 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 1231072000206 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 1231072000207 ATP-dependent protease, Lon family; Region: spore_lon_C; TIGR02903 1231072000208 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 1231072000209 Walker A motif; other site 1231072000210 ATP binding site [chemical binding]; other site 1231072000211 Walker B motif; other site 1231072000212 arginine finger; other site 1231072000213 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 1231072000214 replicative DNA helicase; Provisional; Region: PRK05595 1231072000215 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 1231072000216 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 1231072000217 Walker A motif; other site 1231072000218 ATP binding site [chemical binding]; other site 1231072000219 Walker B motif; other site 1231072000220 DNA binding loops [nucleotide binding] 1231072000221 Bacterial SH3 domain; Region: SH3_3; cl17532 1231072000222 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 1231072000223 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 1231072000224 hypothetical protein; Provisional; Region: PRK04435 1231072000225 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; cl17393 1231072000226 DNA-binding interface [nucleotide binding]; DNA binding site 1231072000227 C-terminal ACT domain of a small (; 147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains; Region: ACT_PheB-BS; cd04888 1231072000228 Protein of unknown function (DUF3006); Region: DUF3006; pfam11213 1231072000229 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 1231072000230 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 1231072000231 hydroxyglutarate oxidase; Provisional; Region: PRK11728 1231072000232 hybrid cluster protein-associated redox disulfide domain; Region: prismane_assoc; TIGR03980 1231072000233 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 1231072000234 Acyl-ACP thioesterase; Region: Acyl-ACP_TE; pfam01643 1231072000235 active site 1231072000236 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 1231072000237 active site 1231072000238 HI0933-like protein; Region: HI0933_like; pfam03486 1231072000239 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1231072000240 CoA binding domain; Region: CoA_binding_2; pfam13380 1231072000241 PEP synthetase regulatory protein; Provisional; Region: PRK05339 1231072000242 DNA replication protein DnaC; Validated; Region: PRK06835 1231072000243 DNA replication protein DnaC; Validated; Region: PRK06835 1231072000244 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 1231072000245 Walker A motif; other site 1231072000246 ATP binding site [chemical binding]; other site 1231072000247 Putative primosome component and related proteins [DNA replication, recombination, and repair]; Region: DnaD; COG3935 1231072000248 Replication initiation and membrane attachment; Region: DnaB_2; pfam07261 1231072000249 DnaD and phage-associated domain; Region: DnaD_dom; TIGR01446 1231072000250 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 1231072000251 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 1231072000252 FMN binding site [chemical binding]; other site 1231072000253 substrate binding site [chemical binding]; other site 1231072000254 putative catalytic residue [active] 1231072000255 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 1231072000256 MarR family; Region: MarR_2; pfam12802 1231072000257 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 1231072000258 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 1231072000259 dimer interface [polypeptide binding]; other site 1231072000260 active site 1231072000261 CoA binding pocket [chemical binding]; other site 1231072000262 acyl carrier protein; Provisional; Region: acpP; PRK00982 1231072000263 putative enoyl-[acyl-carrier-protein] reductase II; Region: enACPred_II; TIGR03151 1231072000264 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 1231072000265 FMN binding site [chemical binding]; other site 1231072000266 substrate binding site [chemical binding]; other site 1231072000267 putative catalytic residue [active] 1231072000268 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 1231072000269 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 1231072000270 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 1231072000271 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 1231072000272 NAD(P) binding site [chemical binding]; other site 1231072000273 homotetramer interface [polypeptide binding]; other site 1231072000274 homodimer interface [polypeptide binding]; other site 1231072000275 active site 1231072000276 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 1231072000277 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 1231072000278 dimer interface [polypeptide binding]; other site 1231072000279 active site 1231072000280 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 1231072000281 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 1231072000282 carboxyltransferase (CT) interaction site; other site 1231072000283 biotinylation site [posttranslational modification]; other site 1231072000284 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 1231072000285 biotin carboxylase; Validated; Region: PRK05586 1231072000286 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1231072000287 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1231072000288 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 1231072000289 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 1231072000290 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 1231072000291 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 1231072000292 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 1231072000293 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 1231072000294 Ferritin-like domain; Region: Ferritin; pfam00210 1231072000295 ferroxidase diiron center [ion binding]; other site 1231072000296 Subtilisin-like serine proteases [Posttranslational modification, protein turnover, chaperones]; Region: AprE; COG1404 1231072000297 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 1231072000298 active site 1231072000299 catalytic residues [active] 1231072000300 Protein of unknown function, DUF606; Region: DUF606; pfam04657 1231072000301 dUTPase; Region: dUTPase_2; pfam08761 1231072000302 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 1231072000303 active site 1231072000304 homodimer interface [polypeptide binding]; other site 1231072000305 metal binding site [ion binding]; metal-binding site 1231072000306 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 1231072000307 4Fe-4S binding domain; Region: Fer4_5; pfam12801 1231072000308 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 1231072000309 EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB...; Region: EcAsnRS_like_N; cd04318 1231072000310 putative dimer interface [polypeptide binding]; other site 1231072000311 putative anticodon binding site; other site 1231072000312 Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as...; Region: AsxRS_core; cd00776 1231072000313 homodimer interface [polypeptide binding]; other site 1231072000314 motif 1; other site 1231072000315 motif 2; other site 1231072000316 active site 1231072000317 motif 3; other site 1231072000318 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 1231072000319 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1231072000320 Coenzyme A binding pocket [chemical binding]; other site 1231072000321 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; pfam02683 1231072000322 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 1231072000323 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 1231072000324 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 1231072000325 catalytic residues [active] 1231072000326 stationary phase survival protein SurE; Provisional; Region: PRK13933 1231072000327 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 1231072000328 EamA-like transporter family; Region: EamA; pfam00892 1231072000329 EamA-like transporter family; Region: EamA; pfam00892 1231072000330 methionine sulfoxide reductase A; Provisional; Region: PRK14054 1231072000331 TraX protein; Region: TraX; cl05434 1231072000332 biotin synthase; Region: bioB; TIGR00433 1231072000333 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 1231072000334 FeS/SAM binding site; other site 1231072000335 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 1231072000336 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 1231072000337 M20 Peptidase Aminoacylase 1-like protein 2-like, amidohydrolase subfamily; Region: M20_ACY1L2_like; cd05672 1231072000338 metal binding site [ion binding]; metal-binding site 1231072000339 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1231072000340 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1231072000341 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 1231072000342 dimerization interface [polypeptide binding]; other site 1231072000343 F420-0:Gamma-glutamyl ligase; Region: F420_ligase; pfam01996 1231072000344 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 1231072000345 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 1231072000346 RNA binding surface [nucleotide binding]; other site 1231072000347 Pseudouridine synthase, Escherichia coli RluF like; Region: PseudoU_synth_RluF; cd02554 1231072000348 probable active site [active] 1231072000349 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 1231072000350 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 1231072000351 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 1231072000352 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1231072000353 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 1231072000354 dimer interface [polypeptide binding]; other site 1231072000355 phosphorylation site [posttranslational modification] 1231072000356 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 1231072000357 ATP binding site [chemical binding]; other site 1231072000358 Mg2+ binding site [ion binding]; other site 1231072000359 G-X-G motif; other site 1231072000360 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 1231072000361 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1231072000362 Walker A/P-loop; other site 1231072000363 ATP binding site [chemical binding]; other site 1231072000364 Q-loop/lid; other site 1231072000365 ABC transporter signature motif; other site 1231072000366 Walker B; other site 1231072000367 D-loop; other site 1231072000368 H-loop/switch region; other site 1231072000369 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1231072000370 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 1231072000371 active site 1231072000372 phosphorylation site [posttranslational modification] 1231072000373 intermolecular recognition site; other site 1231072000374 dimerization interface [polypeptide binding]; other site 1231072000375 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 1231072000376 DNA binding site [nucleotide binding] 1231072000377 TraX protein; Region: TraX; cl05434 1231072000378 Fibronectin-binding protein (FBP); Region: FBP; pfam07299 1231072000379 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 1231072000380 hypothetical protein; Provisional; Region: PRK05590 1231072000381 YyzF-like protein; Region: YyzF; pfam14116 1231072000382 Sporulation and spore germination; Region: Germane; pfam10646 1231072000383 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 1231072000384 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 1231072000385 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 1231072000386 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 1231072000387 hinge; other site 1231072000388 active site 1231072000389 AKAP7 2'5' RNA ligase-like domain; Region: AKAP7_NLS; pfam10469 1231072000390 glutamine synthetase, type I; Region: GlnA; TIGR00653 1231072000391 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 1231072000392 Domain of unknown function (DUF3783); Region: DUF3783; pfam12646 1231072000393 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 1231072000394 non-specific DNA binding site [nucleotide binding]; other site 1231072000395 salt bridge; other site 1231072000396 sequence-specific DNA binding site [nucleotide binding]; other site 1231072000397 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 1231072000398 Catalytic site [active] 1231072000399 Heme NO binding; Region: HNOB; pfam07700 1231072000400 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1231072000401 dimer interface [polypeptide binding]; other site 1231072000402 putative CheW interface [polypeptide binding]; other site 1231072000403 Uncharacterized membrane protein [Function unknown]; Region: COG3949 1231072000404 Predicted Fe-S oxidoreductase [General function prediction only]; Region: COG1242 1231072000405 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 1231072000406 FeS/SAM binding site; other site 1231072000407 Phosphosulfolactate phosphohydrolase and related enzymes [Coenzyme metabolism / General function prediction only]; Region: COG2045 1231072000408 2-phosphosulfolactate phosphatase; Provisional; Region: PRK00886 1231072000409 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 1231072000410 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 1231072000411 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 1231072000412 motif II; other site 1231072000413 Iron only hydrogenase large subunit, C-terminal domain [General function prediction only]; Region: COG4624 1231072000414 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 1231072000415 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 1231072000416 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1231072000417 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1231072000418 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1231072000419 pur operon repressor; Provisional; Region: PRK09213 1231072000420 Bacterial purine repressor, N-terminal; Region: PuR_N; pfam09182 1231072000421 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1231072000422 active site 1231072000423 regulatory protein SpoVG; Reviewed; Region: PRK13259 1231072000424 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14354 1231072000425 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 1231072000426 Substrate binding site; other site 1231072000427 Mg++ binding site; other site 1231072000428 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 1231072000429 active site 1231072000430 substrate binding site [chemical binding]; other site 1231072000431 CoA binding site [chemical binding]; other site 1231072000432 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 1231072000433 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 1231072000434 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1231072000435 active site 1231072000436 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1231072000437 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 1231072000438 active site 1231072000439 phosphorylation site [posttranslational modification] 1231072000440 intermolecular recognition site; other site 1231072000441 dimerization interface [polypeptide binding]; other site 1231072000442 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 1231072000443 DNA binding site [nucleotide binding] 1231072000444 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1231072000445 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 1231072000446 dimerization interface [polypeptide binding]; other site 1231072000447 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 1231072000448 dimer interface [polypeptide binding]; other site 1231072000449 phosphorylation site [posttranslational modification] 1231072000450 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 1231072000451 ATP binding site [chemical binding]; other site 1231072000452 Mg2+ binding site [ion binding]; other site 1231072000453 G-X-G motif; other site 1231072000454 periplasmic serine pepetdase DegS; Region: protease_degS; TIGR02038 1231072000455 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 1231072000456 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 1231072000457 protein binding site [polypeptide binding]; other site 1231072000458 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 1231072000459 putative active site [active] 1231072000460 catalytic residue [active] 1231072000461 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 1231072000462 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 1231072000463 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 1231072000464 ATP binding site [chemical binding]; other site 1231072000465 putative Mg++ binding site [ion binding]; other site 1231072000466 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 1231072000467 nucleotide binding region [chemical binding]; other site 1231072000468 ATP-binding site [chemical binding]; other site 1231072000469 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 1231072000470 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 1231072000471 SurA N-terminal domain; Region: SurA_N_3; cl07813 1231072000472 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 1231072000473 stage V sporulation protein T; Region: spore_V_T; TIGR02851 1231072000474 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 1231072000475 Stage V sporulation protein B, also known as Stage III sporulation protein F, and related proteins; Region: MATE_SpoVB_like; cd13124 1231072000476 Protein containing tetrapyrrole methyltransferase domain and MazG-like (predicted pyrophosphatase) domain [General function prediction only]; Region: COG3956 1231072000477 N-terminal S-AdoMet dependent methylase domain of Bacillus subtilis YabN and related proteins; Region: YabN_N; cd11723 1231072000478 putative SAM binding site [chemical binding]; other site 1231072000479 putative homodimer interface [polypeptide binding]; other site 1231072000480 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 1231072000481 homodimer interface [polypeptide binding]; other site 1231072000482 metal binding site [ion binding]; metal-binding site 1231072000483 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 1231072000484 homodimer interface [polypeptide binding]; other site 1231072000485 active site 1231072000486 putative chemical substrate binding site [chemical binding]; other site 1231072000487 metal binding site [ion binding]; metal-binding site 1231072000488 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 1231072000489 IHF dimer interface [polypeptide binding]; other site 1231072000490 IHF - DNA interface [nucleotide binding]; other site 1231072000491 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 1231072000492 RNA binding surface [nucleotide binding]; other site 1231072000493 YabP family; Region: YabP; cl06766 1231072000494 Spore cortex protein YabQ (Spore_YabQ); Region: Spore_YabQ; cl09801 1231072000495 Septum formation initiator; Region: DivIC; pfam04977 1231072000496 hypothetical protein; Provisional; Region: PRK05807 1231072000497 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_hs4; cd05692 1231072000498 RNA binding site [nucleotide binding]; other site 1231072000499 stage II sporulation protein E; Region: spore_II_E; TIGR02865 1231072000500 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 1231072000501 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 1231072000502 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 1231072000503 Ligand Binding Site [chemical binding]; other site 1231072000504 TilS substrate C-terminal domain; Region: TilS_C; smart00977 1231072000505 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1231072000506 active site 1231072000507 FtsH Extracellular; Region: FtsH_ext; pfam06480 1231072000508 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 1231072000509 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 1231072000510 Walker A motif; other site 1231072000511 ATP binding site [chemical binding]; other site 1231072000512 Walker B motif; other site 1231072000513 arginine finger; other site 1231072000514 Peptidase family M41; Region: Peptidase_M41; pfam01434 1231072000515 Predicted thioesterase [General function prediction only]; Region: COG5496 1231072000516 pantothenate kinase; Reviewed; Region: PRK13318 1231072000517 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 1231072000518 FMN binding site [chemical binding]; other site 1231072000519 active site 1231072000520 catalytic residues [active] 1231072000521 substrate binding site [chemical binding]; other site 1231072000522 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 1231072000523 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 1231072000524 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 1231072000525 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 1231072000526 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 1231072000527 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 1231072000528 dimer interface [polypeptide binding]; other site 1231072000529 putative anticodon binding site; other site 1231072000530 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 1231072000531 motif 1; other site 1231072000532 active site 1231072000533 motif 2; other site 1231072000534 motif 3; other site 1231072000535 glycyl-tRNA synthetase; Provisional; Region: PRK04173 1231072000536 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 1231072000537 motif 1; other site 1231072000538 Glycyl-tRNA synthetase (GlyRS)-like class II core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes. It is responsible for the attachment of glycine to the 3...; Region: GlyRS-like_core; cd00774 1231072000539 active site 1231072000540 motif 2; other site 1231072000541 motif 3; other site 1231072000542 GlyRS Glycyl-anticodon binding domain. GlyRS 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: GlyRS_anticodon; cd00858 1231072000543 anticodon binding site; other site 1231072000544 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01710 1231072000545 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1231072000546 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1231072000547 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 1231072000548 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 1231072000549 NAD-dependent deacetylase; Provisional; Region: PRK00481 1231072000550 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 1231072000551 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 1231072000552 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 1231072000553 metal binding site [ion binding]; metal-binding site 1231072000554 Inhibitor of sigma-G Gin; Region: Gin; pfam10764 1231072000555 Orn/Lys/Arg decarboxylase, major domain; Region: OKR_DC_1; pfam01276 1231072000556 Ornithine decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to ornithine decarboxylase (ODC), arginine decarboxylase (ADC) and lysine...; Region: Orn_deC_like; cd00615 1231072000557 homodimer interface [polypeptide binding]; other site 1231072000558 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1231072000559 catalytic residue [active] 1231072000560 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 1231072000561 Thymidylate kinase; Region: Thymidylate_kin; pfam02223 1231072000562 TMP-binding site; other site 1231072000563 ATP-binding site [chemical binding]; other site 1231072000564 Protein of unknown function (DUF970); Region: DUF970; pfam06153 1231072000565 DNA polymerase III subunit delta'; Validated; Region: PRK05564 1231072000566 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 1231072000567 Walker A motif; other site 1231072000568 ATP binding site [chemical binding]; other site 1231072000569 Walker B motif; other site 1231072000570 arginine finger; other site 1231072000571 PSP1 C-terminal conserved region; Region: PSP1; cl00770 1231072000572 PSP1 C-terminal conserved region; Region: PSP1; cl00770 1231072000573 Copper chaperone [Inorganic ion transport and metabolism]; Region: CopZ; COG2608 1231072000574 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 1231072000575 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 1231072000576 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 1231072000577 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 1231072000578 S-adenosylmethionine binding site [chemical binding]; other site 1231072000579 Predicted methyltransferases [General function prediction only]; Region: COG0313 1231072000580 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 1231072000581 putative SAM binding site [chemical binding]; other site 1231072000582 putative homodimer interface [polypeptide binding]; other site 1231072000583 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3883 1231072000584 The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; Region: BAR; cl12013 1231072000585 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 1231072000586 NlpC/P60 family; Region: NLPC_P60; pfam00877 1231072000587 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 1231072000588 SpoVT / AbrB like domain; Region: SpoVT_AbrB; smart00966 1231072000589 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea; Region: Transaldolase_FSA; cd00956 1231072000590 active site 1231072000591 intersubunit interactions; other site 1231072000592 catalytic residue [active] 1231072000593 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 1231072000594 Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a deformed (beta/alpha)8 barrel fold with 5- or 6-strands; Region: CE4_NodB_like_5s_6s; cd10918 1231072000595 putative active site [active] 1231072000596 putative metal binding site [ion binding]; other site 1231072000597 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 1231072000598 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 1231072000599 nucleotide binding site [chemical binding]; other site 1231072000600 MutS domain III; Region: MutS_III; pfam05192 1231072000601 ATP-binding cassette domain of MutS-like homolog; Region: ABC_MutS-like; cd03283 1231072000602 Walker A/P-loop; other site 1231072000603 ATP binding site [chemical binding]; other site 1231072000604 Q-loop/lid; other site 1231072000605 ABC transporter signature motif; other site 1231072000606 Walker B; other site 1231072000607 D-loop; other site 1231072000608 H-loop/switch region; other site 1231072000609 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 1231072000610 homotrimer interaction site [polypeptide binding]; other site 1231072000611 zinc binding site [ion binding]; other site 1231072000612 CDP-binding sites; other site 1231072000613 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 1231072000614 homotrimer interaction site [polypeptide binding]; other site 1231072000615 putative active site [active] 1231072000616 Bacterial Ig-like domain; Region: Big_5; pfam13205 1231072000617 Beta- N-acetylglucosaminidase [Carbohydrate transport and metabolism]; Region: LytD; COG4193 1231072000618 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; cl17361 1231072000619 Cation transport protein; Region: TrkH; cl17365 1231072000620 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 1231072000621 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 1231072000622 TrkA-N domain; Region: TrkA_N; pfam02254 1231072000623 TrkA-C domain; Region: TrkA_C; pfam02080 1231072000624 TrkA-N domain; Region: TrkA_N; pfam02254 1231072000625 TrkA-C domain; Region: TrkA_C; pfam02080 1231072000626 Uncharacterized membrane protein, required for spore maturation in B.subtilis. [General function prediction only]; Region: SpmA; COG2715 1231072000627 Uncharacterized membrane protein [Function unknown]; Region: SpmB; COG0700 1231072000628 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 1231072000629 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 1231072000630 Walker A/P-loop; other site 1231072000631 ATP binding site [chemical binding]; other site 1231072000632 Q-loop/lid; other site 1231072000633 ABC transporter signature motif; other site 1231072000634 Walker B; other site 1231072000635 D-loop; other site 1231072000636 H-loop/switch region; other site 1231072000637 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 1231072000638 Fe-S cluster binding site [ion binding]; other site 1231072000639 active site 1231072000640 methionyl-tRNA synthetase; Reviewed; Region: PRK12267 1231072000641 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 1231072000642 active site 1231072000643 HIGH motif; other site 1231072000644 KMSKS motif; other site 1231072000645 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 1231072000646 tRNA binding surface [nucleotide binding]; other site 1231072000647 anticodon binding site; other site 1231072000648 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 1231072000649 putative tRNA-binding site [nucleotide binding]; other site 1231072000650 dimer interface [polypeptide binding]; other site 1231072000651 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 1231072000652 active site 1231072000653 Domain of unknown function (DUF348); Region: DUF348; pfam03990 1231072000654 Domain of unknown function (DUF348); Region: DUF348; pfam03990 1231072000655 G5 domain; Region: G5; pfam07501 1231072000656 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3584 1231072000657 ribonuclease M5; Region: 5S_RNA_mat_M5; TIGR00334 1231072000658 TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea. RNase M5 catalyzes the maturation of 5S rRNA in low...; Region: TOPRIM_RNase_M5_like; cd01027 1231072000659 putative active site [active] 1231072000660 putative metal binding site [ion binding]; other site 1231072000661 Domain of unknown function (DUF4093); Region: DUF4093; pfam13331 1231072000662 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 1231072000663 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 1231072000664 S-adenosylmethionine binding site [chemical binding]; other site 1231072000665 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 1231072000666 Prolipoprotein diacylglyceryl transferase; Region: LGT; pfam01790 1231072000667 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 1231072000668 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Mrp; COG0489 1231072000669 Ferredoxin [Energy production and conversion]; Region: Fer; COG1141 1231072000670 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 1231072000671 putative proton-coupled thiamine transporter YuaJ; Region: thia_yuaJ; TIGR02357 1231072000672 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK07111 1231072000673 ATP cone domain; Region: ATP-cone; pfam03477 1231072000674 Class III ribonucleotide reductase; Region: RNR_III; cd01675 1231072000675 effector binding site; other site 1231072000676 active site 1231072000677 Zn binding site [ion binding]; other site 1231072000678 glycine loop; other site 1231072000679 4Fe-4S single cluster domain; Region: Fer4_12; pfam13353 1231072000680 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 1231072000681 FeS/SAM binding site; other site 1231072000682 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 1231072000683 dimerization interface [polypeptide binding]; other site 1231072000684 putative DNA binding site [nucleotide binding]; other site 1231072000685 putative Zn2+ binding site [ion binding]; other site 1231072000686 glutamate racemase; Provisional; Region: PRK00865 1231072000687 Domain of unknown function (DUF3870); Region: DUF3870; pfam12986 1231072000688 Bacterial Ig-like domain; Region: Big_5; pfam13205 1231072000689 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 1231072000690 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 1231072000691 active site 1231072000692 metal binding site [ion binding]; metal-binding site 1231072000693 Bacterial Ig-like domain (group 4); Region: Big_4; pfam07532 1231072000694 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 1231072000695 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 1231072000696 active site 1231072000697 metal binding site [ion binding]; metal-binding site 1231072000698 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 1231072000699 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1231072000700 HIGH motif; other site 1231072000701 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1231072000702 active site 1231072000703 KMSKS motif; other site 1231072000704 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 1231072000705 tRNA binding surface [nucleotide binding]; other site 1231072000706 anticodon binding site; other site 1231072000707 Transcriptional regulators [Transcription]; Region: PurR; COG1609 1231072000708 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 1231072000709 DNA binding site [nucleotide binding] 1231072000710 domain linker motif; other site 1231072000711 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 1231072000712 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 1231072000713 AAA domain; Region: AAA_12; pfam13087 1231072000714 Mannose-1-phosphate guanylyltransferase [Cell envelope biogenesis, outer membrane]; Region: {ManC}; COG0836 1231072000715 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 1231072000716 Substrate binding site; other site 1231072000717 Cupin domain; Region: Cupin_2; cl17218 1231072000718 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 1231072000719 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 1231072000720 FeS/SAM binding site; other site 1231072000721 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 1231072000722 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 1231072000723 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1231072000724 spore coat protein, CotS family; Region: spore_CotS; TIGR02906 1231072000725 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; cl17270 1231072000726 active site 1231072000727 ATP binding site [chemical binding]; other site 1231072000728 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 1231072000729 substrate binding site [chemical binding]; other site 1231072000730 spore coat protein, CotS family; Region: spore_CotS; TIGR02906 1231072000731 spore coat protein, CotS family; Region: spore_CotS; TIGR02906 1231072000732 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; cl17270 1231072000733 active site 1231072000734 ATP binding site [chemical binding]; other site 1231072000735 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 1231072000736 substrate binding site [chemical binding]; other site 1231072000737 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 1231072000738 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1231072000739 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; cl17270 1231072000740 spore coat protein, CotS family; Region: spore_CotS; TIGR02906 1231072000741 active site 1231072000742 ATP binding site [chemical binding]; other site 1231072000743 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 1231072000744 substrate binding site [chemical binding]; other site 1231072000745 2-aminoethylphosphonate ABC transporter substrate-binding protein; Provisional; Region: PRK15046 1231072000746 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 1231072000747 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 1231072000748 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 1231072000749 dimer interface [polypeptide binding]; other site 1231072000750 conserved gate region; other site 1231072000751 putative PBP binding loops; other site 1231072000752 ABC-ATPase subunit interface; other site 1231072000753 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 1231072000754 dimer interface [polypeptide binding]; other site 1231072000755 conserved gate region; other site 1231072000756 putative PBP binding loops; other site 1231072000757 ABC-ATPase subunit interface; other site 1231072000758 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 1231072000759 ATP-binding cassette domain of the polyamine transporter; Region: ABC_PotA_N; cd03300 1231072000760 Walker A/P-loop; other site 1231072000761 ATP binding site [chemical binding]; other site 1231072000762 Q-loop/lid; other site 1231072000763 ABC transporter signature motif; other site 1231072000764 Walker B; other site 1231072000765 D-loop; other site 1231072000766 H-loop/switch region; other site 1231072000767 Transcriptional antiterminator [Transcription]; Region: BglG; COG3711 1231072000768 Mga helix-turn-helix domain; Region: Mga; pfam05043 1231072000769 PRD domain; Region: PRD; pfam00874 1231072000770 PRD domain; Region: PRD; pfam00874 1231072000771 PTS_IIB_bgl_like: the PTS (phosphotransferase system) IIB domain of a family of sensory systems composed of a membrane-bound sugar-sensor (similar to BglF) and a transcription antiterminator (similar to BglG) which regulate expression of genes involved...; Region: PTS_IIB_bgl_like; cd05568 1231072000772 active site 1231072000773 P-loop; other site 1231072000774 phosphorylation site [posttranslational modification] 1231072000775 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 1231072000776 active site 1231072000777 phosphorylation site [posttranslational modification] 1231072000778 PTS_IIB: subunit IIB of enzyme II (EII) is the central energy-coupling domain of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In the multienzyme PTS complex, EII is a carbohydrate-specific permease consisting of two cytoplasmic...; Region: PTS_IIB; cl10014 1231072000779 active site 1231072000780 P-loop; other site 1231072000781 phosphorylation site [posttranslational modification] 1231072000782 PTS system sugar-specific permease component; Region: EIIC-GAT; cl04451 1231072000783 transcriptional antiterminator BglG; Provisional; Region: PRK09772 1231072000784 CAT RNA binding domain; Region: CAT_RBD; smart01061 1231072000785 PRD domain; Region: PRD; pfam00874 1231072000786 PRD domain; Region: PRD; pfam00874 1231072000787 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; COG1263 1231072000788 PTS system N-acetyl glucosamine specific transporter subunits IIABC; Provisional; Region: PRK10255 1231072000789 PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIB_glc; cd00212 1231072000790 active site turn [active] 1231072000791 phosphorylation site [posttranslational modification] 1231072000792 PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIA_glc; cd00210 1231072000793 HPr interaction site; other site 1231072000794 glycerol kinase (GK) interaction site [polypeptide binding]; other site 1231072000795 active site 1231072000796 phosphorylation site [posttranslational modification] 1231072000797 YabG peptidase U57; Region: Peptidase_U57; pfam05582 1231072000798 Protein of unknown function (DUF1021); Region: DUF1021; pfam06257 1231072000799 Domain of unknown function (DUF3794); Region: DUF3794; pfam12673 1231072000800 Domain of unknown function (DUF3794); Region: DUF3794; pfam12673 1231072000801 Domain of unknown function (DUF3794); Region: DUF3794; pfam12673 1231072000802 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 1231072000803 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 1231072000804 Type 1 glutamine amidotransferase (GATase1)-like domain found in cyanophycinase; Region: GAT1_cyanophycinase; cd03145 1231072000805 proposed catalytic triad [active] 1231072000806 active site nucleophile [active] 1231072000807 cyanophycin synthetase; Provisional; Region: PRK14016 1231072000808 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1231072000809 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1231072000810 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1231072000811 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00128 1231072000812 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 1231072000813 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 1231072000814 Bacillus/Clostridium GerA spore germination protein; Region: GerA; pfam03323 1231072000815 Spore germination protein; Region: Spore_permease; cl17796 1231072000816 germination protein, Ger(x)C family; Region: spore_ger_x_C; TIGR02887 1231072000817 Spore germination B3/ GerAC like, C-terminal; Region: Spore_GerAC; pfam05504 1231072000818 Stage II sporulation protein R (spore_II_R); Region: Spore_II_R; pfam09551 1231072000819 UDP-N-acetylglucosamine:LPS N-acetylglucosamine transferase [Cell envelope biogenesis, outer membrane]; Region: MurG; COG0707 1231072000820 Monogalactosyldiacylglycerol (MGDG) synthase; Region: MGDG_synth; pfam06925 1231072000821 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 1231072000822 germination protein YpeB; Region: spore_YpeB; TIGR02889 1231072000823 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 1231072000824 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 1231072000825 D-ala D-ala ligase C-terminus; Region: Dala_Dala_lig_C; pfam07478 1231072000826 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 1231072000827 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 1231072000828 Ligand Binding Site [chemical binding]; other site 1231072000829 Domain of unknown function (DUF814); Region: DUF814; pfam05670 1231072000830 Domain of unknown function (DUF1934); Region: DUF1934; pfam09148 1231072000831 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 1231072000832 transcription termination factor Rho; Provisional; Region: PRK12608 1231072000833 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 1231072000834 RNA binding site [nucleotide binding]; other site 1231072000835 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 1231072000836 multimer interface [polypeptide binding]; other site 1231072000837 Walker A motif; other site 1231072000838 ATP binding site [chemical binding]; other site 1231072000839 Walker B motif; other site 1231072000840 ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: PhnD; COG3221 1231072000841 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00019 1231072000842 thymidine kinase; Provisional; Region: PRK04296 1231072000843 Protein of unknown function (DUF1385); Region: DUF1385; cl01595 1231072000844 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 1231072000845 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 1231072000846 S-adenosylmethionine binding site [chemical binding]; other site 1231072000847 peptide chain release factor 1; Validated; Region: prfA; PRK00591 1231072000848 This domain is found in peptide chain release factors; Region: PCRF; smart00937 1231072000849 RF-1 domain; Region: RF-1; pfam00472 1231072000850 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 1231072000851 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 1231072000852 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 1231072000853 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 1231072000854 Low molecular weight phosphatase family; Region: LMWPc; cd00115 1231072000855 active site 1231072000856 ribose-5-phosphate isomerase B; Provisional; Region: PRK05571 1231072000857 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1231072000858 active site 1231072000859 Deoxycytidylate deaminase [Nucleotide transport and metabolism]; Region: ComEB; COG2131 1231072000860 active site 1231072000861 Zn binding site [ion binding]; other site 1231072000862 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 1231072000863 This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins. WecA is an UDP-N-acetylglucosamine (GlcNAc):undecaprenyl-phosphate (Und-P) GlcNAc-1-phosphate transferase that catalyzes the formation of a phosphodiester bond...; Region: GT_WecA_like; cd06853 1231072000864 Mg++ binding site [ion binding]; other site 1231072000865 putative catalytic motif [active] 1231072000866 substrate binding site [chemical binding]; other site 1231072000867 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 1231072000868 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 1231072000869 active site 1231072000870 homodimer interface [polypeptide binding]; other site 1231072000871 putative acyltransferase; Provisional; Region: PRK05790 1231072000872 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 1231072000873 dimer interface [polypeptide binding]; other site 1231072000874 active site 1231072000875 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 1231072000876 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 1231072000877 hinge; other site 1231072000878 active site 1231072000879 SpoIID/LytB domain; Region: SpoIID_LytB; TIGR02669 1231072000880 Stage II sporulation protein; Region: SpoIID; pfam08486 1231072000881 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1231072000882 Peptidase family M23; Region: Peptidase_M23; pfam01551 1231072000883 Stage III sporulation protein D; Region: SpoIIID; pfam12116 1231072000884 rod shape-determining protein Mbl; Provisional; Region: PRK13928 1231072000885 MreB and similar proteins; Region: MreB_like; cd10225 1231072000886 nucleotide binding site [chemical binding]; other site 1231072000887 Mg binding site [ion binding]; other site 1231072000888 putative protofilament interaction site [polypeptide binding]; other site 1231072000889 RodZ interaction site [polypeptide binding]; other site 1231072000890 Protein of unknown function (DUF1256); Region: DUF1256; pfam06866 1231072000891 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 1231072000892 Ligand Binding Site [chemical binding]; other site 1231072000893 S-adenosylmethionine synthetase; Validated; Region: PRK05250 1231072000894 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 1231072000895 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 1231072000896 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 1231072000897 helicase, putative, RecD/TraA family; Region: recD_rel; TIGR01448 1231072000898 AAA domain; Region: AAA_30; pfam13604 1231072000899 Family description; Region: UvrD_C_2; pfam13538 1231072000900 Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]; Region: comFA; COG4098 1231072000901 comF family protein; Region: comF; TIGR00201 1231072000902 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1231072000903 active site 1231072000904 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 1231072000905 30S subunit binding site; other site 1231072000906 Haloacid dehalogenase-like hydrolase; Region: Hydrolase_6; pfam13344 1231072000907 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 1231072000908 DEAD/DEAH box helicase; Region: DEAD; pfam00270 1231072000909 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 1231072000910 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 1231072000911 nucleotide binding region [chemical binding]; other site 1231072000912 ATP-binding site [chemical binding]; other site 1231072000913 Secretory pathway protein Sec39; Region: Sec39; pfam08314 1231072000914 SEC-C motif; Region: SEC-C; pfam02810 1231072000915 peptide chain release factor 2; Provisional; Region: PRK05589 1231072000916 This domain is found in peptide chain release factors; Region: PCRF; smart00937 1231072000917 RF-1 domain; Region: RF-1; pfam00472 1231072000918 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 1231072000919 M28 Zn-Peptidases containing a PA domain insert; Region: M28_like_PA; cd03877 1231072000920 Peptidase family M28; Region: Peptidase_M28; pfam04389 1231072000921 metal binding site [ion binding]; metal-binding site 1231072000922 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 1231072000923 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 1231072000924 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 1231072000925 S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression; Region: S1_Tex; cd05685 1231072000926 RNA binding site [nucleotide binding]; other site 1231072000927 Predicted membrane protein [Function unknown]; Region: COG3601 1231072000928 Protein of unknown function (DUF3816); Region: DUF3816; pfam12822 1231072000929 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 1231072000930 Predicted phosphohydrolase [General function prediction only]; Region: COG1768 1231072000931 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 1231072000932 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1655 1231072000933 Uncharacterized protein conserved in bacteria (DUF2225); Region: DUF2225; pfam09986 1231072000934 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 1231072000935 synthetase active site [active] 1231072000936 NTP binding site [chemical binding]; other site 1231072000937 metal binding site [ion binding]; metal-binding site 1231072000938 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 1231072000939 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 1231072000940 HIGH motif; other site 1231072000941 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1231072000942 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1231072000943 active site 1231072000944 KMSKS motif; other site 1231072000945 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 1231072000946 tRNA binding surface [nucleotide binding]; other site 1231072000947 Adenylyl cyclase (AC) class IV-like, a subgroup of the CYTH-like superfamily; Region: CYTH-like_AC_IV-like; cd07890 1231072000948 putative active site [active] 1231072000949 signature motif; other site 1231072000950 putative metal binding residues [ion binding]; other site 1231072000951 putative triphosphate binding site [ion binding]; other site 1231072000952 dimer interface [polypeptide binding]; other site 1231072000953 Coat F domain; Region: Coat_F; pfam07875 1231072000954 Phosphomannose isomerase [Carbohydrate transport and metabolism]; Region: ManA; COG1482 1231072000955 Alpha-Mannosidase Binding Domain of Atg19/34; Region: ABD; cl15429 1231072000956 37-kD nucleoid-associated bacterial protein; Region: NA37; pfam04245 1231072000957 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1; Region: TBP_aldolase_IIB; cd00947 1231072000958 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 1231072000959 intersubunit interface [polypeptide binding]; other site 1231072000960 active site 1231072000961 zinc binding site [ion binding]; other site 1231072000962 Na+ binding site [ion binding]; other site 1231072000963 Domain of unknown function (DUF4363); Region: DUF4363; pfam14276 1231072000964 Predicted membrane protein [Function unknown]; Region: COG2323 1231072000965 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 1231072000966 Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK); Region: UMPK_like; cd02028 1231072000967 active site 1231072000968 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 1231072000969 CDP-diacylglycerol--serine O-phosphatidyltransferase; Region: pssA; TIGR00473 1231072000970 FOG: CBS domain [General function prediction only]; Region: COG0517 1231072000971 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 1231072000972 putative lipid kinase; Reviewed; Region: PRK13059 1231072000973 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 1231072000974 spore cortex-lytic enzyme; Region: spore_SleB; TIGR02869 1231072000975 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 1231072000976 Cell Wall Hydrolase; Region: Hydrolase_2; pfam07486 1231072000977 serine O-acetyltransferase; Region: cysE; TIGR01172 1231072000978 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of...; Region: LbH_SAT; cd03354 1231072000979 trimer interface [polypeptide binding]; other site 1231072000980 active site 1231072000981 substrate binding site [chemical binding]; other site 1231072000982 CoA binding site [chemical binding]; other site 1231072000983 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 1231072000984 Reductive dehalogenase subunit; Region: Dehalogenase; pfam13486 1231072000985 4Fe-4S double cluster binding domain; Region: Fer4_16; pfam13484 1231072000986 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 1231072000987 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1231072000988 putative acyl-acceptor binding pocket; other site 1231072000989 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 1231072000990 endonuclease III; Region: ENDO3c; smart00478 1231072000991 minor groove reading motif; other site 1231072000992 helix-hairpin-helix signature motif; other site 1231072000993 substrate binding pocket [chemical binding]; other site 1231072000994 active site 1231072000995 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 1231072000996 Malic enzyme, N-terminal domain; Region: malic; pfam00390 1231072000997 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 1231072000998 putative NAD(P) binding site [chemical binding]; other site 1231072000999 competence damage-inducible protein A; Provisional; Region: PRK00549 1231072001000 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 1231072001001 putative MPT binding site; other site 1231072001002 Competence-damaged protein; Region: CinA; pfam02464 1231072001003 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 1231072001004 Repair protein; Region: Repair_PSII; pfam04536 1231072001005 Putative peptidoglycan binding domain; Region: PG_binding_4; pfam12229 1231072001006 VanW like protein; Region: VanW; pfam04294 1231072001007 G5 domain; Region: G5; pfam07501 1231072001008 MoxR-like ATPases [General function prediction only]; Region: COG0714 1231072001009 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 1231072001010 Walker A motif; other site 1231072001011 ATP binding site [chemical binding]; other site 1231072001012 Walker B motif; other site 1231072001013 arginine finger; other site 1231072001014 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 1231072001015 Protein of unknown function DUF58; Region: DUF58; pfam01882 1231072001016 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 1231072001017 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 1231072001018 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 1231072001019 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 1231072001020 active site 1231072001021 metal binding site [ion binding]; metal-binding site 1231072001022 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 1231072001023 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 1231072001024 active site 1231072001025 motif I; other site 1231072001026 motif II; other site 1231072001027 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 1231072001028 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 1231072001029 EDD domain protein, DegV family; Region: DegV; TIGR00762 1231072001030 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 1231072001031 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 1231072001032 Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea; Region: PBP1_BmpA_PnrA_like; cd06354 1231072001033 ligand binding site [chemical binding]; other site 1231072001034 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 1231072001035 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1231072001036 Walker A/P-loop; other site 1231072001037 ATP binding site [chemical binding]; other site 1231072001038 Q-loop/lid; other site 1231072001039 ABC transporter signature motif; other site 1231072001040 Walker B; other site 1231072001041 D-loop; other site 1231072001042 H-loop/switch region; other site 1231072001043 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 1231072001044 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 1231072001045 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 1231072001046 TM-ABC transporter signature motif; other site 1231072001047 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 1231072001048 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 1231072001049 TM-ABC transporter signature motif; other site 1231072001050 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 1231072001051 dimer interface [polypeptide binding]; other site 1231072001052 conserved gate region; other site 1231072001053 putative PBP binding loops; other site 1231072001054 ABC-ATPase subunit interface; other site 1231072001055 ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism]; Region: ProX; cl17891 1231072001056 Periplasmic glycine betaine/choline-binding (lipo)protein of an ABC-type transport system (osmoprotectant binding protein) [Cell envelope biogenesis, outer membrane]; Region: OpuBC; COG1732 1231072001057 ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]; Region: OpuBA; COG1125 1231072001058 ATP-binding cassette domain of the osmoprotectant transporter; Region: ABC_OpuCA_Osmoprotection; cd03295 1231072001059 Walker A/P-loop; other site 1231072001060 ATP binding site [chemical binding]; other site 1231072001061 Q-loop/lid; other site 1231072001062 ABC transporter signature motif; other site 1231072001063 Walker B; other site 1231072001064 D-loop; other site 1231072001065 H-loop/switch region; other site 1231072001066 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the ABC transporter OpuCA. OpuCA is the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing...; Region: CBS_pair_ABC_OpuCA_assoc2; cd04583 1231072001067 N(5)-(carboxyethyl)ornithine synthase; Region: ceo_syn; cd12181 1231072001068 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 1231072001069 putative active site [active] 1231072001070 putative ligand binding site [chemical binding]; other site 1231072001071 putative NAD(P) binding site [chemical binding]; other site 1231072001072 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 1231072001073 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 1231072001074 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 1231072001075 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 1231072001076 Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]; Region: DeoR; COG2390 1231072001077 Putative sugar-binding domain; Region: Sugar-bind; pfam04198 1231072001078 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 1231072001079 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 1231072001080 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 1231072001081 Phosphoglycerate kinase; Region: PGK; pfam00162 1231072001082 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 1231072001083 substrate binding site [chemical binding]; other site 1231072001084 hinge regions; other site 1231072001085 ADP binding site [chemical binding]; other site 1231072001086 catalytic site [active] 1231072001087 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 1231072001088 dimer interface [polypeptide binding]; other site 1231072001089 substrate binding site [chemical binding]; other site 1231072001090 catalytic triad [active] 1231072001091 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 1231072001092 phosphoglyceromutase; Provisional; Region: PRK05434 1231072001093 BPG-independent PGAM N-terminus (iPGM_N); Region: iPGM_N; cl17463 1231072001094 enolase; Provisional; Region: eno; PRK00077 1231072001095 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 1231072001096 dimer interface [polypeptide binding]; other site 1231072001097 metal binding site [ion binding]; metal-binding site 1231072001098 substrate binding pocket [chemical binding]; other site 1231072001099 H(+) -translocating inorganic pyrophosphatase; Region: PLN02255; cl11452 1231072001100 Inorganic H+ pyrophosphatase; Region: H_PPase; pfam03030 1231072001101 ribonuclease R; Region: RNase_R; TIGR02063 1231072001102 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 1231072001103 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 1231072001104 RNB domain; Region: RNB; pfam00773 1231072001105 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 1231072001106 RNA binding site [nucleotide binding]; other site 1231072001107 Uncharacterized protein conserved in bacteria (DUF2325); Region: DUF2325; cl01811 1231072001108 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 1231072001109 SmpB-tmRNA interface; other site 1231072001110 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1231072001111 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 1231072001112 active site 1231072001113 phosphorylation site [posttranslational modification] 1231072001114 intermolecular recognition site; other site 1231072001115 dimerization interface [polypeptide binding]; other site 1231072001116 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 1231072001117 DNA binding site [nucleotide binding] 1231072001118 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1231072001119 His Kinase A (phosphoacceptor) domain; Region: HisKA; smart00388 1231072001120 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 1231072001121 ATP binding site [chemical binding]; other site 1231072001122 Mg2+ binding site [ion binding]; other site 1231072001123 G-X-G motif; other site 1231072001124 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1231072001125 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1231072001126 Walker A/P-loop; other site 1231072001127 ATP binding site [chemical binding]; other site 1231072001128 Q-loop/lid; other site 1231072001129 ABC transporter signature motif; other site 1231072001130 Walker B; other site 1231072001131 D-loop; other site 1231072001132 H-loop/switch region; other site 1231072001133 putative selenium metabolism protein, YedE family; Region: seleno_YedE; TIGR04112 1231072001134 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 1231072001135 CPxP motif; other site 1231072001136 Sulphur transport; Region: Sulf_transp; pfam04143 1231072001137 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1231072001138 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1231072001139 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 1231072001140 putative dimerization interface [polypeptide binding]; other site 1231072001141 putative inner membrane protein; Provisional; Region: PRK11099 1231072001142 Sulphur transport; Region: Sulf_transp; pfam04143 1231072001143 Sulphur transport; Region: Sulf_transp; pfam04143 1231072001144 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4868 1231072001145 hypothetical protein; Provisional; Region: PRK13663 1231072001146 DNA topoisomerase III; Provisional; Region: PRK07726 1231072001147 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 1231072001148 active site 1231072001149 putative interdomain interaction site [polypeptide binding]; other site 1231072001150 putative metal-binding site [ion binding]; other site 1231072001151 putative nucleotide binding site [chemical binding]; other site 1231072001152 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 1231072001153 domain I; other site 1231072001154 DNA binding groove [nucleotide binding] 1231072001155 phosphate binding site [ion binding]; other site 1231072001156 domain II; other site 1231072001157 domain III; other site 1231072001158 nucleotide binding site [chemical binding]; other site 1231072001159 catalytic site [active] 1231072001160 domain IV; other site 1231072001161 Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]; Region: TopA; COG0551 1231072001162 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 1231072001163 DNA-binding site [nucleotide binding]; DNA binding site 1231072001164 RNA-binding motif; other site 1231072001165 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 1231072001166 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 1231072001167 Walker A/P-loop; other site 1231072001168 ATP binding site [chemical binding]; other site 1231072001169 Q-loop/lid; other site 1231072001170 ABC transporter signature motif; other site 1231072001171 Walker B; other site 1231072001172 D-loop; other site 1231072001173 H-loop/switch region; other site 1231072001174 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 1231072001175 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 1231072001176 dimer interface [polypeptide binding]; other site 1231072001177 conserved gate region; other site 1231072001178 putative PBP binding loops; other site 1231072001179 ABC-ATPase subunit interface; other site 1231072001180 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 1231072001181 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 1231072001182 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]; Region: COG1979 1231072001183 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 1231072001184 dimer interface [polypeptide binding]; other site 1231072001185 active site 1231072001186 metal binding site [ion binding]; metal-binding site 1231072001187 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; pfam01177 1231072001188 hybrid cluster protein; Provisional; Region: PRK05290 1231072001189 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 1231072001190 ACS interaction site; other site 1231072001191 CODH interaction site; other site 1231072001192 Hybrid cluster protein (HCP), formerly known as prismane, is thought to play a role in nitrogen metabolism but its specific function is unknown. HCP has three structural domains, an N-terminal alpha-helical domain, and two similar domains comprising a...; Region: HCP; cd01914 1231072001193 hybrid metal cluster; other site 1231072001194 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1231072001195 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 1231072001196 active site 1231072001197 phosphorylation site [posttranslational modification] 1231072001198 intermolecular recognition site; other site 1231072001199 dimerization interface [polypeptide binding]; other site 1231072001200 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 1231072001201 DNA binding site [nucleotide binding] 1231072001202 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1231072001203 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 1231072001204 dimer interface [polypeptide binding]; other site 1231072001205 phosphorylation site [posttranslational modification] 1231072001206 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 1231072001207 ATP binding site [chemical binding]; other site 1231072001208 Mg2+ binding site [ion binding]; other site 1231072001209 G-X-G motif; other site 1231072001210 Pleckstrin homology (PH)-like domains in bacteria (PHb); Region: PH-like_bacteria; cd13225 1231072001211 pentamer interface [polypeptide binding]; other site 1231072001212 dodecaamer interface [polypeptide binding]; other site 1231072001213 Predicted membrane protein [Function unknown]; Region: COG2323 1231072001214 Domain of unknown function (DUF4363); Region: DUF4363; pfam14276 1231072001215 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 1231072001216 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 1231072001217 Rieske Fe-S protein [Energy production and conversion]; Region: QcrA; COG0723 1231072001218 YhfW family, C-terminal Rieske domain; YhfW is a protein of unknown function with an N-terminal DadA-like (glycine/D-amino acid dehydrogenase) domain and a C-terminal Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain involved in...; Region: Rieske_YhfW_C; cd03477 1231072001219 [2Fe-2S] cluster binding site [ion binding]; other site 1231072001220 CGGC domain; Region: CGGC; pfam08821 1231072001221 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 1231072001222 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 1231072001223 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 1231072001224 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 1231072001225 Putative RNA methylase family UPF0020; Region: UPF0020; pfam01170 1231072001226 Region found in RelA / SpoT proteins; Region: RelA_SpoT; pfam04607 1231072001227 metal binding triad [ion binding]; metal-binding site 1231072001228 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 1231072001229 Ferritin-like domain; Region: Ferritin; pfam00210 1231072001230 dinuclear metal binding motif [ion binding]; other site 1231072001231 M20 Peptidase T like enzymes specifically cleave tripeptides; Region: M20_peptT_like; cd05683 1231072001232 peptidase T-like protein; Region: PepT-like; TIGR01883 1231072001233 metal binding site [ion binding]; metal-binding site 1231072001234 putative dimer interface [polypeptide binding]; other site 1231072001235 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 1231072001236 MarR family; Region: MarR; pfam01047 1231072001237 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1231072001238 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1231072001239 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1231072001240 Walker A/P-loop; other site 1231072001241 ATP binding site [chemical binding]; other site 1231072001242 Q-loop/lid; other site 1231072001243 ABC transporter signature motif; other site 1231072001244 Walker B; other site 1231072001245 D-loop; other site 1231072001246 H-loop/switch region; other site 1231072001247 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1231072001248 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1231072001249 ATP-binding cassette domain of glucan transporter and related proteins, subfamily C; Region: ABCC_Glucan_exporter_like; cd03254 1231072001250 Walker A/P-loop; other site 1231072001251 ATP binding site [chemical binding]; other site 1231072001252 Q-loop/lid; other site 1231072001253 ABC transporter signature motif; other site 1231072001254 Walker B; other site 1231072001255 D-loop; other site 1231072001256 H-loop/switch region; other site 1231072001257 Membrane domain of glycerophosphoryl diester phosphodiesterase; Region: GPDPase_memb; pfam10110 1231072001258 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 1231072001259 catalytic site [active] 1231072001260 active site 1231072001261 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 1231072001262 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 1231072001263 active site 1231072001264 conjugal transfer protein TraL; Provisional; Region: PRK13886 1231072001265 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 1231072001266 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1231072001267 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 1231072001268 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 1231072001269 flavodoxin; Provisional; Region: PRK05568 1231072001270 Protein of unknown function (DUF3793); Region: DUF3793; pfam12672 1231072001271 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 1231072001272 metal binding site [ion binding]; metal-binding site 1231072001273 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 1231072001274 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1231072001275 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 1231072001276 active site 1231072001277 phosphorylation site [posttranslational modification] 1231072001278 intermolecular recognition site; other site 1231072001279 dimerization interface [polypeptide binding]; other site 1231072001280 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 1231072001281 DNA binding site [nucleotide binding] 1231072001282 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1231072001283 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 1231072001284 dimerization interface [polypeptide binding]; other site 1231072001285 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 1231072001286 dimer interface [polypeptide binding]; other site 1231072001287 phosphorylation site [posttranslational modification] 1231072001288 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 1231072001289 ATP binding site [chemical binding]; other site 1231072001290 Mg2+ binding site [ion binding]; other site 1231072001291 G-X-G motif; other site 1231072001292 tol-pal system beta propeller repeat protein TolB; Region: propeller_TolB; TIGR02800 1231072001293 Dipeptidyl peptidase IV (DPP IV) N-terminal region; Region: DPPIV_N; pfam00930 1231072001294 Protein of unknown function (DUF3888); Region: DUF3888; pfam13027 1231072001295 DNA polymerase IV; Provisional; Region: PRK14133 1231072001296 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 1231072001297 active site 1231072001298 DNA binding site [nucleotide binding] 1231072001299 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 1231072001300 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 1231072001301 Clostripain family; Region: Peptidase_C11; pfam03415 1231072001302 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 1231072001303 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 1231072001304 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_8; cd13134 1231072001305 hypothetical protein; Reviewed; Region: PRK12275 1231072001306 four helix bundle protein; Region: TIGR02436 1231072001307 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 1231072001308 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 1231072001309 CoA enzyme activase uncharacterized domain (DUF2229); Region: DUF2229; cl17855 1231072001310 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3581 1231072001311 Activator of 2-hydroxyglutaryl-CoA dehydratase (HSP70-class ATPase domain) [Lipid metabolism]; Region: COG1924 1231072001312 BadF/BadG/BcrA/BcrD ATPase family; Region: BcrAD_BadFG; cl17271 1231072001313 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 1231072001314 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 1231072001315 G1 box; other site 1231072001316 GTP/Mg2+ binding site [chemical binding]; other site 1231072001317 Switch I region; other site 1231072001318 G2 box; other site 1231072001319 G3 box; other site 1231072001320 Switch II region; other site 1231072001321 G4 box; other site 1231072001322 G5 box; other site 1231072001323 Nucleoside recognition; Region: Gate; pfam07670 1231072001324 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 1231072001325 Nucleoside recognition; Region: Gate; pfam07670 1231072001326 FeoA domain; Region: FeoA; pfam04023 1231072001327 Iron dependent repressor, N-terminal DNA binding domain; Region: Fe_dep_repress; pfam01325 1231072001328 Helix-turn-helix diphteria tox regulatory element; Region: HTH_DTXR; smart00529 1231072001329 Iron dependent repressor, metal binding and dimerisation domain; Region: Fe_dep_repr_C; pfam02742 1231072001330 phosphoglucosamine mutase; Region: Arch_GlmM; TIGR03990 1231072001331 The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a...; Region: PMM_PGM; cd03089 1231072001332 active site 1231072001333 substrate binding site [chemical binding]; other site 1231072001334 metal binding site [ion binding]; metal-binding site 1231072001335 Putative rRNA methylase; Region: rRNA_methylase; pfam06962 1231072001336 Sensory domain found in PocR; Region: PocR; pfam10114 1231072001337 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1231072001338 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 1231072001339 dimer interface [polypeptide binding]; other site 1231072001340 phosphorylation site [posttranslational modification] 1231072001341 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 1231072001342 ATP binding site [chemical binding]; other site 1231072001343 Mg2+ binding site [ion binding]; other site 1231072001344 G-X-G motif; other site 1231072001345 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 1231072001346 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 1231072001347 hypothetical protein; Provisional; Region: PRK05590 1231072001348 SEC-C motif; Region: SEC-C; pfam02810 1231072001349 Acyltransferase family; Region: Acyl_transf_3; pfam01757 1231072001350 Predicted O-acyltransferase [General function prediction only]; Region: COG3274 1231072001351 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001352 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001353 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001354 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 1231072001355 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 1231072001356 Collagen binding domain; Region: Collagen_bind; pfam05737 1231072001357 Cna protein B-type domain; Region: Cna_B; pfam05738 1231072001358 Cna protein B-type domain; Region: Cna_B; pfam05738 1231072001359 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 1231072001360 Domain of unknown function (DUF2935); Region: DUF2935; pfam11155 1231072001361 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 1231072001362 HAMP domain; Region: HAMP; pfam00672 1231072001363 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1231072001364 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1231072001365 dimer interface [polypeptide binding]; other site 1231072001366 putative CheW interface [polypeptide binding]; other site 1231072001367 Citrate transporter; Region: CitMHS; pfam03600 1231072001368 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1231072001369 Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA dehydrogenases; Region: SCAD_SBCAD; cd01158 1231072001370 FAD binding site [chemical binding]; other site 1231072001371 homotetramer interface [polypeptide binding]; other site 1231072001372 substrate binding pocket [chemical binding]; other site 1231072001373 catalytic base [active] 1231072001374 Acyl CoA:acetate/3-ketoacid CoA transferase [Lipid metabolism]; Region: COG4670 1231072001375 Coenzyme A transferase; Region: CoA_trans; smart00882 1231072001376 Coenzyme A transferase; Region: CoA_trans; cl17247 1231072001377 3-hydroxybutyryl-CoA dehydratase; Validated; Region: PRK05809 1231072001378 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 1231072001379 substrate binding site [chemical binding]; other site 1231072001380 oxyanion hole (OAH) forming residues; other site 1231072001381 trimer interface [polypeptide binding]; other site 1231072001382 Predicted transcriptional regulators [Transcription]; Region: COG1733 1231072001383 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 1231072001384 putative DNA binding site [nucleotide binding]; other site 1231072001385 dimerization interface [polypeptide binding]; other site 1231072001386 putative Zn2+ binding site [ion binding]; other site 1231072001387 mechanosensitive channel MscS; Provisional; Region: PRK10334 1231072001388 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1231072001389 Acetyl-CoA hydrolase [Energy production and conversion]; Region: ACH1; COG0427 1231072001390 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 1231072001391 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 1231072001392 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 1231072001393 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 1231072001394 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1231072001395 HlyD family secretion protein; Region: HlyD_3; pfam13437 1231072001396 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1231072001397 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1231072001398 Walker A/P-loop; other site 1231072001399 ATP binding site [chemical binding]; other site 1231072001400 Q-loop/lid; other site 1231072001401 ABC transporter signature motif; other site 1231072001402 Walker B; other site 1231072001403 D-loop; other site 1231072001404 H-loop/switch region; other site 1231072001405 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 1231072001406 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 1231072001407 FtsX-like permease family; Region: FtsX; pfam02687 1231072001408 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 1231072001409 Outer membrane efflux protein; Region: OEP; pfam02321 1231072001410 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001411 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001412 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001413 Predicted membrane protein [Function unknown]; Region: COG1511 1231072001414 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 1231072001415 Predicted membrane protein [Function unknown]; Region: COG1511 1231072001416 YhgE/Pip C-terminal domain; Region: pip_yhgE_Cterm; TIGR03062 1231072001417 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 1231072001418 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 1231072001419 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 1231072001420 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 1231072001421 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 1231072001422 Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond...; Region: LRR_RI; cl15309 1231072001423 Leucine-rich repeats; other site 1231072001424 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 1231072001425 Substrate binding site [chemical binding]; other site 1231072001426 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 1231072001427 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 1231072001428 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 1231072001429 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 1231072001430 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 1231072001431 Leucine rich repeat; Region: LRR_8; pfam13855 1231072001432 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 1231072001433 Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond...; Region: LRR_RI; cl15309 1231072001434 Leucine rich repeat; Region: LRR_8; pfam13855 1231072001435 Leucine-rich repeats; other site 1231072001436 Substrate binding site [chemical binding]; other site 1231072001437 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 1231072001438 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 1231072001439 Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond...; Region: LRR_RI; cl15309 1231072001440 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 1231072001441 Leucine-rich repeats; other site 1231072001442 Substrate binding site [chemical binding]; other site 1231072001443 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 1231072001444 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 1231072001445 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 1231072001446 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 1231072001447 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 1231072001448 Transposase IS200 like; Region: Y1_Tnp; pfam01797 1231072001449 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; cl07055 1231072001450 DnaA box-binding interface [nucleotide binding]; other site 1231072001451 Pyridoxal kinase plays a key role in the synthesis of the active coenzyme pyridoxal-5'-phosphate (PLP), by catalyzing the phosphorylation of the precursor vitamin B6 in the presence of Zn2+ and ATP. Mammals are unable to synthesize PLP de novo and...; Region: pyridoxal_pyridoxamine_kinase; cd01173 1231072001452 dimer interface [polypeptide binding]; other site 1231072001453 pyridoxal binding site [chemical binding]; other site 1231072001454 ATP binding site [chemical binding]; other site 1231072001455 Fe-S oxidoreductases [Energy production and conversion]; Region: COG0731 1231072001456 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 1231072001457 FeS/SAM binding site; other site 1231072001458 Predicted integral membrane protein [Function unknown]; Region: COG5652 1231072001459 N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism]; Region: NagA; COG1820 1231072001460 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of N-acetyl-glucosamine-6-phosphate (GlcNAc-6-P) to glucosamine 6-phosphate and acetate. This is the first committed step in the biosynthetic pathway to...; Region: NagA; cd00854 1231072001461 active site 1231072001462 dimer interface [polypeptide binding]; other site 1231072001463 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001464 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001465 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001466 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 1231072001467 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1231072001468 DNA-binding site [nucleotide binding]; DNA binding site 1231072001469 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 1231072001470 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 1231072001471 Iron-containing alcohol dehydrogenases-like; Region: Fe-ADH6; cd08194 1231072001472 putative active site [active] 1231072001473 metal binding site [ion binding]; metal-binding site 1231072001474 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1; Region: TBP_aldolase_IIB; cd00947 1231072001475 intersubunit interface [polypeptide binding]; other site 1231072001476 active site 1231072001477 zinc binding site [ion binding]; other site 1231072001478 Na+ binding site [ion binding]; other site 1231072001479 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 1231072001480 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the...; Region: KdgK; cd01166 1231072001481 substrate binding site [chemical binding]; other site 1231072001482 ATP binding site [chemical binding]; other site 1231072001483 KduI/IolB family; Region: KduI; pfam04962 1231072001484 Acetolactate synthase [Amino acid transport and metabolism]; Region: COG3962 1231072001485 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 1231072001486 PYR/PP interface [polypeptide binding]; other site 1231072001487 dimer interface [polypeptide binding]; other site 1231072001488 TPP binding site [chemical binding]; other site 1231072001489 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 1231072001490 Thiamine pyrophosphate (TPP) family, IolD subfamily, TPP-binding module; composed of proteins similar to Rhizobium leguminosarum bv. viciae IolD. IolD plays an important role in myo-inositol catabolism; Region: TPP_IolD; cd02003 1231072001491 TPP-binding site; other site 1231072001492 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 1231072001493 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 1231072001494 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 1231072001495 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 1231072001496 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 1231072001497 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 1231072001498 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 1231072001499 putative transporter; Provisional; Region: PRK10484 1231072001500 uncharacterized SLC5 subfamily, Escherichia coli YidK-like; solute binding domain; Region: SLC5sbd_YidK; cd10328 1231072001501 Na binding site [ion binding]; other site 1231072001502 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001503 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001504 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001505 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001506 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001507 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001508 Peptidase M14-like domain; uncharacterized subgroup; Region: M14-like_1_5; cd06242 1231072001509 putative active site [active] 1231072001510 Zn binding site [ion binding]; other site 1231072001511 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001512 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001513 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001514 Leucine rich repeat; Region: LRR_8; pfam13855 1231072001515 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001516 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001517 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001518 Bacterial Ig-like domain (group 4); Region: Big_4; pfam07532 1231072001519 Bacterial Ig-like domain (group 4); Region: Big_4; pfam07532 1231072001520 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001521 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001522 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001523 Transposase IS200 like; Region: Y1_Tnp; cl00848 1231072001524 Predicted membrane protein [Function unknown]; Region: COG1971 1231072001525 Domain of unknown function DUF; Region: DUF204; pfam02659 1231072001526 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 1231072001527 metal binding site 2 [ion binding]; metal-binding site 1231072001528 putative DNA binding helix; other site 1231072001529 metal binding site 1 [ion binding]; metal-binding site 1231072001530 dimer interface [polypeptide binding]; other site 1231072001531 structural Zn2+ binding site [ion binding]; other site 1231072001532 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 1231072001533 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1231072001534 Zn2+ binding site [ion binding]; other site 1231072001535 Mg2+ binding site [ion binding]; other site 1231072001536 Rhomboid family; Region: Rhomboid; pfam01694 1231072001537 Peptidase family M41; Region: Peptidase_M41; pfam01434 1231072001538 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 1231072001539 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 1231072001540 Walker A motif; other site 1231072001541 ATP binding site [chemical binding]; other site 1231072001542 Walker B motif; other site 1231072001543 arginine finger; other site 1231072001544 Peptidase family M41; Region: Peptidase_M41; pfam01434 1231072001545 Uncharacterized conserved protein [Function unknown]; Region: COG3339 1231072001546 RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner; Region: RNase_H; cl14782 1231072001547 active site 1231072001548 RNA/DNA hybrid binding site [nucleotide binding]; other site 1231072001549 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 1231072001550 Catalytic NodB homology domain of Streptococcus mutans polysaccharide deacetylase PgdA, Bacillus subtilis YheN, and similar proteins; Region: CE4_SmPgdA_like; cd10944 1231072001551 NodB motif; other site 1231072001552 active site 1231072001553 catalytic site [active] 1231072001554 Zn binding site [ion binding]; other site 1231072001555 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 1231072001556 Sulfatase; Region: Sulfatase; pfam00884 1231072001557 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 1231072001558 catalytic triad [active] 1231072001559 UDP-N-acetylmuramyl tripeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurE; COG0769 1231072001560 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1231072001561 Domain of unknown function (DUF1727); Region: DUF1727; pfam08353 1231072001562 Bacterial capsule synthesis protein PGA_cap; Region: PGA_cap; smart00854 1231072001563 CapA and related proteins, metallophosphatase domain; Region: MPP_CapA; cd07381 1231072001564 putative active site [active] 1231072001565 putative metal binding site [ion binding]; other site 1231072001566 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 1231072001567 TPR motif; other site 1231072001568 Tetratricopeptide repeat; Region: TPR_12; pfam13424 1231072001569 binding surface 1231072001570 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 1231072001571 Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]; Region: ComEC; COG2333 1231072001572 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 1231072001573 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 1231072001574 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1231072001575 putative acyl-acceptor binding pocket; other site 1231072001576 RNA polymerase sigma factor; Provisional; Region: PRK11924 1231072001577 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1231072001578 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 1231072001579 DNA binding residues [nucleotide binding] 1231072001580 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 1231072001581 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 1231072001582 Walker A motif; other site 1231072001583 ATP binding site [chemical binding]; other site 1231072001584 Walker B motif; other site 1231072001585 arginine finger; other site 1231072001586 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 1231072001587 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1231072001588 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1231072001589 substrate binding pocket [chemical binding]; other site 1231072001590 membrane-bound complex binding site; other site 1231072001591 hinge residues; other site 1231072001592 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1231072001593 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1231072001594 substrate binding pocket [chemical binding]; other site 1231072001595 membrane-bound complex binding site; other site 1231072001596 hinge residues; other site 1231072001597 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 1231072001598 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 1231072001599 dimer interface [polypeptide binding]; other site 1231072001600 conserved gate region; other site 1231072001601 putative PBP binding loops; other site 1231072001602 ABC-ATPase subunit interface; other site 1231072001603 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 1231072001604 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 1231072001605 Walker A/P-loop; other site 1231072001606 ATP binding site [chemical binding]; other site 1231072001607 Q-loop/lid; other site 1231072001608 ABC transporter signature motif; other site 1231072001609 Walker B; other site 1231072001610 D-loop; other site 1231072001611 H-loop/switch region; other site 1231072001612 argininosuccinate synthase; Provisional; Region: PRK13820 1231072001613 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 1231072001614 ANP binding site [chemical binding]; other site 1231072001615 Substrate Binding Site II [chemical binding]; other site 1231072001616 Substrate Binding Site I [chemical binding]; other site 1231072001617 argininosuccinate lyase; Provisional; Region: PRK00855 1231072001618 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 1231072001619 active sites [active] 1231072001620 tetramer interface [polypeptide binding]; other site 1231072001621 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 1231072001622 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 1231072001623 glutaminase A; Region: Gln_ase; TIGR03814 1231072001624 Glutaminase [Amino acid transport and metabolism]; Region: GlsA; COG2066 1231072001625 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 1231072001626 DNA-binding transcriptional regulator AsnC; Provisional; Region: PRK11179 1231072001627 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 1231072001628 putative DNA binding site [nucleotide binding]; other site 1231072001629 putative Zn2+ binding site [ion binding]; other site 1231072001630 AsnC family; Region: AsnC_trans_reg; pfam01037 1231072001631 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 1231072001632 homotrimer interaction site [polypeptide binding]; other site 1231072001633 putative active site [active] 1231072001634 threonine synthase; Validated; Region: PRK06260 1231072001635 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 1231072001636 homodimer interface [polypeptide binding]; other site 1231072001637 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1231072001638 catalytic residue [active] 1231072001639 Zn-dependent dipeptidase, microsomal dipeptidase homolog [Amino acid transport and metabolism]; Region: COG2355 1231072001640 renal dipeptidase (rDP), best studied in mammals and also called membrane or microsomal dipeptidase, is a membrane-bound glycoprotein hydrolyzing dipeptides and is involved in hydrolytic metabolism of penem and carbapenem beta-lactam antibiotics; Region: rDP_like; cd01301 1231072001641 active site 1231072001642 dimer interface [polypeptide binding]; other site 1231072001643 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 1231072001644 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; cl12060 1231072001645 Metal-binding active site; metal-binding site 1231072001646 A type 1 glutamine amidotransferase (GATase1)-like domain found in PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_like; cd03134 1231072001647 intracellular protease, PfpI family; Region: PfpI; TIGR01382 1231072001648 proposed catalytic triad [active] 1231072001649 conserved cys residue [active] 1231072001650 Thioredoxin domain; Region: Thioredoxin_3; pfam13192 1231072001651 vitamin B12-dependent ribonucleotide reductase; Validated; Region: PRK06556 1231072001652 Class II vitamin B12-dependent ribonucleotide reductase; Region: Ribonuc_red_2_N; pfam08471 1231072001653 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 1231072001654 active site 1231072001655 dimer interface [polypeptide binding]; other site 1231072001656 effector binding site; other site 1231072001657 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 1231072001658 TSCPD domain; Region: TSCPD; pfam12637 1231072001659 Rrf2 family protein; Region: rrf2_super; TIGR00738 1231072001660 Transcriptional regulator; Region: Rrf2; pfam02082 1231072001661 Protein of unknown function (DUF1361); Region: DUF1361; pfam07099 1231072001662 nuc_hydro_IU_UC_XIUA: inosine-uridine preferring, xanthosine-inosine-uridine-adenosine-preferring and, uridine-cytidine preferring nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the...; Region: nuc_hydro_IU_UC_XIUA; cd02651 1231072001663 active site 1231072001664 tetramer interface [polypeptide binding]; other site 1231072001665 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 1231072001666 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 1231072001667 active site 1231072001668 metal binding site [ion binding]; metal-binding site 1231072001669 DNA binding site [nucleotide binding] 1231072001670 Type 5 capsule protein repressor C-terminal domain; Region: SbcD_C; pfam12320 1231072001671 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 1231072001672 ATP-binding cassette domain of sbcCD; Region: ABC_sbcCD; cd03279 1231072001673 Walker A/P-loop; other site 1231072001674 ATP binding site [chemical binding]; other site 1231072001675 Q-loop/lid; other site 1231072001676 ATP-binding cassette domain of sbcCD; Region: ABC_sbcCD; cd03279 1231072001677 ABC transporter signature motif; other site 1231072001678 Walker B; other site 1231072001679 D-loop; other site 1231072001680 H-loop/switch region; other site 1231072001681 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 1231072001682 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1231072001683 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1231072001684 ABC transporter; Region: ABC_tran_2; pfam12848 1231072001685 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1231072001686 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 1231072001687 Metallo-dependent hydrolases, subgroup C is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_C; cd01309 1231072001688 active site 1231072001689 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 1231072001690 Metallo-dependent hydrolases, subgroup C is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_C; cd01309 1231072001691 active site 1231072001692 Putative p-aminobenzoyl-glutamate transporter [Coenzyme metabolism]; Region: AbgT; COG2978 1231072001693 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 1231072001694 Nucleoside 2-deoxyribosyltransferase; Region: Nuc_deoxyrib_tr; pfam05014 1231072001695 Haemolysin-III related; Region: HlyIII; cl03831 1231072001696 channel protein, hemolysin III family; Region: hlyIII; TIGR01065 1231072001697 Predicted metal-binding protein (DUF2284); Region: DUF2284; pfam10050 1231072001698 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1231072001699 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1231072001700 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1231072001701 Walker A/P-loop; other site 1231072001702 ATP binding site [chemical binding]; other site 1231072001703 Q-loop/lid; other site 1231072001704 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1231072001705 ABC transporter signature motif; other site 1231072001706 ABC transporter; Region: ABC_tran_2; pfam12848 1231072001707 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1231072001708 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 1231072001709 Cu/Zn superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodC; COG2032 1231072001710 Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the...; Region: Cu-Zn_Superoxide_Dismutase; cd00305 1231072001711 E-class dimer interface [polypeptide binding]; other site 1231072001712 P-class dimer interface [polypeptide binding]; other site 1231072001713 active site 1231072001714 Cu2+ binding site [ion binding]; other site 1231072001715 Zn2+ binding site [ion binding]; other site 1231072001716 DHHW protein; Region: DHHW; pfam14286 1231072001717 DHHW protein; Region: DHHW; pfam14286 1231072001718 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 1231072001719 Domain of unknown function (DUF4358); Region: DUF4358; pfam14270 1231072001720 NnaC (CMP-NeuNAc synthetase) _like subfamily of SGNH_hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its...; Region: NnaC_like; cd01841 1231072001721 active site 1231072001722 catalytic triad [active] 1231072001723 oxyanion hole [active] 1231072001724 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 1231072001725 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 1231072001726 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 1231072001727 Peptidase M14 carboxypeptidase family-like domain of Endopeptidase I; Region: M14_Endopeptidase_I; cd06229 1231072001728 putative active site [active] 1231072001729 Zn binding site [ion binding]; other site 1231072001730 Glycerol dehydrogenase and related enzymes [Energy production and conversion]; Region: GldA; COG0371 1231072001731 Glycerol dehydrogenases (GlyDH) catalyzes oxidation of glycerol to dihydroxyacetone in glycerol dissmilation; Region: GlyDH; cd08170 1231072001732 dimer interface [polypeptide binding]; other site 1231072001733 active site 1231072001734 metal binding site [ion binding]; metal-binding site 1231072001735 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1231072001736 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 1231072001737 active site 1231072001738 phosphorylation site [posttranslational modification] 1231072001739 intermolecular recognition site; other site 1231072001740 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1231072001741 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 1231072001742 DNA binding site [nucleotide binding] 1231072001743 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1231072001744 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 1231072001745 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 1231072001746 dimer interface [polypeptide binding]; other site 1231072001747 phosphorylation site [posttranslational modification] 1231072001748 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 1231072001749 ATP binding site [chemical binding]; other site 1231072001750 Mg2+ binding site [ion binding]; other site 1231072001751 G-X-G motif; other site 1231072001752 Outer membrane lipoprotein-sorting protein [Cell envelope biogenesis, outer membrane]; Region: LolA; COG2834 1231072001753 Domain of unknown function (DUF4412); Region: DUF4412; pfam14371 1231072001754 Predicted transcriptional regulators [Transcription]; Region: COG1695 1231072001755 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 1231072001756 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 1231072001757 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 1231072001758 Firmicute fructose-1,6-bisphosphatase; Region: FBPase_2; pfam06874 1231072001759 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 1231072001760 active site 1 [active] 1231072001761 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 1231072001762 active site 2 [active] 1231072001763 Domain of unknown function (DUF4179); Region: DUF4179; pfam13786 1231072001764 RNA polymerase sigma-70 factor, TIGR02954 family; Region: Sig70_famx3 1231072001765 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 1231072001766 DNA binding residues [nucleotide binding] 1231072001767 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 1231072001768 Tetratricopeptide repeat; Region: TPR_16; pfam13432 1231072001769 binding surface 1231072001770 TPR motif; other site 1231072001771 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 1231072001772 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 1231072001773 FtsX-like permease family; Region: FtsX; pfam02687 1231072001774 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1231072001775 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1231072001776 Walker A/P-loop; other site 1231072001777 ATP binding site [chemical binding]; other site 1231072001778 Q-loop/lid; other site 1231072001779 ABC transporter signature motif; other site 1231072001780 Walker B; other site 1231072001781 D-loop; other site 1231072001782 H-loop/switch region; other site 1231072001783 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]; Region: COG3591 1231072001784 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 1231072001785 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1231072001786 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 1231072001787 DNA binding residues [nucleotide binding] 1231072001788 Predicted transcriptional regulators [Transcription]; Region: COG1695 1231072001789 Transcriptional regulator PadR-like family; Region: PadR; cl17335 1231072001790 Protein of unknown function (DUF2812); Region: DUF2812; pfam11193 1231072001791 ATP-binding cassette domain of the bacitracin-resistance transporter; Region: ABC_BcrA_bacitracin_resist; cd03268 1231072001792 cobalt transport protein ATP-binding subunit; Region: cbiO; TIGR01166 1231072001793 Walker A/P-loop; other site 1231072001794 ATP binding site [chemical binding]; other site 1231072001795 Q-loop/lid; other site 1231072001796 ABC transporter signature motif; other site 1231072001797 Walker B; other site 1231072001798 D-loop; other site 1231072001799 H-loop/switch region; other site 1231072001800 lantibiotic protection ABC transporter permease subunit, MutE/EpiE family; Region: lanti_perm_MutE; TIGR03732 1231072001801 ABC-2 family transporter protein; Region: ABC2_membrane_4; pfam12730 1231072001802 lantibiotic protection ABC transporter permease subunit, MutG family; Region: lanti_perm_MutG; TIGR03733 1231072001803 ABC-2 family transporter protein; Region: ABC2_membrane_4; pfam12730 1231072001804 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1231072001805 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 1231072001806 active site 1231072001807 phosphorylation site [posttranslational modification] 1231072001808 intermolecular recognition site; other site 1231072001809 dimerization interface [polypeptide binding]; other site 1231072001810 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 1231072001811 DNA binding site [nucleotide binding] 1231072001812 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1231072001813 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 1231072001814 dimer interface [polypeptide binding]; other site 1231072001815 phosphorylation site [posttranslational modification] 1231072001816 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 1231072001817 ATP binding site [chemical binding]; other site 1231072001818 Mg2+ binding site [ion binding]; other site 1231072001819 G-X-G motif; other site 1231072001820 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 1231072001821 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 1231072001822 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1231072001823 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1231072001824 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1231072001825 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 1231072001826 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 1231072001827 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 1231072001828 Walker A/P-loop; other site 1231072001829 ATP binding site [chemical binding]; other site 1231072001830 Q-loop/lid; other site 1231072001831 ABC transporter signature motif; other site 1231072001832 Walker B; other site 1231072001833 D-loop; other site 1231072001834 H-loop/switch region; other site 1231072001835 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 1231072001836 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 1231072001837 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 1231072001838 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1231072001839 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1231072001840 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 1231072001841 FeS/SAM binding site; other site 1231072001842 4Fe-4S single cluster domain; Region: Fer4_14; pfam13394 1231072001843 Helix-turn-helix domain; Region: HTH_18; pfam12833 1231072001844 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1231072001845 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; smart00871 1231072001846 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 1231072001847 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1231072001848 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 1231072001849 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 1231072001850 non-specific DNA binding site [nucleotide binding]; other site 1231072001851 salt bridge; other site 1231072001852 sequence-specific DNA binding site [nucleotide binding]; other site 1231072001853 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 1231072001854 active site 1231072001855 putative substrate binding region [chemical binding]; other site 1231072001856 CAAX protease self-immunity; Region: Abi; pfam02517 1231072001857 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 1231072001858 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1231072001859 Coenzyme A binding pocket [chemical binding]; other site 1231072001860 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 1231072001861 ABC-type multidrug transport system, ATPase component; Region: ABC_drug_resistance_like; cd03264 1231072001862 Walker A/P-loop; other site 1231072001863 ATP binding site [chemical binding]; other site 1231072001864 Q-loop/lid; other site 1231072001865 ABC transporter signature motif; other site 1231072001866 Walker B; other site 1231072001867 D-loop; other site 1231072001868 H-loop/switch region; other site 1231072001869 2'-5' RNA ligase superfamily; Region: 2_5_RNA_ligase2; pfam13563 1231072001870 Protein of unknown function (DUF2500); Region: DUF2500; pfam10694 1231072001871 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 1231072001872 S1 domain; Region: S1_2; pfam13509 1231072001873 Uncharacterized conserved protein [Function unknown]; Region: COG2928 1231072001874 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1231072001875 Zn2+ binding site [ion binding]; other site 1231072001876 Mg2+ binding site [ion binding]; other site 1231072001877 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 1231072001878 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 1231072001879 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 1231072001880 N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; Region: PLDc_N_DEXD_b3; cd09205 1231072001881 PLD-like domain; Region: PLDc_2; pfam13091 1231072001882 putative homodimer interface [polypeptide binding]; other site 1231072001883 putative active site [active] 1231072001884 catalytic site [active] 1231072001885 DEAD-like helicases superfamily; Region: DEXDc; smart00487 1231072001886 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 1231072001887 ATP binding site [chemical binding]; other site 1231072001888 putative Mg++ binding site [ion binding]; other site 1231072001889 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 1231072001890 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 1231072001891 nucleotide binding region [chemical binding]; other site 1231072001892 ATP-binding site [chemical binding]; other site 1231072001893 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in a group of uncharacterized proteins from archaea and bacteria; Region: NTP-PPase_COG4997; cd11532 1231072001894 metal binding site [ion binding]; metal-binding site 1231072001895 Alkaline phosphatase [Inorganic ion transport and metabolism]; Region: PhoA; COG1785 1231072001896 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH; Region: alkPPc; cd00016 1231072001897 dimer interface [polypeptide binding]; other site 1231072001898 active site 1231072001899 Chromate transporter; Region: Chromate_transp; pfam02417 1231072001900 Chromate transporter; Region: Chromate_transp; pfam02417 1231072001901 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 1231072001902 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; pfam00690 1231072001903 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 1231072001904 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 1231072001905 Soluble P-type ATPase [General function prediction only]; Region: COG4087 1231072001906 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 1231072001907 RNA polymerase sigma factor; Provisional; Region: PRK12522 1231072001908 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1231072001909 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 1231072001910 DNA binding residues [nucleotide binding] 1231072001911 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 1231072001912 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 1231072001913 Double zinc ribbon; Region: DZR; pfam12773 1231072001914 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 1231072001915 Protein of unknown function (DUF327); Region: DUF327; pfam03885 1231072001916 Protein of unknown function (DUF3100); Region: DUF3100; pfam11299 1231072001917 M20 Peptidase Aminoacylase 1-like protein 2, amidohydrolase family; Region: M20_Acy1L2_like_2; cd09849 1231072001918 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 1231072001919 metal binding site [ion binding]; metal-binding site 1231072001920 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 1231072001921 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 1231072001922 catalytic motif [active] 1231072001923 Zn binding site [ion binding]; other site 1231072001924 RibD C-terminal domain; Region: RibD_C; cl17279 1231072001925 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 1231072001926 Lumazine binding domain; Region: Lum_binding; pfam00677 1231072001927 Lumazine binding domain; Region: Lum_binding; pfam00677 1231072001928 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09311 1231072001929 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 1231072001930 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 1231072001931 dimerization interface [polypeptide binding]; other site 1231072001932 active site 1231072001933 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 1231072001934 homopentamer interface [polypeptide binding]; other site 1231072001935 active site 1231072001936 FMN-binding domain; Region: FMN_bind; cl01081 1231072001937 FMN-binding domain; Region: FMN_bind; pfam04205 1231072001938 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1231072001939 Zn2+ binding site [ion binding]; other site 1231072001940 Mg2+ binding site [ion binding]; other site 1231072001941 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cd00317 1231072001942 active site 1231072001943 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 1231072001944 NAD synthase [Coenzyme metabolism]; Region: NadE; COG0171 1231072001945 homodimer interface [polypeptide binding]; other site 1231072001946 NAD binding pocket [chemical binding]; other site 1231072001947 ATP binding pocket [chemical binding]; other site 1231072001948 Mg binding site [ion binding]; other site 1231072001949 active-site loop [active] 1231072001950 Predicted amidohydrolase [General function prediction only]; Region: COG0388 1231072001951 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 1231072001952 multimer interface [polypeptide binding]; other site 1231072001953 active site 1231072001954 catalytic triad [active] 1231072001955 protein interface 1 [polypeptide binding]; other site 1231072001956 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 1231072001957 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 1231072001958 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 1231072001959 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 1231072001960 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 1231072001961 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1231072001962 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 1231072001963 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1231072001964 DNA-binding site [nucleotide binding]; DNA binding site 1231072001965 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 1231072001966 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1231072001967 homodimer interface [polypeptide binding]; other site 1231072001968 catalytic residue [active] 1231072001969 helicase-exonuclease AddAB, AddB subunit; Region: addB_Gpos; TIGR02773 1231072001970 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 1231072001971 Small, acid-soluble spore proteins, alpha/beta type; Region: SASP; pfam00269 1231072001972 Protein of unknown function DUF262; Region: DUF262; pfam03235 1231072001973 Uncharacterized conserved protein [Function unknown]; Region: COG1479 1231072001974 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 1231072001975 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001976 Putative cell wall-binding domain [Cell envelope biogenesis, outer membrane]; Region: LytB; COG2247 1231072001977 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001978 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072001979 SCP_bacterial: SCP-like extracellular protein domain, as found in bacteria and archaea. The wider family of SCP containing proteins includes plant pathogenesis-related protein 1 (PR-1), CRISPs, mammalian cysteine-rich secretory proteins, and allergen 5...; Region: SCP_bacterial; cd05379 1231072001980 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 1231072001981 Family description; Region: UvrD_C_2; pfam13538 1231072001982 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 1231072001983 Part of AAA domain; Region: AAA_19; pfam13245 1231072001984 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; cl12060 1231072001985 AP (apurinic/apyrimidinic) site pocket; other site 1231072001986 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 1231072001987 DNA interaction; other site 1231072001988 Metal-binding active site; metal-binding site 1231072001989 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK13581 1231072001990 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 1231072001991 ligand binding site [chemical binding]; other site 1231072001992 NAD binding site [chemical binding]; other site 1231072001993 dimerization interface [polypeptide binding]; other site 1231072001994 catalytic site [active] 1231072001995 C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-xct; cd04902 1231072001996 putative L-serine binding site [chemical binding]; other site 1231072001997 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 1231072001998 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 1231072001999 homodimer interface [polypeptide binding]; other site 1231072002000 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1231072002001 catalytic residue [active] 1231072002002 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072002003 Putative cell wall-binding domain [Cell envelope biogenesis, outer membrane]; Region: LytB; COG2247 1231072002004 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072002005 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072002006 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3323 1231072002007 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cl00220 1231072002008 Isochorismatase family; Region: Isochorismatase; pfam00857 1231072002009 catalytic triad [active] 1231072002010 conserved cis-peptide bond; other site 1231072002011 H+/gluconate symporter and related permeases [Carbohydrate transport and metabolism / Amino acid transport and metabolism]; Region: GntT; COG2610 1231072002012 fructuronate transporter; Provisional; Region: PRK10034; cl15264 1231072002013 Glycerate kinase [Carbohydrate transport and metabolism]; Region: COG1929 1231072002014 Putative sugar diacid recognition; Region: Diacid_rec; pfam05651 1231072002015 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1231072002016 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1231072002017 dimer interface [polypeptide binding]; other site 1231072002018 putative CheW interface [polypeptide binding]; other site 1231072002019 Predicted transcriptional regulator [Transcription]; Region: COG2378 1231072002020 WYL domain; Region: WYL; pfam13280 1231072002021 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1231072002022 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1231072002023 metal binding site [ion binding]; metal-binding site 1231072002024 active site 1231072002025 I-site; other site 1231072002026 (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase...; Region: R_hydratase; cd03449 1231072002027 dimer interaction site [polypeptide binding]; other site 1231072002028 substrate-binding tunnel; other site 1231072002029 active site 1231072002030 catalytic site [active] 1231072002031 substrate binding site [chemical binding]; other site 1231072002032 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 1231072002033 PAS domain; Region: PAS; smart00091 1231072002034 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 1231072002035 Walker A motif; other site 1231072002036 ATP binding site [chemical binding]; other site 1231072002037 Walker B motif; other site 1231072002038 arginine finger; other site 1231072002039 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1231072002040 Acyl CoA:acetate/3-ketoacid CoA transferase [Lipid metabolism]; Region: COG4670 1231072002041 Coenzyme A transferase; Region: CoA_trans; smart00882 1231072002042 Coenzyme A transferase; Region: CoA_trans; cl17247 1231072002043 H+/gluconate symporter and related permeases [Carbohydrate transport and metabolism / Amino acid transport and metabolism]; Region: GntT; COG2610 1231072002044 fructuronate transporter; Provisional; Region: PRK10034; cl15264 1231072002045 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1231072002046 Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA dehydrogenases; Region: SCAD_SBCAD; cd01158 1231072002047 FAD binding site [chemical binding]; other site 1231072002048 homotetramer interface [polypeptide binding]; other site 1231072002049 substrate binding pocket [chemical binding]; other site 1231072002050 catalytic base [active] 1231072002051 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_beta; cd01714 1231072002052 Ligand binding site [chemical binding]; other site 1231072002053 Electron transfer flavoprotein domain; Region: ETF; pfam01012 1231072002054 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 1231072002055 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_alpha; cd01715 1231072002056 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 1231072002057 helicase-exonuclease AddAB, AddA subunit, Firmicutes type; Region: addA_Gpos; TIGR02785 1231072002058 Part of AAA domain; Region: AAA_19; pfam13245 1231072002059 Family description; Region: UvrD_C_2; pfam13538 1231072002060 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 1231072002061 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 1231072002062 dimer interface [polypeptide binding]; other site 1231072002063 phosphorylation site [posttranslational modification] 1231072002064 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1231072002065 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 1231072002066 ATP binding site [chemical binding]; other site 1231072002067 Mg2+ binding site [ion binding]; other site 1231072002068 G-X-G motif; other site 1231072002069 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1231072002070 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 1231072002071 ATP binding site [chemical binding]; other site 1231072002072 Mg2+ binding site [ion binding]; other site 1231072002073 G-X-G motif; other site 1231072002074 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 1231072002075 catalytic core [active] 1231072002076 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 1231072002077 Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a...; Region: CobU; cd00544 1231072002078 homotrimer interface [polypeptide binding]; other site 1231072002079 Walker A motif; other site 1231072002080 GTP binding site [chemical binding]; other site 1231072002081 Walker B motif; other site 1231072002082 cobalamin synthase; Reviewed; Region: cobS; PRK00235 1231072002083 cobyric acid synthase; Provisional; Region: PRK00784 1231072002084 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 1231072002085 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 1231072002086 catalytic triad [active] 1231072002087 CobD/Cbib protein; Region: CobD_Cbib; cl00561 1231072002088 cobalamin biosynthesis protein; Provisional; Region: cobD; PRK01209 1231072002089 threonine-phosphate decarboxylase; Provisional; Region: PRK06358 1231072002090 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 1231072002091 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1231072002092 homodimer interface [polypeptide binding]; other site 1231072002093 catalytic residue [active] 1231072002094 cobalt transport protein CbiM; Validated; Region: PRK08319 1231072002095 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; pfam01891 1231072002096 cobalt transport protein CbiN; Provisional; Region: PRK02898 1231072002097 cobalt ABC transporter, permease protein CbiQ; Region: CbiQ_TIGR; TIGR02454 1231072002098 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 1231072002099 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 1231072002100 tRNA; other site 1231072002101 putative tRNA binding site [nucleotide binding]; other site 1231072002102 putative NADP binding site [chemical binding]; other site 1231072002103 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 1231072002104 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 1231072002105 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 1231072002106 domain interfaces; other site 1231072002107 active site 1231072002108 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 1231072002109 active site 1231072002110 SAM binding site [chemical binding]; other site 1231072002111 homodimer interface [polypeptide binding]; other site 1231072002112 Uroporphyrinogen-III synthase [Coenzyme metabolism]; Region: HemD; COG1587 1231072002113 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 1231072002114 active site 1231072002115 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 1231072002116 dimer interface [polypeptide binding]; other site 1231072002117 active site 1231072002118 Schiff base residues; other site 1231072002119 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 1231072002120 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 1231072002121 inhibitor-cofactor binding pocket; inhibition site 1231072002122 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1231072002123 catalytic residue [active] 1231072002124 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 1231072002125 Dethiobiotin synthetase [Coenzyme metabolism]; Region: BioD; COG0132 1231072002126 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 1231072002127 catalytic triad [active] 1231072002128 precorrin-8X methylmutase; Validated; Region: cbiC; PRK05575 1231072002129 cobalt-precorrin-8X methylmutase; Validated; Region: cbiC; cl00913 1231072002130 cobalt-precorrin-6A synthase; Reviewed; Region: cbiD; PRK00075 1231072002131 Precorrin-6Y methyltransferase, the cobalamin biosynthesis enzyme CbiE; Region: Precorrin-6Y-methylase; cd11644 1231072002132 active site 1231072002133 putative homodimer interface [polypeptide binding]; other site 1231072002134 SAM binding site [chemical binding]; other site 1231072002135 Precorrin-6B methylase 2 [Coenzyme metabolism]; Region: CobL; COG2242 1231072002136 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 1231072002137 S-adenosylmethionine binding site [chemical binding]; other site 1231072002138 Precorrin-2 C20-methyltransferase, also named CobI or CbiL; Region: Precorrin_2_C20_MT; cd11645 1231072002139 active site 1231072002140 SAM binding site [chemical binding]; other site 1231072002141 homodimer interface [polypeptide binding]; other site 1231072002142 Precorrin-4 C11-methyltransferase (CbiF/CobM); Region: Precorrin-4_C11-MT; cd11641 1231072002143 active site 1231072002144 SAM binding site [chemical binding]; other site 1231072002145 homodimer interface [polypeptide binding]; other site 1231072002146 cobalamin biosynthesis protein CbiG; Validated; Region: PRK05788 1231072002147 Cobalamin synthesis G N-terminal; Region: CbiG_N; pfam11760 1231072002148 Cobalamin biosynthesis central region; Region: CbiG_mid; pfam11761 1231072002149 Cobalamin synthesis G C-terminus; Region: CbiG_C; pfam01890 1231072002150 Precorrin-3B C(17)-methyltransferase (CobJ/CbiH); Region: Precorrin_3B_C17_MT; cd11646 1231072002151 active site 1231072002152 SAM binding site [chemical binding]; other site 1231072002153 homodimer interface [polypeptide binding]; other site 1231072002154 Precorrin-6x reductase [Coenzyme metabolism]; Region: CobK; COG2099 1231072002155 cobalt-precorrin-6x reductase; Reviewed; Region: PRK08057 1231072002156 AIR synthase related protein, N-terminal domain; Region: AIRS; pfam00586 1231072002157 Cobalt chelatase (CbiK); Region: CbiK; pfam06180 1231072002158 Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), N-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the...; Region: CbiK_N; cd03412 1231072002159 active site 1231072002160 C-terminal domain interface [polypeptide binding]; other site 1231072002161 Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), C-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the...; Region: CbiK_C; cd03413 1231072002162 active site 1231072002163 N-terminal domain interface [polypeptide binding]; other site 1231072002164 ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer; Region: CobA_CobO_BtuR; cd00561 1231072002165 homodimer interface [polypeptide binding]; other site 1231072002166 Walker A motif; other site 1231072002167 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 1231072002168 ATP binding site [chemical binding]; other site 1231072002169 hydroxycobalamin binding site [chemical binding]; other site 1231072002170 Walker B motif; other site 1231072002171 Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits [Energy production and conversion]; Region: COG4231 1231072002172 ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer; Region: CobA_CobO_BtuR; cd00561 1231072002173 homodimer interface [polypeptide binding]; other site 1231072002174 Walker A motif; other site 1231072002175 ATP binding site [chemical binding]; other site 1231072002176 hydroxycobalamin binding site [chemical binding]; other site 1231072002177 Walker B motif; other site 1231072002178 Prenyltransferase-like; Region: Prenyltrans_2; pfam13249 1231072002179 Bacterial surface proteins containing Ig-like domains [Cell motility and secretion]; Region: COG5492 1231072002180 Bacterial Ig-like domain (group 2); Region: Big_2; pfam02368 1231072002181 Bacterial surface proteins containing Ig-like domains [Cell motility and secretion]; Region: COG5492 1231072002182 Bacterial Ig-like domain (group 2); Region: Big_2; pfam02368 1231072002183 Bacterial Ig-like domain (group 2); Region: Big_2; pfam02368 1231072002184 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072002185 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072002186 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072002187 This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate...; Region: ISOPREN_C2_like; cd00688 1231072002188 Prenyltransferase-like; Region: Prenyltrans_2; pfam13249 1231072002189 Prenyltransferase-like; Region: Prenyltrans_2; pfam13249 1231072002190 Prenyltransferase-like; Region: Prenyltrans_2; pfam13249 1231072002191 Prenyltransferase-like; Region: Prenyltrans_2; pfam13249 1231072002192 Bacterial surface proteins containing Ig-like domains [Cell motility and secretion]; Region: COG5492 1231072002193 Bacterial Ig-like domain (group 2); Region: Big_2; pfam02368 1231072002194 Bacterial Ig-like domain (group 2); Region: Big_2; pfam02368 1231072002195 Bacterial Ig-like domain (group 2); Region: Big_2; cl02708 1231072002196 This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate...; Region: ISOPREN_C2_like; cd00688 1231072002197 Prenyltransferase-like; Region: Prenyltrans_2; pfam13249 1231072002198 Bacterial Ig-like domain (group 4); Region: Big_4; pfam07532 1231072002199 Bacterial surface proteins containing Ig-like domains [Cell motility and secretion]; Region: COG5492 1231072002200 Bacterial Ig-like domain (group 2); Region: Big_2; pfam02368 1231072002201 Cobalt transport protein; Region: CbiQ; cl00463 1231072002202 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 1231072002203 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 1231072002204 Walker A/P-loop; other site 1231072002205 ATP binding site [chemical binding]; other site 1231072002206 Q-loop/lid; other site 1231072002207 ABC transporter signature motif; other site 1231072002208 Walker B; other site 1231072002209 D-loop; other site 1231072002210 H-loop/switch region; other site 1231072002211 Second domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain2; cd03226 1231072002212 Walker A/P-loop; other site 1231072002213 ATP binding site [chemical binding]; other site 1231072002214 Q-loop/lid; other site 1231072002215 ABC transporter signature motif; other site 1231072002216 Walker B; other site 1231072002217 D-loop; other site 1231072002218 H-loop/switch region; other site 1231072002219 Protein of unknown function (DUF3816); Region: DUF3816; pfam12822 1231072002220 ECF-type riboflavin transporter, S component; Region: ECF-ribofla_trS; pfam07155 1231072002221 delta-lactam-biosynthetic de-N-acetylase; Region: spore_pdaA; TIGR02884 1231072002222 Catalytic NodB homology domain of Streptococcus mutans polysaccharide deacetylase PgdA, Bacillus subtilis YheN, and similar proteins; Region: CE4_SmPgdA_like; cd10944 1231072002223 NodB motif; other site 1231072002224 active site 1231072002225 catalytic site [active] 1231072002226 Zn binding site [ion binding]; other site 1231072002227 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 1231072002228 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1231072002229 Walker A/P-loop; other site 1231072002230 ATP binding site [chemical binding]; other site 1231072002231 Q-loop/lid; other site 1231072002232 ABC transporter signature motif; other site 1231072002233 Walker B; other site 1231072002234 D-loop; other site 1231072002235 H-loop/switch region; other site 1231072002236 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814; cl03223 1231072002237 Uncharacterized protein family (UPF0051); Region: UPF0051; pfam01458 1231072002238 MoxR-like ATPases [General function prediction only]; Region: COG0714 1231072002239 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 1231072002240 Walker A motif; other site 1231072002241 ATP binding site [chemical binding]; other site 1231072002242 Walker B motif; other site 1231072002243 arginine finger; other site 1231072002244 Protein of unknown function DUF58; Region: DUF58; pfam01882 1231072002245 Aerotolerance regulator N-terminal; Region: BatA; pfam07584 1231072002246 von Willebrand factor type A domain; Region: VWA_2; pfam13519 1231072002247 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 1231072002248 metal ion-dependent adhesion site (MIDAS); other site 1231072002249 Protein of unknown function (DUF1355); Region: DUF1355; cl17712 1231072002250 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 1231072002251 metal ion-dependent adhesion site (MIDAS); other site 1231072002252 Protein of unknown function (DUF1355); Region: DUF1355; cl17712 1231072002253 This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate...; Region: ISOPREN_C2_like; cl08267 1231072002254 Prenyltransferase-like; Region: Prenyltrans_2; pfam13249 1231072002255 This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate...; Region: ISOPREN_C2_like; cd00688 1231072002256 S-layer homology domain; Region: SLH; pfam00395 1231072002257 This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate...; Region: ISOPREN_C2_like; cd00688 1231072002258 Prenyltransferase-like; Region: Prenyltrans_2; pfam13249 1231072002259 Bacterial surface proteins containing Ig-like domains [Cell motility and secretion]; Region: COG5492 1231072002260 Bacterial Ig-like domain (group 2); Region: Big_2; pfam02368 1231072002261 This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate...; Region: ISOPREN_C2_like; cd00688 1231072002262 Prenyltransferase-like; Region: Prenyltrans_2; pfam13249 1231072002263 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072002264 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072002265 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072002266 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072002267 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072002268 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072002269 This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate...; Region: ISOPREN_C2_like; cd00688 1231072002270 Prenyltransferase-like; Region: Prenyltrans_2; pfam13249 1231072002271 Bacterial Ig-like domain (group 2); Region: Big_2; cl02708 1231072002272 This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate...; Region: ISOPREN_C2_like; cd00688 1231072002273 Prenyltransferase-like; Region: Prenyltrans_2; pfam13249 1231072002274 phosphoglucomutase-2-like protein; Provisional; Region: PTZ00150 1231072002275 This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2 is thought to be a phosphopentomutase that catalyzes the conversion of the nucleoside breakdown products, ribose-1-phosphate and...; Region: PGM2; cd05799 1231072002276 active site 1231072002277 substrate binding site [chemical binding]; other site 1231072002278 metal binding site [ion binding]; metal-binding site 1231072002279 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: COG4667 1231072002280 Hypothetical patatin similar to yjju protein of Escherichia coli; Region: Pat_hypo_Ecoli_yjju_like; cd07208 1231072002281 active site 1231072002282 nucleophile elbow; other site 1231072002283 Asparagine synthetase (aspartate-ammonia ligase) (AsnA) catalyses the conversion of L-aspartate to L-asparagine in the presence of ATP and ammonia. AsnA is a homodimeric enzyme which is structurally similiar to the catalytic core domain of class II...; Region: AsnA; cd00645 1231072002284 dimer interface [polypeptide binding]; other site 1231072002285 active site 1231072002286 Protein of unknown function (DUF3793); Region: DUF3793; pfam12672 1231072002287 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 1231072002288 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 1231072002289 Walker A/P-loop; other site 1231072002290 ATP binding site [chemical binding]; other site 1231072002291 Q-loop/lid; other site 1231072002292 ABC transporter signature motif; other site 1231072002293 Walker B; other site 1231072002294 D-loop; other site 1231072002295 H-loop/switch region; other site 1231072002296 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 1231072002297 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 1231072002298 ABC-ATPase subunit interface; other site 1231072002299 dimer interface [polypeptide binding]; other site 1231072002300 putative PBP binding regions; other site 1231072002301 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 1231072002302 Periplasmic binding protein YvrC. These proteins are predicted to function as initial receptors in ABC transport of metal ions in eubacteria and archaea. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct...; Region: YvrC; cd01143 1231072002303 putative binding site residues; other site 1231072002304 Protein involved in propanediol utilization, and related proteins (includes coumermycin biosynthetic protein), possible kinase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PduX; COG4542 1231072002305 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 1231072002306 Branched-chain amino acid transport protein; Region: Branch_AA_trans; pfam05525 1231072002307 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1231072002308 Exopolysaccharide biosynthesis protein related to N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase [Carbohydrate transport and metabolism]; Region: EpsL; COG4632 1231072002309 Peptidase family M50; Region: Peptidase_M50; pfam02163 1231072002310 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 1231072002311 active site 1231072002312 putative substrate binding region [chemical binding]; other site 1231072002313 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 1231072002314 S-adenosylmethionine binding site [chemical binding]; other site 1231072002315 RNA polymerase beta'' subunit; Reviewed; Region: rpoC2; CHL00117 1231072002316 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 1231072002317 dimer interface [polypeptide binding]; other site 1231072002318 catalytic triad [active] 1231072002319 peroxidatic and resolving cysteines [active] 1231072002320 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 1231072002321 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1231072002322 NAD(P) binding site [chemical binding]; other site 1231072002323 active site 1231072002324 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 1231072002325 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 1231072002326 Walker A/P-loop; other site 1231072002327 ATP binding site [chemical binding]; other site 1231072002328 Q-loop/lid; other site 1231072002329 ABC transporter signature motif; other site 1231072002330 Walker B; other site 1231072002331 D-loop; other site 1231072002332 H-loop/switch region; other site 1231072002333 Predicted transcriptional regulators [Transcription]; Region: COG1725 1231072002334 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1231072002335 DNA-binding site [nucleotide binding]; DNA binding site 1231072002336 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1231072002337 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 1231072002338 active site 1231072002339 phosphorylation site [posttranslational modification] 1231072002340 intermolecular recognition site; other site 1231072002341 dimerization interface [polypeptide binding]; other site 1231072002342 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 1231072002343 DNA binding site [nucleotide binding] 1231072002344 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1231072002345 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 1231072002346 dimerization interface [polypeptide binding]; other site 1231072002347 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 1231072002348 dimer interface [polypeptide binding]; other site 1231072002349 phosphorylation site [posttranslational modification] 1231072002350 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 1231072002351 ATP binding site [chemical binding]; other site 1231072002352 Mg2+ binding site [ion binding]; other site 1231072002353 G-X-G motif; other site 1231072002354 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 1231072002355 EamA-like transporter family; Region: EamA; cl17759 1231072002356 EamA-like transporter family; Region: EamA; pfam00892 1231072002357 OsmC-like protein; Region: OsmC; pfam02566 1231072002358 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 1231072002359 SpoVT / AbrB like domain; Region: SpoVT_AbrB; smart00966 1231072002360 Predicted Zn-dependent peptidases, insulinase-like [General function prediction only]; Region: COG1026 1231072002361 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 1231072002362 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 1231072002363 Peptidase M16C associated; Region: M16C_assoc; pfam08367 1231072002364 FMN-binding domain; Region: FMN_bind; cl01081 1231072002365 flavocytochrome c; Region: flavo_cyto_c; TIGR01813 1231072002366 L-aspartate oxidase; Provisional; Region: PRK06175 1231072002367 putative FAD-binding dehydrogenase; Reviewed; Region: PRK12834 1231072002368 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 1231072002369 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 1231072002370 Uncharacterized conserved protein (DUF2156); Region: DUF2156; cl12090 1231072002371 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 1231072002372 active site 1231072002373 NTP binding site [chemical binding]; other site 1231072002374 metal binding triad [ion binding]; metal-binding site 1231072002375 dihydropyrimidine dehydrogenase subunit A; Provisional; Region: PRK11749 1231072002376 dihydropyrimidine dehydrogenase subunit B; Validated; Region: PRK08318 1231072002377 Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN, and...; Region: DHPD_FMN; cd02940 1231072002378 homodimer interface [polypeptide binding]; other site 1231072002379 active site 1231072002380 FMN binding site [chemical binding]; other site 1231072002381 substrate binding site [chemical binding]; other site 1231072002382 4Fe-4S binding domain; Region: Fer4; pfam00037 1231072002383 Integrase core domain; Region: rve; pfam00665 1231072002384 Integrase core domain; Region: rve_3; pfam13683 1231072002385 Transposase; Region: HTH_Tnp_1; cl17663 1231072002386 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 1231072002387 tyrosine phenol-lyase; Provisional; Region: PRK13237 1231072002388 Tryptophanase family (Tnase). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to tryptophanase (Tnase) and tyrosine phenol-lyase (TPL). Tnase and TPL are...; Region: Tnase_like; cd00617 1231072002389 substrate binding site [chemical binding]; other site 1231072002390 tetramer interface [polypeptide binding]; other site 1231072002391 catalytic residue [active] 1231072002392 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 1231072002393 Na2 binding site [ion binding]; other site 1231072002394 putative substrate binding site 1 [chemical binding]; other site 1231072002395 Na binding site 1 [ion binding]; other site 1231072002396 putative substrate binding site 2 [chemical binding]; other site 1231072002397 Transcriptional regulators [Transcription]; Region: FadR; COG2186 1231072002398 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1231072002399 DNA-binding site [nucleotide binding]; DNA binding site 1231072002400 FCD domain; Region: FCD; pfam07729 1231072002401 Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]; Region: ComEC; COG2333 1231072002402 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1231072002403 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 1231072002404 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 1231072002405 Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]; Region: MalY; COG1168 1231072002406 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 1231072002407 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1231072002408 homodimer interface [polypeptide binding]; other site 1231072002409 catalytic residue [active] 1231072002410 Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and...; Region: rubredoxin_SM; cd00729 1231072002411 Rubredoxin; Region: Rubredoxin; pfam00301 1231072002412 iron binding site [ion binding]; other site 1231072002413 Rubrerythrin [Energy production and conversion]; Region: COG1592 1231072002414 rubrerythrin-like, diiron-binding domain; Region: Rubrerythrin_like; cd01046 1231072002415 diiron binding motif [ion binding]; other site 1231072002416 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 1231072002417 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 1231072002418 active site 1231072002419 motif I; other site 1231072002420 motif II; other site 1231072002421 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 1231072002422 ThiC family; Region: ThiC; cl08031 1231072002423 thiamine biosynthesis protein ThiC; Provisional; Region: PRK13352 1231072002424 HesB-like selenoprotein; Region: HesB_rel_seleno; TIGR01911 1231072002425 HutD; Region: HutD; pfam05962 1231072002426 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1231072002427 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1231072002428 metal binding site [ion binding]; metal-binding site 1231072002429 active site 1231072002430 I-site; other site 1231072002431 Putative NodB-like catalytic domain of uncharacterized proteins found in bacteria; Region: CE4_COG5298; cd10923 1231072002432 Uncharacterized protein conserved in bacteria (DUF2334); Region: DUF2334; pfam10096 1231072002433 NodB motif; other site 1231072002434 putative active site [active] 1231072002435 putative catalytic site [active] 1231072002436 putative Zn binding site [ion binding]; other site 1231072002437 Glycosyltransferases, probably involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG1215 1231072002438 CESA_like is the cellulose synthase superfamily; Region: CESA_like; cd06423 1231072002439 DXD motif; other site 1231072002440 Bacterial cellulose synthase subunit; Region: BcsB; pfam03170 1231072002441 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3314 1231072002442 Nucleoside recognition; Region: Gate; pfam07670 1231072002443 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 1231072002444 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1231072002445 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1231072002446 NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide reductase...; Region: NrdH; cd02976 1231072002447 catalytic residues [active] 1231072002448 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 1231072002449 MgtC family; Region: MgtC; pfam02308 1231072002450 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 1231072002451 Putative glycerate dehydrogenase and related proteins of the D-specific 2-hydroxy dehydrogenase family; Region: GDH_like_1; cd12161 1231072002452 putative ligand binding site [chemical binding]; other site 1231072002453 putative NAD binding site [chemical binding]; other site 1231072002454 catalytic site [active] 1231072002455 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 1231072002456 non-specific DNA binding site [nucleotide binding]; other site 1231072002457 salt bridge; other site 1231072002458 sequence-specific DNA binding site [nucleotide binding]; other site 1231072002459 Radical SAM superfamily; Region: Radical_SAM; pfam04055 1231072002460 Ethanolamine utilisation protein, EutH; Region: EutH; cl01248 1231072002461 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1231072002462 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 1231072002463 active site 1231072002464 phosphorylation site [posttranslational modification] 1231072002465 intermolecular recognition site; other site 1231072002466 dimerization interface [polypeptide binding]; other site 1231072002467 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 1231072002468 DNA binding site [nucleotide binding] 1231072002469 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1231072002470 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 1231072002471 dimerization interface [polypeptide binding]; other site 1231072002472 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 1231072002473 dimer interface [polypeptide binding]; other site 1231072002474 phosphorylation site [posttranslational modification] 1231072002475 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 1231072002476 ATP binding site [chemical binding]; other site 1231072002477 Mg2+ binding site [ion binding]; other site 1231072002478 G-X-G motif; other site 1231072002479 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 1231072002480 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 1231072002481 Biotin operon repressor [Transcription]; Region: BirA; COG1654 1231072002482 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 1231072002483 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 1231072002484 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 1231072002485 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 1231072002486 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 1231072002487 FeS/SAM binding site; other site 1231072002488 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1231072002489 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1231072002490 dimer interface [polypeptide binding]; other site 1231072002491 putative CheW interface [polypeptide binding]; other site 1231072002492 3-oxoacyl-[acyl-carrier-protein]; Region: FabH; COG0332 1231072002493 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 1231072002494 dimer interface [polypeptide binding]; other site 1231072002495 active site 1231072002496 CoA binding pocket [chemical binding]; other site 1231072002497 methyl-galactoside ABC transporter galactose-binding periplasmic protein MglB; Provisional; Region: PRK15395 1231072002498 Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species; Region: PBP1_GGBP; cd01539 1231072002499 ligand binding site [chemical binding]; other site 1231072002500 calcium binding site [ion binding]; other site 1231072002501 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 1231072002502 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1231072002503 Walker A/P-loop; other site 1231072002504 ATP binding site [chemical binding]; other site 1231072002505 Q-loop/lid; other site 1231072002506 ABC transporter signature motif; other site 1231072002507 Walker B; other site 1231072002508 D-loop; other site 1231072002509 H-loop/switch region; other site 1231072002510 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 1231072002511 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 1231072002512 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 1231072002513 TM-ABC transporter signature motif; other site 1231072002514 Transcriptional regulators [Transcription]; Region: PurR; COG1609 1231072002515 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 1231072002516 DNA binding site [nucleotide binding] 1231072002517 domain linker motif; other site 1231072002518 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 1231072002519 dimerization interface [polypeptide binding]; other site 1231072002520 ligand binding site [chemical binding]; other site 1231072002521 galactose-1-phosphate uridylyltransferase; Provisional; Region: PRK05270 1231072002522 Galactose-1-phosphate uridyl transferase, N-terminal domain; Region: GalP_UDP_transf; pfam01087 1231072002523 Galactose-1-phosphate uridyl transferase, C-terminal domain; Region: GalP_UDP_tr_C; pfam02744 1231072002524 galactokinase; Provisional; Region: PRK05322 1231072002525 Galactokinase galactose-binding signature; Region: GalKase_gal_bdg; pfam10509 1231072002526 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 1231072002527 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 1231072002528 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 1231072002529 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 1231072002530 NAD binding site [chemical binding]; other site 1231072002531 homodimer interface [polypeptide binding]; other site 1231072002532 active site 1231072002533 substrate binding site [chemical binding]; other site 1231072002534 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1231072002535 RNA polymerase sigma factor RpoD, C-terminal domain; Region: RpoD_Cterm; TIGR02393 1231072002536 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1231072002537 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 1231072002538 Sigma-70, region 4; Region: Sigma70_r4; pfam04545 1231072002539 DNA binding residues [nucleotide binding] 1231072002540 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 1231072002541 Family of activating enzymes (E1) of ubiquitin-like proteins related to the E.coli hypothetical protein ygdL. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like...; Region: YgdL_like; cd00755 1231072002542 putative ATP binding site [chemical binding]; other site 1231072002543 putative substrate interface [chemical binding]; other site 1231072002544 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 1231072002545 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1231072002546 Manganese catalase, ferritin-like diiron-binding domain; Region: Mn_catalase; cd01051 1231072002547 dimanganese center [ion binding]; other site 1231072002548 CotJB protein; Region: CotJB; pfam12652 1231072002549 Protein of unknown function (DUF1517); Region: DUF1517; cl01807 1231072002550 Short C-terminal domain; Region: SHOCT; pfam09851 1231072002551 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1231072002552 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 1231072002553 active site 1231072002554 phosphorylation site [posttranslational modification] 1231072002555 intermolecular recognition site; other site 1231072002556 dimerization interface [polypeptide binding]; other site 1231072002557 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 1231072002558 DNA binding site [nucleotide binding] 1231072002559 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 1231072002560 dimer interface [polypeptide binding]; other site 1231072002561 phosphorylation site [posttranslational modification] 1231072002562 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 1231072002563 ATP binding site [chemical binding]; other site 1231072002564 Mg2+ binding site [ion binding]; other site 1231072002565 G-X-G motif; other site 1231072002566 Uncharacterized family 2; belongs to a superfamily containing transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this family was previously known as part of DUF156; Region: CsoR-like_DUF156_2; cd10159 1231072002567 putative homodimer interface [polypeptide binding]; other site 1231072002568 putative homotetramer interface [polypeptide binding]; other site 1231072002569 putative allosteric switch controlling residues; other site 1231072002570 putative metal binding site [ion binding]; other site 1231072002571 putative homodimer-homodimer interface [polypeptide binding]; other site 1231072002572 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 1231072002573 metal-binding site [ion binding] 1231072002574 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 1231072002575 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 1231072002576 metal-binding site [ion binding] 1231072002577 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 1231072002578 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 1231072002579 motif II; other site 1231072002580 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 1231072002581 metal-binding site [ion binding] 1231072002582 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 1231072002583 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 1231072002584 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 1231072002585 PhoU domain; Region: PhoU; pfam01895 1231072002586 PhoU domain; Region: PhoU; pfam01895 1231072002587 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 1231072002588 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 1231072002589 5S rRNA interface [nucleotide binding]; other site 1231072002590 CTC domain interface [polypeptide binding]; other site 1231072002591 L16 interface [polypeptide binding]; other site 1231072002592 nylC-like family; composed of proteins with similarity to Flavobacterium endo-type 6-aminohexanoate-oligomer hydrolase (EIII), the product of the nylon oligomer degradation gene, nylC. EIII is an amide hydrolase that catalyzes the degradation of...; Region: nylC_like; cd02252 1231072002593 putative active site pocket [active] 1231072002594 cleavage site 1231072002595 Predicted membrane protein [Function unknown]; Region: COG4684 1231072002596 Protein of unknown function (DUF3816); Region: DUF3816; pfam12822 1231072002597 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cl01053 1231072002598 active site 1231072002599 catalytic triad [active] 1231072002600 oxyanion hole [active] 1231072002601 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 1231072002602 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 1231072002603 protein binding site [polypeptide binding]; other site 1231072002604 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 1231072002605 Catalytic dyad [active] 1231072002606 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 1231072002607 catalytic residues [active] 1231072002608 EDD domain protein, DegV family; Region: DegV; TIGR00762 1231072002609 EDD domain protein, DegV family; Region: DegV; TIGR00762 1231072002610 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 1231072002611 Predicted transcriptional regulators [Transcription]; Region: COG1695 1231072002612 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 1231072002613 homoserine dehydrogenase; Validated; Region: PRK06813 1231072002614 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 1231072002615 Cache domain; Region: Cache_1; pfam02743 1231072002616 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 1231072002617 dimerization interface [polypeptide binding]; other site 1231072002618 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1231072002619 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1231072002620 dimer interface [polypeptide binding]; other site 1231072002621 putative CheW interface [polypeptide binding]; other site 1231072002622 lysine-2,3-aminomutase; Region: lys_2_3_AblA; TIGR03820 1231072002623 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 1231072002624 FeS/SAM binding site; other site 1231072002625 Lysine-2,3-aminomutase; Region: LAM_C; pfam12544 1231072002626 Glycosyl hydrolases family 35; Region: Glyco_hydro_35; pfam01301 1231072002627 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 1231072002628 Alanine dehydrogenase and related dehydrogenases; Region: Ala_dh_like; cd01620 1231072002629 putative ligand binding site [chemical binding]; other site 1231072002630 NAD(P) binding site [chemical binding]; other site 1231072002631 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 1231072002632 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1231072002633 DNA-binding site [nucleotide binding]; DNA binding site 1231072002634 TrkA-C domain; Region: TrkA_C; pfam02080 1231072002635 peroxiredoxin; Provisional; Region: PRK13189 1231072002636 Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by...; Region: PRX_1cys; cd03016 1231072002637 dimer interface [polypeptide binding]; other site 1231072002638 decamer (pentamer of dimers) interface [polypeptide binding]; other site 1231072002639 catalytic triad [active] 1231072002640 PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_2; cd03392 1231072002641 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 1231072002642 active site 1231072002643 methionine sulfoxide reductase B; Provisional; Region: PRK00222 1231072002644 SelR domain; Region: SelR; pfam01641 1231072002645 Domain of unknown function (DUF4179); Region: DUF4179; pfam13786 1231072002646 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 1231072002647 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1231072002648 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 1231072002649 DNA binding residues [nucleotide binding] 1231072002650 spore photoproduct lyase; Region: photo_TT_lyase; TIGR04070 1231072002651 Radical SAM superfamily; Region: Radical_SAM; pfam04055 1231072002652 Na+/H+ antiporter NhaC; Region: antiport_nhaC; TIGR00931 1231072002653 Metal-dependent hydrolases of the beta-lactamase superfamily III [General function prediction only]; Region: ElaC; COG1234 1231072002654 RbsD / FucU transport protein family; Region: RbsD_FucU; pfam05025 1231072002655 Transcriptional regulators [Transcription]; Region: PurR; COG1609 1231072002656 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 1231072002657 DNA binding site [nucleotide binding] 1231072002658 domain linker motif; other site 1231072002659 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 1231072002660 dimerization interface [polypeptide binding]; other site 1231072002661 ligand binding site [chemical binding]; other site 1231072002662 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 1231072002663 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 1231072002664 Walker A/P-loop; other site 1231072002665 ATP binding site [chemical binding]; other site 1231072002666 Q-loop/lid; other site 1231072002667 ABC transporter signature motif; other site 1231072002668 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 1231072002669 Q-loop/lid; other site 1231072002670 ABC transporter signature motif; other site 1231072002671 Walker B; other site 1231072002672 D-loop; other site 1231072002673 H-loop/switch region; other site 1231072002674 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 1231072002675 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1231072002676 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 1231072002677 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 1231072002678 TM-ABC transporter signature motif; other site 1231072002679 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 1231072002680 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Region: PBP1_ABC_sugar_binding_like_2; cd06310 1231072002681 putative ligand binding site [chemical binding]; other site 1231072002682 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 1231072002683 putative active site [active] 1231072002684 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 1231072002685 Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of nucleotides...; Region: ribokinase; cd01174 1231072002686 substrate binding site [chemical binding]; other site 1231072002687 dimer interface [polypeptide binding]; other site 1231072002688 ATP binding site [chemical binding]; other site 1231072002689 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 1231072002690 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 1231072002691 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 1231072002692 Domain of unknown function (DUF336); Region: DUF336; cl01249 1231072002693 HD supefamily hydrolase [General function prediction only]; Region: COG3294 1231072002694 CRISPR/Cas system-associated protein Cas3'' Region: Cas3''_I; cl17503 1231072002695 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1231072002696 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1231072002697 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1231072002698 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1231072002699 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1231072002700 Walker A/P-loop; other site 1231072002701 ATP binding site [chemical binding]; other site 1231072002702 Q-loop/lid; other site 1231072002703 ABC transporter signature motif; other site 1231072002704 Walker B; other site 1231072002705 D-loop; other site 1231072002706 H-loop/switch region; other site 1231072002707 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1231072002708 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1231072002709 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1231072002710 Walker A/P-loop; other site 1231072002711 ATP binding site [chemical binding]; other site 1231072002712 Q-loop/lid; other site 1231072002713 ABC transporter signature motif; other site 1231072002714 Walker B; other site 1231072002715 D-loop; other site 1231072002716 H-loop/switch region; other site 1231072002717 maltose O-acetyltransferase; Provisional; Region: PRK10092 1231072002718 Maltose O-acetyltransferase (MAT) and Galactoside O-acetyltransferase (GAT): MAT and GAT catalyze the CoA-dependent acetylation of the 6-hydroxyl group of their respective sugar substrates. MAT acetylates maltose and glucose exclusively at the C6...; Region: LbH_MAT_GAT; cd03357 1231072002719 active site 1231072002720 substrate binding site [chemical binding]; other site 1231072002721 trimer interface [polypeptide binding]; other site 1231072002722 CoA binding site [chemical binding]; other site 1231072002723 Predicted transcriptional regulators [Transcription]; Region: COG1695 1231072002724 Transcriptional regulator PadR-like family; Region: PadR; cl17335 1231072002725 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 1231072002726 Bacterial cell division membrane protein [Cell division and chromosome partitioning]; Region: FtsW; COG0772 1231072002727 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional; Region: ribB; PRK03353 1231072002728 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism]; Region: RibB; COG0108 1231072002729 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 1231072002730 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 1231072002731 non-specific DNA binding site [nucleotide binding]; other site 1231072002732 salt bridge; other site 1231072002733 sequence-specific DNA binding site [nucleotide binding]; other site 1231072002734 Formate/nitrite transporter; Region: Form_Nir_trans; pfam01226 1231072002735 Cache domain; Region: Cache_1; pfam02743 1231072002736 HAMP domain; Region: HAMP; pfam00672 1231072002737 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1231072002738 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1231072002739 dimer interface [polypeptide binding]; other site 1231072002740 putative CheW interface [polypeptide binding]; other site 1231072002741 Purine catabolism regulatory protein-like family; Region: PucR; pfam07905 1231072002742 DRTGG domain; Region: DRTGG; pfam07085 1231072002743 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 1231072002744 allantoate amidohydrolase; Reviewed; Region: PRK12893 1231072002745 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 1231072002746 active site 1231072002747 metal binding site [ion binding]; metal-binding site 1231072002748 dimer interface [polypeptide binding]; other site 1231072002749 dihydroorotase; Validated; Region: pyrC; PRK09357 1231072002750 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 1231072002751 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 1231072002752 active site 1231072002753 putative transporter; Provisional; Region: PRK10484 1231072002754 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 1231072002755 Na binding site [ion binding]; other site 1231072002756 dihydroorotate dehydrogenase electron transfer subunit; Reviewed; Region: PRK00054 1231072002757 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 1231072002758 FAD binding pocket [chemical binding]; other site 1231072002759 FAD binding motif [chemical binding]; other site 1231072002760 phosphate binding motif [ion binding]; other site 1231072002761 beta-alpha-beta structure motif; other site 1231072002762 NAD binding pocket [chemical binding]; other site 1231072002763 Iron coordination center [ion binding]; other site 1231072002764 dihydroorotate dehydrogenase (subfamily 1) family protein; Region: pyrD_sub1_fam; TIGR01037 1231072002765 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 1231072002766 heterodimer interface [polypeptide binding]; other site 1231072002767 active site 1231072002768 FMN binding site [chemical binding]; other site 1231072002769 homodimer interface [polypeptide binding]; other site 1231072002770 substrate binding site [chemical binding]; other site 1231072002771 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 1231072002772 Aspartase; Region: Aspartase; cd01357 1231072002773 active sites [active] 1231072002774 tetramer interface [polypeptide binding]; other site 1231072002775 RNA polymerase sigma-70 factor, TIGR02952 family; Region: Sig70_famx2 1231072002776 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 1231072002777 DNA binding residues [nucleotide binding] 1231072002778 Domain of unknown function (DUF4367); Region: DUF4367; pfam14285 1231072002779 amino acid transporter; Region: 2A0306; TIGR00909 1231072002780 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 1231072002781 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 1231072002782 Metallo-dependent hydrolases, subgroup A is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_A; cd01299 1231072002783 active site 1231072002784 Sensory domain found in PocR; Region: PocR; pfam10114 1231072002785 Predicted sensor domain [Signal transduction mechanisms / Transcription]; Region: PocR; COG4936 1231072002786 Histidine kinase; Region: His_kinase; pfam06580 1231072002787 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 1231072002788 ATP binding site [chemical binding]; other site 1231072002789 Mg2+ binding site [ion binding]; other site 1231072002790 G-X-G motif; other site 1231072002791 Response regulator receiver domain; Region: Response_reg; pfam00072 1231072002792 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 1231072002793 active site 1231072002794 phosphorylation site [posttranslational modification] 1231072002795 intermolecular recognition site; other site 1231072002796 dimerization interface [polypeptide binding]; other site 1231072002797 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1231072002798 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1231072002799 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1231072002800 glycyl radical enzyme, PFL2/glycerol dehydratase family; Region: PFL2-3; TIGR01774 1231072002801 Pyruvate formate lyase 2 and related enzymes; Region: PFL2_DhaB_BssA; cd01677 1231072002802 dimer interface [polypeptide binding]; other site 1231072002803 active site 1231072002804 glycine loop; other site 1231072002805 glycyl-radical enzyme activating protein family; Region: PFLE_PFLC; TIGR02494 1231072002806 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 1231072002807 FeS/SAM binding site; other site 1231072002808 TIGR03943 family protein; Region: TIGR03943 1231072002809 Predicted permeases [General function prediction only]; Region: COG0701 1231072002810 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 1231072002811 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 1231072002812 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 1231072002813 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 1231072002814 Cache domain; Region: Cache_1; pfam02743 1231072002815 HAMP domain; Region: HAMP; pfam00672 1231072002816 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1231072002817 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1231072002818 dimer interface [polypeptide binding]; other site 1231072002819 putative CheW interface [polypeptide binding]; other site 1231072002820 Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]; Region: DeoR; COG2390 1231072002821 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 1231072002822 DNA binding residues [nucleotide binding] 1231072002823 Putative sugar-binding domain; Region: Sugar-bind; pfam04198 1231072002824 L-fuculose phosphate aldolase; Provisional; Region: PRK06833 1231072002825 L-ribulose-5-phosphate 4-epimerase; Reviewed; Region: araD; PRK08193 1231072002826 intersubunit interface [polypeptide binding]; other site 1231072002827 active site 1231072002828 Zn2+ binding site [ion binding]; other site 1231072002829 Na+/H+ antiporter family; Region: Na_H_antiporter; pfam03553 1231072002830 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]; Region: COG0182; cl00348 1231072002831 methylthioribose-1-phosphate isomerase; Reviewed; Region: mtnA; PRK05720 1231072002832 methylthioribose kinase; Reviewed; Region: mtnK; PRK09550 1231072002833 Phosphotransferase enzyme family; Region: APH; pfam01636 1231072002834 Predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold [General function prediction only]; Region: LipA; COG1075 1231072002835 Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Region: HTH_BmrR; cd01107 1231072002836 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 1231072002837 DNA binding residues [nucleotide binding] 1231072002838 drug binding residues [chemical binding]; other site 1231072002839 dimer interface [polypeptide binding]; other site 1231072002840 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; smart00871 1231072002841 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 1231072002842 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 1231072002843 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 1231072002844 active site 1231072002845 phosphorylation site [posttranslational modification] 1231072002846 intermolecular recognition site; other site 1231072002847 dimerization interface [polypeptide binding]; other site 1231072002848 LytTr DNA-binding domain; Region: LytTR; pfam04397 1231072002849 Cache domain; Region: Cache_2; pfam08269 1231072002850 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 1231072002851 dimerization interface [polypeptide binding]; other site 1231072002852 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1231072002853 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1231072002854 dimer interface [polypeptide binding]; other site 1231072002855 putative CheW interface [polypeptide binding]; other site 1231072002856 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 1231072002857 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 1231072002858 Walker A/P-loop; other site 1231072002859 ATP binding site [chemical binding]; other site 1231072002860 Q-loop/lid; other site 1231072002861 ABC transporter signature motif; other site 1231072002862 Walker B; other site 1231072002863 D-loop; other site 1231072002864 H-loop/switch region; other site 1231072002865 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 1231072002866 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 1231072002867 ABC-ATPase subunit interface; other site 1231072002868 dimer interface [polypeptide binding]; other site 1231072002869 putative PBP binding regions; other site 1231072002870 Metal binding protein TroA_a. These proteins are predicted to function as initial receptors in ABC transport of metal ions in eubacteria. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and...; Region: TroA_a; cd01148 1231072002871 proposed F420-0 ABC transporter, periplasmic F420-0 binding protein; Region: F420-O_ABCperi; TIGR03868 1231072002872 putative ligand binding residues [chemical binding]; other site 1231072002873 bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase protein; Reviewed; Region: aroDE; PRK09310 1231072002874 bacteriocin-associated integral membrane (putative immunity) protein; Region: bact_immun_7tm; TIGR01654 1231072002875 Protein of unknown function (DUF1430); Region: DUF1430; pfam07242 1231072002876 Metal binding protein TroA_a. These proteins are predicted to function as initial receptors in ABC transport of metal ions in eubacteria. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and...; Region: TroA_a; cd01148 1231072002877 proposed F420-0 ABC transporter, periplasmic F420-0 binding protein; Region: F420-O_ABCperi; TIGR03868 1231072002878 putative ligand binding residues [chemical binding]; other site 1231072002879 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 1231072002880 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 1231072002881 ABC-ATPase subunit interface; other site 1231072002882 dimer interface [polypeptide binding]; other site 1231072002883 putative PBP binding regions; other site 1231072002884 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 1231072002885 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 1231072002886 Walker A/P-loop; other site 1231072002887 ATP binding site [chemical binding]; other site 1231072002888 Q-loop/lid; other site 1231072002889 ABC transporter signature motif; other site 1231072002890 Walker B; other site 1231072002891 D-loop; other site 1231072002892 H-loop/switch region; other site 1231072002893 This putative domain contains a quite highly conserved sequence of CGGC in its central region; Region: CGGC; smart01078 1231072002894 hypothetical protein; Provisional; Region: PRK09272 1231072002895 Uncharacterized family 1; belongs to a superfamily containing the transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this family was previously known as part of DUF156; Region: CsoR-like_DUF156_1; cd10158 1231072002896 putative homodimer interface [polypeptide binding]; other site 1231072002897 putative homotetramer interface [polypeptide binding]; other site 1231072002898 putative metal binding site [ion binding]; other site 1231072002899 putative homodimer-homodimer interface [polypeptide binding]; other site 1231072002900 putative allosteric switch controlling residues; other site 1231072002901 Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones]; Region: COG1331 1231072002902 TRX domain, SSP411 protein family; members of this family are highly conserved proteins present in eukaryotes, bacteria and archaea, about 600-800 amino acids in length, which contain a TRX domain with a redox active CXXC motif. The human/rat protein; Region: SSP411; cd02955 1231072002903 catalytic residues [active] 1231072002904 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 1231072002905 putative active cleft [active] 1231072002906 LanC-like proteins. LanC is the cyclase enzyme of the lanthionine synthetase. Lanthionine is a lantibiotic, a unique class of peptide antibiotics. They are ribosomally synthesized as a precursor peptide and then post-translationally modified to contain...; Region: LanC_like; cl04955 1231072002907 arginyl-tRNA synthetase; Reviewed; Region: PRK12451 1231072002908 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 1231072002909 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 1231072002910 active site 1231072002911 HIGH motif; other site 1231072002912 KMSK motif region; other site 1231072002913 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 1231072002914 tRNA binding surface [nucleotide binding]; other site 1231072002915 anticodon binding site; other site 1231072002916 RNase_H superfamily; Region: RNase_H_2; pfam13482 1231072002917 active site 1231072002918 catalytic site [active] 1231072002919 substrate binding site [chemical binding]; other site 1231072002920 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 1231072002921 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 1231072002922 G1 box; other site 1231072002923 GTP/Mg2+ binding site [chemical binding]; other site 1231072002924 Switch I region; other site 1231072002925 G2 box; other site 1231072002926 G3 box; other site 1231072002927 Switch II region; other site 1231072002928 G4 box; other site 1231072002929 G5 box; other site 1231072002930 Nucleoside recognition; Region: Gate; pfam07670 1231072002931 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 1231072002932 Nucleoside recognition; Region: Gate; pfam07670 1231072002933 Fe2+ transport system protein A [Inorganic ion transport and metabolism]; Region: FeoA; COG1918 1231072002934 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 1231072002935 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 1231072002936 motif II; other site 1231072002937 RNase_H superfamily; Region: RNase_H_2; pfam13482 1231072002938 Transcriptional regulators [Transcription]; Region: FadR; COG2186 1231072002939 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1231072002940 DNA-binding site [nucleotide binding]; DNA binding site 1231072002941 FCD domain; Region: FCD; pfam07729 1231072002942 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 1231072002943 L-lactate permease; Region: Lactate_perm; cl00701 1231072002944 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_beta; cd01714 1231072002945 Ligand binding site [chemical binding]; other site 1231072002946 Electron transfer flavoprotein domain; Region: ETF; pfam01012 1231072002947 Ferredoxin [Energy production and conversion]; Region: NapF; COG1145 1231072002948 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 1231072002949 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_alpha; cd01715 1231072002950 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 1231072002951 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 1231072002952 FAD binding domain; Region: FAD_binding_4; pfam01565 1231072002953 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 1231072002954 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1231072002955 active site 1231072002956 HIGH motif; other site 1231072002957 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1231072002958 active site 1231072002959 KMSKS motif; other site 1231072002960 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 1231072002961 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1231072002962 Beta-Casp domain; Region: Beta-Casp; smart01027 1231072002963 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 1231072002964 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 1231072002965 EamA-like transporter family; Region: EamA; pfam00892 1231072002966 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 1231072002967 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 1231072002968 Coenzyme A pyrophosphatase (CoAse), a member of the Nudix hydrolase superfamily, functions to catalyze the elimination of oxidized inactive CoA, which can inhibit CoA-utilizing enzymes. The need of CoAses mainly arises under conditions of oxidative...; Region: CoAse; cd03426 1231072002969 putative active site [active] 1231072002970 putative CoA binding site [chemical binding]; other site 1231072002971 nudix motif; other site 1231072002972 metal binding site [ion binding]; metal-binding site 1231072002973 nicotinate phosphoribosyltransferase; Validated; Region: PRK09243 1231072002974 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 1231072002975 active site 1231072002976 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 1231072002977 Part of AAA domain; Region: AAA_19; pfam13245 1231072002978 Family description; Region: UvrD_C_2; pfam13538 1231072002979 cell division protein FtsA; Region: ftsA; TIGR01174 1231072002980 Cell division protein FtsA; Region: FtsA; smart00842 1231072002981 Cell division protein FtsA; Region: FtsA; pfam14450 1231072002982 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1231072002983 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1231072002984 active site 1231072002985 stage V sporulation protein B; Region: spore_V_B; TIGR02900 1231072002986 Stage V sporulation protein B, also known as Stage III sporulation protein F, and related proteins; Region: MATE_SpoVB_like; cd13124 1231072002987 stage V sporulation protein B; Region: spore_V_B; TIGR02900 1231072002988 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 1231072002989 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 1231072002990 dinuclear metal binding motif [ion binding]; other site 1231072002991 Zinc dependent phospholipase C (alpha toxin); Region: Zn_dep_PLPC; cd11009 1231072002992 Zn binding site [ion binding]; other site 1231072002993 Fe-S oxidoreductase [Energy production and conversion]; Region: COG1032 1231072002994 B12 binding domain_like associated with radical SAM domain. This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the...; Region: radical_SAM_B12_BD; cd02068 1231072002995 Protein of unknown function (DUF4080); Region: DUF4080; pfam13311 1231072002996 V-type ATP synthase subunit H; Validated; Region: PRK08404 1231072002997 V-type ATP synthase subunit I; Validated; Region: PRK05771 1231072002998 V-type ATP synthase subunit K; Validated; Region: PRK06558 1231072002999 ATP synthase subunit C; Region: ATP-synt_C; pfam00137 1231072003000 Archaeal/vacuolar-type H+-ATPase subunit E [Energy production and conversion]; Region: NtpE; COG1390 1231072003001 V-type ATP synthase subunit E; Provisional; Region: PRK03963; cl17074 1231072003002 V-type ATP synthase subunit C; Provisional; Region: PRK01198 1231072003003 Archaeal/vacuolar-type H+-ATPase subunit C [Energy production and conversion]; Region: NtpC; COG1527 1231072003004 V-type ATP synthase subunit F; Provisional; Region: PRK01395 1231072003005 V-type ATP synthase subunit A; Provisional; Region: PRK04192 1231072003006 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1231072003007 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 1231072003008 Walker A motif/ATP binding site; other site 1231072003009 Walker B motif; other site 1231072003010 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1231072003011 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1231072003012 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 1231072003013 Walker A motif; other site 1231072003014 ATP binding site [chemical binding]; other site 1231072003015 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 1231072003016 Walker B motif; other site 1231072003017 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1231072003018 V-type ATP synthase subunit D; Reviewed; Region: PRK00373 1231072003019 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 1231072003020 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1231072003021 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 1231072003022 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 1231072003023 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 1231072003024 Bacterial fructose-1,6-bisphosphatase, glpX-encoded. A dimeric enzyme dependent on Mg(2+). glpX-encoded FPBase (FBPase class II) differs from other members of the inositol-phosphatase superfamily by permutation of secondary structure elements. The core...; Region: FBPase_glpX; cd01516 1231072003025 Bacterial fructose-1,6-bisphosphatase, glpX-encoded; Region: FBPase_glpX; pfam03320 1231072003026 putative active site [active] 1231072003027 Bacterial Ig-like domain; Region: Big_5; pfam13205 1231072003028 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 1231072003029 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 1231072003030 active site 1231072003031 metal binding site [ion binding]; metal-binding site 1231072003032 Bacterial Ig-like domain (group 4); Region: Big_4; pfam07532 1231072003033 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 1231072003034 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 1231072003035 active site 1231072003036 metal binding site [ion binding]; metal-binding site 1231072003037 HPr kinase/phosphorylase; Provisional; Region: PRK05428 1231072003038 HPr Serine kinase N terminus; Region: Hpr_kinase_N; pfam02603 1231072003039 HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent...; Region: HprK_C; cd01918 1231072003040 Hpr binding site; other site 1231072003041 active site 1231072003042 homohexamer subunit interaction site [polypeptide binding]; other site 1231072003043 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 1231072003044 5,10-methenyltetrahydrofolate synthetase; Region: MTHFS_bact; TIGR02727 1231072003045 M18 Peptidase Aminopeptidase I; Region: M18_API; cd05659 1231072003046 Aminopeptidase I zinc metalloprotease (M18); Region: Peptidase_M18; pfam02127 1231072003047 oligomer interface [polypeptide binding]; other site 1231072003048 putative active site [active] 1231072003049 metal binding site [ion binding]; metal-binding site 1231072003050 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 1231072003051 cation diffusion facilitator family transporter; Region: CDF; TIGR01297 1231072003052 Sm and related proteins; Region: Sm_like; cl00259 1231072003053 Sm1 motif; other site 1231072003054 RNA binding site [nucleotide binding]; other site 1231072003055 Transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this domain superfamily was previously known as DUF156; Region: CsoR-like_DUF156; cd10148 1231072003056 putative homodimer interface [polypeptide binding]; other site 1231072003057 putative homotetramer interface [polypeptide binding]; other site 1231072003058 putative allosteric switch controlling residues; other site 1231072003059 putative metal binding site [ion binding]; other site 1231072003060 putative homodimer-homodimer interface [polypeptide binding]; other site 1231072003061 Protein of unknown function (DUF3815); Region: DUF3815; pfam12821 1231072003062 Uncharacterized conserved protein [Function unknown]; Region: COG2966 1231072003063 Protein of unknown function (DUF1212); Region: DUF1212; pfam06738 1231072003064 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 1231072003065 SLBB domain; Region: SLBB; pfam10531 1231072003066 4Fe-4S binding domain; Region: Fer4_6; pfam12837 1231072003067 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; pfam03116 1231072003068 FMN-binding domain; Region: FMN_bind; cl01081 1231072003069 electron transport complex RsxE subunit; Provisional; Region: PRK12405 1231072003070 electron transport complex, RnfABCDGE type, A subunit; Region: rnfA; TIGR01943 1231072003071 ferredoxin; Validated; Region: PRK07118 1231072003072 4Fe-4S binding domain; Region: Fer4; pfam00037 1231072003073 4Fe-4S binding domain; Region: Fer4; pfam00037 1231072003074 Heptaprenyl diphosphate synthase component I; Region: Hpre_diP_synt_I; pfam07456 1231072003075 Listerrria innocua Lin0431 is similar to the N-Utilization Substance G (NusG) N terminal (NGN) insert (DII); Region: Lin0431_like; cd09911 1231072003076 trimer interface [polypeptide binding]; other site 1231072003077 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 1231072003078 ApbE family; Region: ApbE; pfam02424 1231072003079 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 1231072003080 Sulfatase; Region: Sulfatase; cl17466 1231072003081 phosphoribosylformylglycinamidine synthase, clade II; Region: FGAM-synthase; TIGR01857 1231072003082 AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal domain...; Region: PurM-like; cl10019 1231072003083 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 1231072003084 dimerization interface [polypeptide binding]; other site 1231072003085 ATP binding site [chemical binding]; other site 1231072003086 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 1231072003087 dimerization interface [polypeptide binding]; other site 1231072003088 ATP binding site [chemical binding]; other site 1231072003089 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 1231072003090 putative active site [active] 1231072003091 catalytic triad [active] 1231072003092 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 1231072003093 active site 1231072003094 DNA binding site [nucleotide binding] 1231072003095 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 1231072003096 TPR motif; other site 1231072003097 binding surface 1231072003098 ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein; Region: ACT_1ZPV; cd04872 1231072003099 Uncharacterized proteins with similarity to Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL_like_DUF711; cd08025 1231072003100 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as Mg2+; Region: ADPRase_NUDT5; cd03424 1231072003101 dimer interface [polypeptide binding]; other site 1231072003102 ADP-ribose binding site [chemical binding]; other site 1231072003103 active site 1231072003104 nudix motif; other site 1231072003105 metal binding site [ion binding]; metal-binding site 1231072003106 Sporulation and spore germination; Region: Germane; pfam10646 1231072003107 Low-specificity threonine aldolase (TA). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). TA catalyzes the conversion of L-threonine or L-allo-threonine to glycine and acetaldehyde in a...; Region: TA_like; cd06502 1231072003108 Beta-eliminating lyase; Region: Beta_elim_lyase; pfam01212 1231072003109 tetramer interface [polypeptide binding]; other site 1231072003110 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1231072003111 catalytic residue [active] 1231072003112 Putative Ser protein kinase [Signal transduction mechanisms]; Region: PrkA; COG2766 1231072003113 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 1231072003114 Protein of unknown function (DUF444); Region: DUF444; cl17371 1231072003115 SpoVR like protein; Region: SpoVR; pfam04293 1231072003116 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 1231072003117 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 1231072003118 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 1231072003119 putative catalytic cysteine [active] 1231072003120 gamma-glutamyl kinase; Provisional; Region: PRK05429 1231072003121 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 1231072003122 nucleotide binding site [chemical binding]; other site 1231072003123 homotetrameric interface [polypeptide binding]; other site 1231072003124 putative phosphate binding site [ion binding]; other site 1231072003125 putative allosteric binding site; other site 1231072003126 Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase; Region: AAT; pfam03417 1231072003127 histidinol-phosphatase; Provisional; Region: PRK05588 1231072003128 Polymerase and Histidinol Phosphatase domain; Region: PHP; cl17102 1231072003129 active site 1231072003130 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 1231072003131 recombination factor protein RarA; Reviewed; Region: PRK13342 1231072003132 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 1231072003133 Walker A motif; other site 1231072003134 ATP binding site [chemical binding]; other site 1231072003135 Walker B motif; other site 1231072003136 arginine finger; other site 1231072003137 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 1231072003138 Predicted transcriptional regulator [Transcription]; Region: COG1959 1231072003139 Transcriptional regulator; Region: Rrf2; cl17282 1231072003140 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 1231072003141 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 1231072003142 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1231072003143 catalytic residue [active] 1231072003144 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 1231072003145 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 1231072003146 trimerization site [polypeptide binding]; other site 1231072003147 active site 1231072003148 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 1231072003149 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 1231072003150 Ligand Binding Site [chemical binding]; other site 1231072003151 PRC-barrel domain containing protein [General function prediction only]; Region: COG3881 1231072003152 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 1231072003153 Domain of unknown function DUF20; Region: UPF0118; pfam01594 1231072003154 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 1231072003155 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 1231072003156 motif 1; other site 1231072003157 active site 1231072003158 motif 2; other site 1231072003159 motif 3; other site 1231072003160 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 1231072003161 hypothetical protein; Provisional; Region: PRK05473 1231072003162 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 1231072003163 Protein of unknown function (DUF1292); Region: DUF1292; pfam06949 1231072003164 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 1231072003165 metal binding site 2 [ion binding]; metal-binding site 1231072003166 putative DNA binding helix; other site 1231072003167 metal binding site 1 [ion binding]; metal-binding site 1231072003168 dimer interface [polypeptide binding]; other site 1231072003169 structural Zn2+ binding site [ion binding]; other site 1231072003170 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 1231072003171 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1231072003172 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 1231072003173 hypothetical protein; Provisional; Region: PRK13676 1231072003174 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 1231072003175 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 1231072003176 G1 box; other site 1231072003177 putative GEF interaction site [polypeptide binding]; other site 1231072003178 GTP/Mg2+ binding site [chemical binding]; other site 1231072003179 Switch I region; other site 1231072003180 G2 box; other site 1231072003181 G3 box; other site 1231072003182 Switch II region; other site 1231072003183 G4 box; other site 1231072003184 G5 box; other site 1231072003185 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 1231072003186 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 1231072003187 YceG-like family; Region: YceG; pfam02618 1231072003188 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 1231072003189 dimerization interface [polypeptide binding]; other site 1231072003190 Predicted O-methyltransferase [General function prediction only]; Region: COG4122 1231072003191 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 1231072003192 S-adenosylmethionine binding site [chemical binding]; other site 1231072003193 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 1231072003194 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 1231072003195 Peptidase family U32; Region: Peptidase_U32; pfam01136 1231072003196 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 1231072003197 Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway; Region: UMPK; cd02023 1231072003198 Sugar specificity; other site 1231072003199 Pyrimidine base specificity; other site 1231072003200 ATP-binding site [chemical binding]; other site 1231072003201 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 1231072003202 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1231072003203 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1231072003204 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 1231072003205 catalytic residues [active] 1231072003206 catalytic nucleophile [active] 1231072003207 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 1231072003208 Recombinase; Region: Recombinase; pfam07508 1231072003209 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 1231072003210 Domain of unknown function (DUF955); Region: DUF955; pfam06114 1231072003211 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 1231072003212 non-specific DNA binding site [nucleotide binding]; other site 1231072003213 salt bridge; other site 1231072003214 sequence-specific DNA binding site [nucleotide binding]; other site 1231072003215 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 1231072003216 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 1231072003217 non-specific DNA binding site [nucleotide binding]; other site 1231072003218 salt bridge; other site 1231072003219 sequence-specific DNA binding site [nucleotide binding]; other site 1231072003220 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 1231072003221 non-specific DNA binding site [nucleotide binding]; other site 1231072003222 salt bridge; other site 1231072003223 sequence-specific DNA binding site [nucleotide binding]; other site 1231072003224 Prophage antirepressor [Transcription]; Region: COG3617 1231072003225 BRO family, N-terminal domain; Region: Bro-N; smart01040 1231072003226 Phage antirepressor protein KilAC domain; Region: ANT; pfam03374 1231072003227 Protein of unknown function (DUF1250); Region: DUF1250; cl11485 1231072003228 Protein of unknown function (DUF2800); Region: DUF2800; pfam10926 1231072003229 Protein of unknown function (DUF2815); Region: DUF2815; pfam10991 1231072003230 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_A; cd08642 1231072003231 active site 1231072003232 DNA binding site [nucleotide binding] 1231072003233 catalytic site [active] 1231072003234 Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A; cl02626 1231072003235 Virulence-associated protein E; Region: VirE; pfam05272 1231072003236 This model contains proteins with the VRR-NUC domain; Region: VRR_NUC; smart00990 1231072003237 Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]; Region: HepA; COG0553 1231072003238 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 1231072003239 nucleotide binding region [chemical binding]; other site 1231072003240 ATP-binding site [chemical binding]; other site 1231072003241 Phage portal protein, SPP1 Gp6-like; Region: Phage_prot_Gp6; pfam05133 1231072003242 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 1231072003243 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 1231072003244 YjzC-like protein; Region: YjzC; pfam14168 1231072003245 Phage minor structural protein GP20; Region: Phage_GP20; pfam06810 1231072003246 Phage major capsid protein E; Region: Phage_cap_E; pfam03864 1231072003247 Bacterial Ig-like domain; Region: Big_5; pfam13205 1231072003248 Phage-related minor tail protein; Region: PhageMin_Tail; pfam10145 1231072003249 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 1231072003250 metal ion-dependent adhesion site (MIDAS); other site 1231072003251 Restriction endonuclease [Defense mechanisms]; Region: COG3587 1231072003252 Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes; Region: FA58C; cl12042 1231072003253 Haemolysin XhlA; Region: XhlA; pfam10779 1231072003254 Muramidase (flagellum-specific) [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlgJ; COG1705 1231072003255 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 1231072003256 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 1231072003257 P-loop; other site 1231072003258 Magnesium ion binding site [ion binding]; other site 1231072003259 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 1231072003260 Magnesium ion binding site [ion binding]; other site 1231072003261 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 1231072003262 DNA binding residues [nucleotide binding] 1231072003263 Shikimate 5-dehydrogenase [Amino acid transport and metabolism]; Region: AroE; COG0169 1231072003264 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 1231072003265 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 1231072003266 shikimate binding site; other site 1231072003267 NAD(P) binding site [chemical binding]; other site 1231072003268 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 1231072003269 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 1231072003270 Walker A motif; other site 1231072003271 ATP binding site [chemical binding]; other site 1231072003272 Walker B motif; other site 1231072003273 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 1231072003274 EpsO protein participates in the methanolan synthesis; Region: EpsO_like; cd06438 1231072003275 DXD motif; other site 1231072003276 cell division protein FtsA; Region: ftsA; TIGR01174 1231072003277 Cell division protein FtsA; Region: FtsA; smart00842 1231072003278 Cell division protein FtsA; Region: FtsA; pfam14450 1231072003279 cell division protein FtsZ; Validated; Region: PRK09330 1231072003280 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 1231072003281 nucleotide binding site [chemical binding]; other site 1231072003282 SulA interaction site; other site 1231072003283 Sporulation factor SpoIIGA; Region: Peptidase_U4; pfam03419 1231072003284 sigma-E processing peptidase SpoIIGA; Region: spore_II_GA; TIGR02854 1231072003285 sporulation sigma factor SigE; Reviewed; Region: PRK08301 1231072003286 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1231072003287 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 1231072003288 DNA binding residues [nucleotide binding] 1231072003289 sporulation sigma factor SigG; Reviewed; Region: PRK08215 1231072003290 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1231072003291 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 1231072003292 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 1231072003293 DNA binding residues [nucleotide binding] 1231072003294 Protein implicated in RNA metabolism, contains PRC-barrel domain [General function prediction only]; Region: COG1873; cl17889 1231072003295 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 1231072003296 ATP cone domain; Region: ATP-cone; pfam03477 1231072003297 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1231072003298 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 1231072003299 active site 1231072003300 phosphorylation site [posttranslational modification] 1231072003301 intermolecular recognition site; other site 1231072003302 dimerization interface [polypeptide binding]; other site 1231072003303 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 1231072003304 DNA binding site [nucleotide binding] 1231072003305 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 1231072003306 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 1231072003307 dimerization interface [polypeptide binding]; other site 1231072003308 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 1231072003309 PAS domain; Region: PAS; smart00091 1231072003310 putative active site [active] 1231072003311 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 1231072003312 dimer interface [polypeptide binding]; other site 1231072003313 phosphorylation site [posttranslational modification] 1231072003314 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 1231072003315 ATP binding site [chemical binding]; other site 1231072003316 Mg2+ binding site [ion binding]; other site 1231072003317 G-X-G motif; other site 1231072003318 PBP superfamily domain; Region: PBP_like_2; cl17296 1231072003319 phosphate ABC transporter, permease protein PstC; Region: phosphate_pstC; TIGR02138 1231072003320 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 1231072003321 dimer interface [polypeptide binding]; other site 1231072003322 conserved gate region; other site 1231072003323 putative PBP binding loops; other site 1231072003324 ABC-ATPase subunit interface; other site 1231072003325 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstA; COG0581 1231072003326 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 1231072003327 dimer interface [polypeptide binding]; other site 1231072003328 conserved gate region; other site 1231072003329 putative PBP binding loops; other site 1231072003330 ABC-ATPase subunit interface; other site 1231072003331 ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: PstB; COG1117 1231072003332 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 1231072003333 Walker A/P-loop; other site 1231072003334 ATP binding site [chemical binding]; other site 1231072003335 Q-loop/lid; other site 1231072003336 ABC transporter signature motif; other site 1231072003337 Walker B; other site 1231072003338 D-loop; other site 1231072003339 H-loop/switch region; other site 1231072003340 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated; Region: PDZ; cl00117 1231072003341 putative FeS-containing Cyanobacterial-specific oxidoreductase; Region: cyano_FeS_chp; TIGR03279 1231072003342 Protein of unknown function (DUF512); Region: DUF512; pfam04459 1231072003343 GTP-binding protein Der; Reviewed; Region: PRK00093 1231072003344 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 1231072003345 G1 box; other site 1231072003346 GTP/Mg2+ binding site [chemical binding]; other site 1231072003347 Switch I region; other site 1231072003348 G2 box; other site 1231072003349 Switch II region; other site 1231072003350 G3 box; other site 1231072003351 G4 box; other site 1231072003352 G5 box; other site 1231072003353 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 1231072003354 G1 box; other site 1231072003355 GTP/Mg2+ binding site [chemical binding]; other site 1231072003356 Switch I region; other site 1231072003357 G2 box; other site 1231072003358 G3 box; other site 1231072003359 Switch II region; other site 1231072003360 G4 box; other site 1231072003361 G5 box; other site 1231072003362 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 1231072003363 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 1231072003364 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 1231072003365 Stage IV sporulation protein A (spore_IV_A); Region: Spore_IV_A; pfam09547 1231072003366 stage IV sporulation protein A; Region: spore_IV_A; TIGR02836 1231072003367 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1231072003368 Alpha/beta hydrolase of unknown function (DUF1057); Region: DUF1057; pfam06342 1231072003369 TAP-like protein; Region: Abhydrolase_4; pfam08386 1231072003370 Domain of Unknown Function (DUF1259); Region: DUF1529; pfam07485 1231072003371 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 1231072003372 Predicted membrane protein [Function unknown]; Region: COG3212 1231072003373 Homoserine O-succinyltransferase; Region: HTS; pfam04204 1231072003374 Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS); Region: GATase1_HTS; cd03131 1231072003375 proposed active site lysine [active] 1231072003376 conserved cys residue [active] 1231072003377 Bacterial protein of unknown function (DUF903); Region: DUF903; pfam06004 1231072003378 O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]; Region: MET17; COG2873 1231072003379 CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of...; Region: CGS_like; cd00614 1231072003380 homodimer interface [polypeptide binding]; other site 1231072003381 substrate-cofactor binding pocket; other site 1231072003382 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1231072003383 catalytic residue [active] 1231072003384 Predicted flavoproteins [General function prediction only]; Region: COG2081 1231072003385 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1231072003386 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1231072003387 dimer interface [polypeptide binding]; other site 1231072003388 putative CheW interface [polypeptide binding]; other site 1231072003389 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 1231072003390 Carbon monoxide dehydrogenase (CODH) is found in acetogenic and methanogenic organisms and is responsible for the synthesis and breakdown of acetyl-CoA, respectively. CODH has two types of metal clusters, a cubane [Fe4-S4] center (B-cluster) similar to...; Region: CODH; cd01915 1231072003391 carbon-monoxide dehydrogenase, catalytic subunit; Region: CO_DH_cata; TIGR01702 1231072003392 ACS interaction site; other site 1231072003393 CODH interaction site; other site 1231072003394 cubane metal cluster (B-cluster) [ion binding]; other site 1231072003395 Ni-Fe-S cluster (C-cluster) [ion binding]; other site 1231072003396 Protein of unknown function (DUF1294); Region: DUF1294; pfam06961 1231072003397 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 1231072003398 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 1231072003399 putative active site [active] 1231072003400 putative metal binding site [ion binding]; other site 1231072003401 hypothetical protein; Provisional; Region: PRK06771 1231072003402 Transposase IS200 like; Region: Y1_Tnp; pfam01797 1231072003403 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; cl07055 1231072003404 DnaA box-binding interface [nucleotide binding]; other site 1231072003405 pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric; Region: pyruv_ox_red; TIGR02176 1231072003406 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 1231072003407 PYR/PP interface [polypeptide binding]; other site 1231072003408 TPP binding site [chemical binding]; other site 1231072003409 dimer interface [polypeptide binding]; other site 1231072003410 substrate binding site [chemical binding]; other site 1231072003411 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 1231072003412 Domain of unknown function; Region: EKR; pfam10371 1231072003413 4Fe-4S binding domain; Region: Fer4_6; pfam12837 1231072003414 4Fe-4S binding domain; Region: Fer4; pfam00037 1231072003415 Thiamine pyrophosphate (TPP family), PFOR_PNO subfamily, TPP-binding module; composed of proteins similar to the single subunit pyruvate ferredoxin oxidoreductase (PFOR) of Desulfovibrio Africanus, present in bacteria and amitochondriate eukaryotes. This...; Region: TPP_PFOR_PNO; cd03377 1231072003416 TPP-binding site [chemical binding]; other site 1231072003417 dimer interface [polypeptide binding]; other site 1231072003418 Domain of unknown function (DUF3787); Region: DUF3787; pfam12655 1231072003419 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 1231072003420 metal binding site [ion binding]; metal-binding site 1231072003421 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 1231072003422 Domain of unknown function (DUF4300); Region: DUF4300; pfam14133 1231072003423 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1231072003424 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1231072003425 Walker A/P-loop; other site 1231072003426 ATP binding site [chemical binding]; other site 1231072003427 Q-loop/lid; other site 1231072003428 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1231072003429 ABC transporter signature motif; other site 1231072003430 Walker B; other site 1231072003431 D-loop; other site 1231072003432 ABC transporter; Region: ABC_tran_2; pfam12848 1231072003433 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1231072003434 Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]; Region: HtpX; COG0501 1231072003435 YcxB-like protein; Region: YcxB; pfam14317 1231072003436 Radical SAM superfamily; Region: Radical_SAM; pfam04055 1231072003437 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 1231072003438 FeS/SAM binding site; other site 1231072003439 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1231072003440 Coenzyme A binding pocket [chemical binding]; other site 1231072003441 Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; Region: HTH_TipAL-Mta; cd01106 1231072003442 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 1231072003443 DNA binding residues [nucleotide binding] 1231072003444 dimer interface [polypeptide binding]; other site 1231072003445 TipAS antibiotic-recognition domain; Region: TipAS; pfam07739 1231072003446 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt; cl00231 1231072003447 ATP binding site [chemical binding]; other site 1231072003448 active site 1231072003449 substrate binding site [chemical binding]; other site 1231072003450 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 1231072003451 helix_turn_helix, Deoxyribose operon repressor; Region: HTH_DEOR; smart00420 1231072003452 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 1231072003453 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 1231072003454 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 1231072003455 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 1231072003456 Major Facilitator Superfamily; Region: MFS_1; pfam07690 1231072003457 putative substrate translocation pore; other site 1231072003458 DRE-TIM metallolyase superfamily; Region: DRE_TIM_metallolyase; cl07974 1231072003459 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 1231072003460 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; cl12060 1231072003461 Metal-binding active site; metal-binding site 1231072003462 Sulphur transport; Region: Sulf_transp; pfam04143 1231072003463 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 1231072003464 CPxP motif; other site 1231072003465 putative inner membrane protein; Provisional; Region: PRK11099 1231072003466 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1231072003467 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1231072003468 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 1231072003469 putative dimerization interface [polypeptide binding]; other site 1231072003470 CoA-disulfide reductase; Region: CoA_CoA_reduc; TIGR03385 1231072003471 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1231072003472 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1231072003473 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1231072003474 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 1231072003475 active site residue [active] 1231072003476 putative inner membrane protein; Provisional; Region: PRK11099 1231072003477 Sulphur transport; Region: Sulf_transp; pfam04143 1231072003478 Sulphur transport; Region: Sulf_transp; pfam04143 1231072003479 Predicted glycosyl hydrolase [General function prediction only]; Region: COG3858 1231072003480 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 1231072003481 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 1231072003482 Cortical fragment-lytic enzyme (CFLE) is a peptidoglycan hydrolase involved in bacterial endospore germination. CFLE is expressed as an inactive preprotein (called SleB) in the forespore compartment of sporulating cells. SleB translocates across the...; Region: GH18_CFLE_spore_hydrolase; cd02874 1231072003483 active site 1231072003484 Arsenate Reductase (ArsC) family, unknown subfamily; uncharacterized proteins containing a CXXC motif with similarity to thioredoxin (TRX)-fold arsenic reductases, ArsC. Proteins containing a redox active CXXC motif like TRX and glutaredoxin (GRX)...; Region: ArsC_like; cd03036 1231072003485 ArsC family; Region: ArsC; pfam03960 1231072003486 putative ArsC-like catalytic residues; other site 1231072003487 putative TRX-like catalytic residues [active] 1231072003488 Rubrerythrin [Energy production and conversion]; Region: COG1592 1231072003489 Rubrerythrin, ferritin-like diiron-binding domain; Region: Rubrerythrin; cd01041 1231072003490 binuclear metal center [ion binding]; other site 1231072003491 Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and...; Region: rubredoxin_SM; cd00729 1231072003492 iron binding site [ion binding]; other site 1231072003493 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 1231072003494 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 1231072003495 Domain of unknown function (DUF348); Region: DUF348; pfam03990 1231072003496 Domain of unknown function (DUF348); Region: DUF348; pfam03990 1231072003497 G5 domain; Region: G5; pfam07501 1231072003498 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3584 1231072003499 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 1231072003500 Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a deformed (beta/alpha)8 barrel fold with 5- or 6-strands; Region: CE4_NodB_like_5s_6s; cd10918 1231072003501 putative active site [active] 1231072003502 putative metal binding site [ion binding]; other site 1231072003503 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 1231072003504 Sodium:alanine symporter family; Region: Na_Ala_symp; pfam01235 1231072003505 Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators; Region: HTH_MerR-like; cd00592 1231072003506 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 1231072003507 DNA binding residues [nucleotide binding] 1231072003508 dimer interface [polypeptide binding]; other site 1231072003509 Acetyltransferase (GNAT) domain; Region: Acetyltransf_8; pfam13523 1231072003510 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1231072003511 Coenzyme A binding pocket [chemical binding]; other site 1231072003512 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 1231072003513 Na2 binding site [ion binding]; other site 1231072003514 putative substrate binding site 1 [chemical binding]; other site 1231072003515 Na binding site 1 [ion binding]; other site 1231072003516 putative substrate binding site 2 [chemical binding]; other site 1231072003517 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072003518 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072003519 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072003520 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 1231072003521 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 1231072003522 intersubunit interface [polypeptide binding]; other site 1231072003523 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 1231072003524 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 1231072003525 NEAr Transport domain, a component of cell surface proteins; Region: NEAT; cd06920 1231072003526 heme-binding site [chemical binding]; other site 1231072003527 NEAr Transport domain, a component of cell surface proteins; Region: NEAT; cd06920 1231072003528 heme-binding site [chemical binding]; other site 1231072003529 NEAr Transport domain, a component of cell surface proteins; Region: NEAT; cd06920 1231072003530 heme-binding site [chemical binding]; other site 1231072003531 NEAr Transport domain, a component of cell surface proteins; Region: NEAT; cd06920 1231072003532 heme-binding site [chemical binding]; other site 1231072003533 NEAr Transport domain, a component of cell surface proteins; Region: NEAT; cd06920 1231072003534 heme-binding site [chemical binding]; other site 1231072003535 NEAr Transport domain, a component of cell surface proteins; Region: NEAT; cd06920 1231072003536 heme-binding site [chemical binding]; other site 1231072003537 NEAr Transport domain, a component of cell surface proteins; Region: NEAT; cl02760 1231072003538 heme-binding site [chemical binding]; other site 1231072003539 NEAr Transport domain, a component of cell surface proteins; Region: NEAT; cd06920 1231072003540 heme-binding site [chemical binding]; other site 1231072003541 heme ABC transporter, heme-binding protein isdE; Region: IsdE; TIGR03659 1231072003542 Siderophore binding protein FatB. These proteins have been shown to function as ABC-type initial receptors in the siderophore-mediated iron uptake in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins...; Region: FatB; cd01140 1231072003543 putative ligand binding residues [chemical binding]; other site 1231072003544 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 1231072003545 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 1231072003546 ABC-ATPase subunit interface; other site 1231072003547 dimer interface [polypeptide binding]; other site 1231072003548 putative PBP binding regions; other site 1231072003549 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 1231072003550 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 1231072003551 Walker A/P-loop; other site 1231072003552 ATP binding site [chemical binding]; other site 1231072003553 Q-loop/lid; other site 1231072003554 ABC transporter signature motif; other site 1231072003555 Walker B; other site 1231072003556 D-loop; other site 1231072003557 H-loop/switch region; other site 1231072003558 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved...; Region: Sortase_D_5; cd06166 1231072003559 active site 1231072003560 catalytic site [active] 1231072003561 ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]; Region: CydD; COG4988 1231072003562 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1231072003563 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1231072003564 Walker A/P-loop; other site 1231072003565 ATP binding site [chemical binding]; other site 1231072003566 Q-loop/lid; other site 1231072003567 ABC transporter signature motif; other site 1231072003568 Walker B; other site 1231072003569 D-loop; other site 1231072003570 H-loop/switch region; other site 1231072003571 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1231072003572 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1231072003573 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1231072003574 Walker A/P-loop; other site 1231072003575 ATP binding site [chemical binding]; other site 1231072003576 Q-loop/lid; other site 1231072003577 ABC transporter signature motif; other site 1231072003578 Walker B; other site 1231072003579 D-loop; other site 1231072003580 H-loop/switch region; other site 1231072003581 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072003582 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072003583 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072003584 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 1231072003585 HD domain; Region: HD_3; pfam13023 1231072003586 Uncharacterized protein family (UPF0157); Region: UPF0157; pfam04229 1231072003587 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 1231072003588 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 1231072003589 active site 1231072003590 NTP binding site [chemical binding]; other site 1231072003591 metal binding triad [ion binding]; metal-binding site 1231072003592 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 1231072003593 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 1231072003594 tRNA nucleotidyltransferase domain 2 putative; Region: tRNA_NucTran2_2; pfam13735 1231072003595 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 1231072003596 GIY-YIG motif/motif A; other site 1231072003597 putative active site [active] 1231072003598 putative metal binding site [ion binding]; other site 1231072003599 Transposase IS200 like; Region: Y1_Tnp; pfam01797 1231072003600 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 1231072003601 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 1231072003602 G1 box; other site 1231072003603 GTP/Mg2+ binding site [chemical binding]; other site 1231072003604 Switch I region; other site 1231072003605 G2 box; other site 1231072003606 G3 box; other site 1231072003607 Switch II region; other site 1231072003608 G4 box; other site 1231072003609 G5 box; other site 1231072003610 Nucleoside recognition; Region: Gate; pfam07670 1231072003611 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 1231072003612 Nucleoside recognition; Region: Gate; pfam07670 1231072003613 FeoA domain; Region: FeoA; cl00838 1231072003614 FeoA domain; Region: FeoA; pfam04023 1231072003615 putative septicolysin, cholesterol-dependent cytolysin family and related proteins; Region: septicolysin_like; cd12208 1231072003616 oligomer interface [polypeptide binding]; other site 1231072003617 Domain of unknown function found in archaea, bacteria, and plants; Region: DUF296; cd11378 1231072003618 trimer interface [polypeptide binding]; other site 1231072003619 putative Zn binding site [ion binding]; other site 1231072003620 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1231072003621 trimer interface [polypeptide binding]; other site 1231072003622 active site 1231072003623 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 1231072003624 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 1231072003625 HAMP domain; Region: HAMP; pfam00672 1231072003626 dimerization interface [polypeptide binding]; other site 1231072003627 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1231072003628 dimer interface [polypeptide binding]; other site 1231072003629 putative CheW interface [polypeptide binding]; other site 1231072003630 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1231072003631 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1231072003632 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 1231072003633 putative dimerization interface [polypeptide binding]; other site 1231072003634 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 1231072003635 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 1231072003636 Bacterial protein of unknown function (DUF939); Region: DUF939; pfam06081 1231072003637 hypothetical protein; Provisional; Region: PRK11820 1231072003638 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 1231072003639 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 1231072003640 hypothetical protein; Provisional; Region: PRK04323 1231072003641 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 1231072003642 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 1231072003643 catalytic site [active] 1231072003644 G-X2-G-X-G-K; other site 1231072003645 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 1231072003646 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 1231072003647 Flavoprotein; Region: Flavoprotein; pfam02441 1231072003648 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 1231072003649 primosome assembly protein PriA; Validated; Region: PRK05580 1231072003650 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 1231072003651 ATP binding site [chemical binding]; other site 1231072003652 putative Mg++ binding site [ion binding]; other site 1231072003653 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 1231072003654 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 1231072003655 ATP-binding site [chemical binding]; other site 1231072003656 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 1231072003657 active site 1231072003658 catalytic residues [active] 1231072003659 metal binding site [ion binding]; metal-binding site 1231072003660 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 1231072003661 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 1231072003662 putative active site [active] 1231072003663 substrate binding site [chemical binding]; other site 1231072003664 putative cosubstrate binding site; other site 1231072003665 catalytic site [active] 1231072003666 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 1231072003667 substrate binding site [chemical binding]; other site 1231072003668 Putative neutral zinc metallopeptidase; Region: Zn_peptidase_2; pfam04298 1231072003669 16S rRNA methyltransferase B; Provisional; Region: PRK14902 1231072003670 NusB family; Region: NusB; pfam01029 1231072003671 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 1231072003672 S-adenosylmethionine binding site [chemical binding]; other site 1231072003673 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14454 1231072003674 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 1231072003675 FeS/SAM binding site; other site 1231072003676 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 1231072003677 Protein phosphatase 2C; Region: PP2C; pfam00481 1231072003678 active site 1231072003679 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 1231072003680 Catalytic domain of Protein Kinases; Region: PKc; cd00180 1231072003681 active site 1231072003682 ATP binding site [chemical binding]; other site 1231072003683 substrate binding site [chemical binding]; other site 1231072003684 activation loop (A-loop); other site 1231072003685 PASTA domain of bacterial serine/threonine kinase pknB-like proteins. PknB is a member of a group of related transmembrane sensor kinases present in many gram positive bacteria, which has been shown to regulate cell shape in Mycobacterium tubercolosis; Region: PASTA_pknB; cd06577 1231072003686 PASTA domain of bacterial serine/threonine kinase pknB-like proteins. PknB is a member of a group of related transmembrane sensor kinases present in many gram positive bacteria, which has been shown to regulate cell shape in Mycobacterium tubercolosis; Region: PASTA_pknB; cd06577 1231072003687 PASTA domain of bacterial serine/threonine kinase pknB-like proteins. PknB is a member of a group of related transmembrane sensor kinases present in many gram positive bacteria, which has been shown to regulate cell shape in Mycobacterium tubercolosis; Region: PASTA_pknB; cd06577 1231072003688 S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of...; Region: S1_YloQ_GTPase; cd04466 1231072003689 RNA binding site [nucleotide binding]; other site 1231072003690 homodimer interface [polypeptide binding]; other site 1231072003691 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 1231072003692 GTPase/Zn-binding domain interface [polypeptide binding]; other site 1231072003693 GTP/Mg2+ binding site [chemical binding]; other site 1231072003694 G4 box; other site 1231072003695 G5 box; other site 1231072003696 G1 box; other site 1231072003697 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 1231072003698 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 1231072003699 substrate binding site [chemical binding]; other site 1231072003700 hexamer interface [polypeptide binding]; other site 1231072003701 metal binding site [ion binding]; metal-binding site 1231072003702 Thiamine pyrophosphokinase; Region: TPK; cd07995 1231072003703 thiamine pyrophosphokinase; Region: thi_PPkinase; TIGR01378 1231072003704 active site 1231072003705 dimerization interface [polypeptide binding]; other site 1231072003706 thiamine binding site [chemical binding]; other site 1231072003707 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 1231072003708 Asp23 family; Region: Asp23; pfam03780 1231072003709 DAK2 domain fusion protein YloV; Region: YloV; TIGR03599 1231072003710 DAK2 domain; Region: Dak2; pfam02734 1231072003711 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 1231072003712 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 1231072003713 ssDNA binding site; other site 1231072003714 generic binding surface II; other site 1231072003715 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 1231072003716 ATP binding site [chemical binding]; other site 1231072003717 putative Mg++ binding site [ion binding]; other site 1231072003718 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 1231072003719 nucleotide binding region [chemical binding]; other site 1231072003720 ATP-binding site [chemical binding]; other site 1231072003721 Conserved hypothetical protein 95; Region: Cons_hypoth95; pfam03602 1231072003722 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 1231072003723 S-adenosylmethionine binding site [chemical binding]; other site 1231072003724 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 1231072003725 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 1231072003726 active site 1231072003727 (T/H)XGH motif; other site 1231072003728 sporulation integral membrane protein YlbJ; Region: spore_ylbJ; TIGR02871 1231072003729 Nucleoside recognition; Region: Gate; pfam07670 1231072003730 HIGH Nucleotidyl Transferase; Region: HIGH_NTase1; cl17673 1231072003731 HIGH Nucleotidyl Transferase; Region: HIGH_NTase1; cl17673 1231072003732 phosphotransacetylase; Reviewed; Region: eutD; PRK09653 1231072003733 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 1231072003734 propionate/acetate kinase; Provisional; Region: PRK12379 1231072003735 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 1231072003736 50S ribosomal protein L32; Reviewed; Region: rpmF; PRK12286 1231072003737 putative phosphate acyltransferase; Provisional; Region: PRK05331 1231072003738 acyl carrier protein; Provisional; Region: acpP; PRK00982 1231072003739 ribonuclease III; Reviewed; Region: rnc; PRK00102 1231072003740 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 1231072003741 dimerization interface [polypeptide binding]; other site 1231072003742 active site 1231072003743 metal binding site [ion binding]; metal-binding site 1231072003744 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 1231072003745 dsRNA binding site [nucleotide binding]; other site 1231072003746 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 1231072003747 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 1231072003748 FeS/SAM binding site; other site 1231072003749 Stage V sporulation protein S (SpoVS); Region: SpoVS; pfam04232 1231072003750 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 1231072003751 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 1231072003752 Walker A/P-loop; other site 1231072003753 ATP binding site [chemical binding]; other site 1231072003754 Q-loop/lid; other site 1231072003755 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; smart00968 1231072003756 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 1231072003757 ABC transporter signature motif; other site 1231072003758 Walker B; other site 1231072003759 D-loop; other site 1231072003760 H-loop/switch region; other site 1231072003761 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 1231072003762 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 1231072003763 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 1231072003764 P loop; other site 1231072003765 GTP binding site [chemical binding]; other site 1231072003766 putative DNA-binding protein; Validated; Region: PRK00118 1231072003767 signal recognition particle protein; Provisional; Region: PRK10867 1231072003768 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 1231072003769 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 1231072003770 P loop; other site 1231072003771 GTP binding site [chemical binding]; other site 1231072003772 Signal peptide binding domain; Region: SRP_SPB; pfam02978 1231072003773 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 1231072003774 Predicted RNA-binding protein (contains KH domain) [General function prediction only]; Region: COG1837 1231072003775 hypothetical protein; Provisional; Region: PRK00468 1231072003776 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 1231072003777 RimM N-terminal domain; Region: RimM; pfam01782 1231072003778 PRC-barrel domain; Region: PRC; pfam05239 1231072003779 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 1231072003780 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 1231072003781 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 1231072003782 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 1231072003783 Catalytic site [active] 1231072003784 GTPase YlqF; Reviewed; Region: rbgA; PRK09563 1231072003785 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 1231072003786 GTP/Mg2+ binding site [chemical binding]; other site 1231072003787 G4 box; other site 1231072003788 G5 box; other site 1231072003789 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 1231072003790 G1 box; other site 1231072003791 G1 box; other site 1231072003792 GTP/Mg2+ binding site [chemical binding]; other site 1231072003793 Switch I region; other site 1231072003794 G2 box; other site 1231072003795 G2 box; other site 1231072003796 G3 box; other site 1231072003797 G3 box; other site 1231072003798 Switch II region; other site 1231072003799 Switch II region; other site 1231072003800 RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner; Region: RNase_H; cl14782 1231072003801 active site 1231072003802 RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner; Region: RNase_H; cl14782 1231072003803 RNA/DNA hybrid binding site [nucleotide binding]; other site 1231072003804 active site 1231072003805 hypothetical protein; Reviewed; Region: PRK12497 1231072003806 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 1231072003807 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 1231072003808 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 1231072003809 Walker A motif; other site 1231072003810 ATP binding site [chemical binding]; other site 1231072003811 Walker B motif; other site 1231072003812 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 1231072003813 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 1231072003814 DNA protecting protein DprA; Region: dprA; TIGR00732 1231072003815 TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the...; Region: TOPRIM_TopoIA_TopoI; cd03363 1231072003816 active site 1231072003817 interdomain interaction site; other site 1231072003818 putative metal-binding site [ion binding]; other site 1231072003819 nucleotide binding site [chemical binding]; other site 1231072003820 Bacterial DNA topoisomeraes I ATP-binding domain; Region: TOP1Bc; smart00436 1231072003821 domain I; other site 1231072003822 phosphate binding site [ion binding]; other site 1231072003823 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 1231072003824 domain III; other site 1231072003825 DNA binding groove [nucleotide binding] 1231072003826 catalytic site [active] 1231072003827 nucleotide binding site [chemical binding]; other site 1231072003828 domain II; other site 1231072003829 domain IV; other site 1231072003830 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 1231072003831 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 1231072003832 Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]; Region: TopA; COG0551 1231072003833 transcriptional repressor CodY; Validated; Region: PRK04158 1231072003834 CodY GAF-like domain; Region: CodY; pfam06018 1231072003835 CodY helix-turn-helix domain; Region: HTH_CodY; pfam08222 1231072003836 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 1231072003837 rRNA interaction site [nucleotide binding]; other site 1231072003838 S8 interaction site; other site 1231072003839 putative laminin-1 binding site; other site 1231072003840 elongation factor Ts; Provisional; Region: tsf; PRK09377 1231072003841 UBA/TS-N domain; Region: UBA; pfam00627 1231072003842 Elongation factor TS; Region: EF_TS; pfam00889 1231072003843 Elongation factor TS; Region: EF_TS; pfam00889 1231072003844 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 1231072003845 putative nucleotide binding site [chemical binding]; other site 1231072003846 uridine monophosphate binding site [chemical binding]; other site 1231072003847 homohexameric interface [polypeptide binding]; other site 1231072003848 ribosome recycling factor; Reviewed; Region: frr; PRK00083 1231072003849 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 1231072003850 hinge region; other site 1231072003851 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 1231072003852 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cd00475 1231072003853 catalytic residue [active] 1231072003854 putative FPP diphosphate binding site; other site 1231072003855 putative FPP binding hydrophobic cleft; other site 1231072003856 dimer interface [polypeptide binding]; other site 1231072003857 putative IPP diphosphate binding site; other site 1231072003858 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 1231072003859 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 1231072003860 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; cl00465 1231072003861 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 1231072003862 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 1231072003863 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 1231072003864 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 1231072003865 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 1231072003866 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 1231072003867 active site 1231072003868 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 1231072003869 protein binding site [polypeptide binding]; other site 1231072003870 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 1231072003871 putative substrate binding region [chemical binding]; other site 1231072003872 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 1231072003873 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 1231072003874 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 1231072003875 DNA polymerase III PolC; Validated; Region: polC; PRK00448 1231072003876 DNA polymerase III polC-type N-terminus; Region: DNA_pol3_alph_N; pfam11490 1231072003877 polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two...; Region: polC_OBF; cd04484 1231072003878 generic binding surface II; other site 1231072003879 generic binding surface I; other site 1231072003880 Polymerase and Histidinol Phosphatase domain; Region: PHP; cl17102 1231072003881 active site 1231072003882 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 1231072003883 active site 1231072003884 catalytic site [active] 1231072003885 substrate binding site [chemical binding]; other site 1231072003886 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at PolC gene; Region: PHP_PolIIIA_POLC; cd07435 1231072003887 ribosome maturation protein RimP; Reviewed; Region: PRK00092 1231072003888 Sm and related proteins; Region: Sm_like; cl00259 1231072003889 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 1231072003890 putative oligomer interface [polypeptide binding]; other site 1231072003891 putative RNA binding site [nucleotide binding]; other site 1231072003892 transcription elongation factor NusA; Provisional; Region: nusA; PRK12327 1231072003893 NusA N-terminal domain; Region: NusA_N; pfam08529 1231072003894 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 1231072003895 RNA binding site [nucleotide binding]; other site 1231072003896 homodimer interface [polypeptide binding]; other site 1231072003897 NusA-like KH domain; Region: KH_5; pfam13184 1231072003898 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 1231072003899 G-X-X-G motif; other site 1231072003900 Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; structure revealed putative RNA binding cleft; proteins are encoded by an operon that includes other proteins involved in transcription and/or translation; Region: YlxR; cd00279 1231072003901 putative RNA binding cleft [nucleotide binding]; other site 1231072003902 ribosomal protein L7Ae family protein; Provisional; Region: PRK05583 1231072003903 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 1231072003904 translation initiation factor IF-2; Region: IF-2; TIGR00487 1231072003905 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 1231072003906 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 1231072003907 G1 box; other site 1231072003908 putative GEF interaction site [polypeptide binding]; other site 1231072003909 GTP/Mg2+ binding site [chemical binding]; other site 1231072003910 Switch I region; other site 1231072003911 G2 box; other site 1231072003912 G3 box; other site 1231072003913 Switch II region; other site 1231072003914 G4 box; other site 1231072003915 G5 box; other site 1231072003916 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 1231072003917 Translation-initiation factor 2; Region: IF-2; pfam11987 1231072003918 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 1231072003919 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 1231072003920 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 1231072003921 DHH family; Region: DHH; pfam01368 1231072003922 DHHA1 domain; Region: DHHA1; pfam02272 1231072003923 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK00130 1231072003924 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 1231072003925 RNA binding site [nucleotide binding]; other site 1231072003926 active site 1231072003927 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 1231072003928 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 1231072003929 active site 1231072003930 Riboflavin kinase; Region: Flavokinase; pfam01687 1231072003931 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 1231072003932 16S/18S rRNA binding site [nucleotide binding]; other site 1231072003933 S13e-L30e interaction site [polypeptide binding]; other site 1231072003934 25S rRNA binding site [nucleotide binding]; other site 1231072003935 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 1231072003936 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 1231072003937 RNase E interface [polypeptide binding]; other site 1231072003938 trimer interface [polypeptide binding]; other site 1231072003939 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 1231072003940 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 1231072003941 RNase E interface [polypeptide binding]; other site 1231072003942 trimer interface [polypeptide binding]; other site 1231072003943 active site 1231072003944 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 1231072003945 putative nucleic acid binding region [nucleotide binding]; other site 1231072003946 G-X-X-G motif; other site 1231072003947 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 1231072003948 RNA binding site [nucleotide binding]; other site 1231072003949 domain interface; other site 1231072003950 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 1231072003951 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 1231072003952 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 1231072003953 sporulation protein, YlmC/YmxH family; Region: spore_YlmC_YmxH; TIGR02888 1231072003954 aspartate kinase I; Reviewed; Region: PRK08210 1231072003955 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 1231072003956 nucleotide binding site [chemical binding]; other site 1231072003957 substrate binding site [chemical binding]; other site 1231072003958 ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI; Region: ACT_AKi-DapG-BS_1; cd04914 1231072003959 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 1231072003960 Caseinolytic protease (ClpP) is an ATP-dependent protease; Region: Clp_protease_like; cl15763 1231072003961 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 1231072003962 active site 1231072003963 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 1231072003964 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 1231072003965 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 1231072003966 ribosomal protein S12 methylthiotransferase RimO; Region: TIGR01125 1231072003967 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1231072003968 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 1231072003969 FeS/SAM binding site; other site 1231072003970 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 1231072003971 recombinase A; Provisional; Region: recA; PRK09354 1231072003972 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 1231072003973 hexamer interface [polypeptide binding]; other site 1231072003974 Walker A motif; other site 1231072003975 ATP binding site [chemical binding]; other site 1231072003976 Walker B motif; other site 1231072003977 phosphodiesterase; Provisional; Region: PRK12704 1231072003978 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1231072003979 Zn2+ binding site [ion binding]; other site 1231072003980 Mg2+ binding site [ion binding]; other site 1231072003981 Stage V sporulation protein S (SpoVS); Region: SpoVS; pfam04232 1231072003982 phosphoribose diphosphate:decaprenyl-phosphate phosphoribosyltransferase; Provisional; Region: PRK12324 1231072003983 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnF; Provisional; Region: PRK02971 1231072003984 aspartate aminotransferase; Provisional; Region: PRK05764 1231072003985 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 1231072003986 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1231072003987 homodimer interface [polypeptide binding]; other site 1231072003988 catalytic residue [active] 1231072003989 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 1231072003990 dimerization domain swap beta strand [polypeptide binding]; other site 1231072003991 regulatory protein interface [polypeptide binding]; other site 1231072003992 active site 1231072003993 regulatory phosphorylation site [posttranslational modification]; other site 1231072003994 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 1231072003995 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 1231072003996 NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Region: NAD_bind_1_Glu_DH; cd01076 1231072003997 NAD(P) binding site [chemical binding]; other site 1231072003998 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 1231072003999 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 1231072004000 active site 1231072004001 DNA binding site [nucleotide binding] 1231072004002 Int/Topo IB signature motif; other site 1231072004003 LexA repressor; Validated; Region: PRK00215 1231072004004 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 1231072004005 putative DNA binding site [nucleotide binding]; other site 1231072004006 putative Zn2+ binding site [ion binding]; other site 1231072004007 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 1231072004008 Catalytic site [active] 1231072004009 Cystathionine beta-lyase family protein involved in aluminum resistance [Inorganic ion transport and metabolism]; Region: COG4100 1231072004010 Aluminium resistance protein; Region: Alum_res; pfam06838 1231072004011 bacterial Hfq-like; Region: Hfq; cd01716 1231072004012 hexamer interface [polypeptide binding]; other site 1231072004013 Sm1 motif; other site 1231072004014 RNA binding site [nucleotide binding]; other site 1231072004015 Sm2 motif; other site 1231072004016 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 1231072004017 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 1231072004018 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 1231072004019 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 1231072004020 Mg2+ binding site [ion binding]; other site 1231072004021 G-X-G motif; other site 1231072004022 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 1231072004023 ATP binding site [chemical binding]; other site 1231072004024 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 1231072004025 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 1231072004026 MutS domain I; Region: MutS_I; pfam01624 1231072004027 MutS domain II; Region: MutS_II; pfam05188 1231072004028 MutS domain III; Region: MutS_III; pfam05192 1231072004029 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 1231072004030 Walker A/P-loop; other site 1231072004031 ATP binding site [chemical binding]; other site 1231072004032 Q-loop/lid; other site 1231072004033 ABC transporter signature motif; other site 1231072004034 Walker B; other site 1231072004035 D-loop; other site 1231072004036 H-loop/switch region; other site 1231072004037 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14328 1231072004038 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1231072004039 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 1231072004040 FeS/SAM binding site; other site 1231072004041 Coat F domain; Region: Coat_F; pfam07875 1231072004042 Domain of Unknown Function (DUF1259); Region: DUF1529; pfam07485 1231072004043 Cache domain; Region: Cache_1; pfam02743 1231072004044 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 1231072004045 dimerization interface [polypeptide binding]; other site 1231072004046 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1231072004047 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1231072004048 dimer interface [polypeptide binding]; other site 1231072004049 putative CheW interface [polypeptide binding]; other site 1231072004050 aspartate aminotransferase; Provisional; Region: PRK07568 1231072004051 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 1231072004052 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1231072004053 homodimer interface [polypeptide binding]; other site 1231072004054 catalytic residue [active] 1231072004055 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1231072004056 Coenzyme A binding pocket [chemical binding]; other site 1231072004057 spore coat protein YsxE; Region: spore_ysxE; TIGR02904 1231072004058 spore coat protein, CotS family; Region: spore_CotS; TIGR02906 1231072004059 S-adenosylmethionine decarboxylase proenzyme; Provisional; Region: PRK03124 1231072004060 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed; Region: PRK00087 1231072004061 LytB protein; Region: LYTB; cl00507 1231072004062 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 1231072004063 RNA binding site [nucleotide binding]; other site 1231072004064 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 1231072004065 RNA binding site [nucleotide binding]; other site 1231072004066 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 1231072004067 RNA binding site [nucleotide binding]; other site 1231072004068 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 1231072004069 RNA binding site [nucleotide binding]; other site 1231072004070 domain interface; other site 1231072004071 cytidylate kinase; Provisional; Region: cmk; PRK00023 1231072004072 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 1231072004073 CMP-binding site; other site 1231072004074 The sites determining sugar specificity; other site 1231072004075 Chorismate mutase (AroH) is one of at least five chorismate-utilizing enzymes present in microorganisms that catalyze the rearrangement of chorismate to prephenic acid, the first committed step in the biosynthesis of aromatic amino acids. In prokaryotes; Region: AroH; cd02185 1231072004076 homotrimer interaction site [polypeptide binding]; other site 1231072004077 active site 1231072004078 HI0933-like protein; Region: HI0933_like; pfam03486 1231072004079 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1231072004080 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 1231072004081 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 1231072004082 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 1231072004083 putative active site [active] 1231072004084 Protein of unknown function (DUF4264); Region: DUF4264; pfam14084 1231072004085 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 1231072004086 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 1231072004087 RNA binding surface [nucleotide binding]; other site 1231072004088 Pseudouridine synthases, RsuA subfamily; Region: PseudoU_synth_RsuA_like; cd02870 1231072004089 active site 1231072004090 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 1231072004091 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1231072004092 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 1231072004093 ZIP Zinc transporter; Region: Zip; pfam02535 1231072004094 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 1231072004095 EpsO protein participates in the methanolan synthesis; Region: EpsO_like; cd06438 1231072004096 DXD motif; other site 1231072004097 Nitroreductase-like family 2. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_2; cd02138 1231072004098 putative FMN binding site [chemical binding]; other site 1231072004099 S-Ribosylhomocysteinase (LuxS); Region: LuxS; cl00802 1231072004100 Putative p-aminobenzoyl-glutamate transporter [Coenzyme metabolism]; Region: AbgT; COG2978 1231072004101 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 1231072004102 [FeFe] hydrogenase H-cluster maturation GTPase HydF; Region: GTP_HydF; TIGR03918 1231072004103 E. coli Ras-like protein (Era)-like GTPase; Region: Era_like; cd00880 1231072004104 G1 box; other site 1231072004105 GTP/Mg2+ binding site [chemical binding]; other site 1231072004106 Switch I region; other site 1231072004107 G2 box; other site 1231072004108 Switch II region; other site 1231072004109 G3 box; other site 1231072004110 G4 box; other site 1231072004111 G5 box; other site 1231072004112 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09613 1231072004113 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 1231072004114 FeS/SAM binding site; other site 1231072004115 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 1231072004116 biotin synthase; Provisional; Region: PRK07094 1231072004117 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 1231072004118 FeS/SAM binding site; other site 1231072004119 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 1231072004120 putative iron-only hydrogenase system regulator; Region: hyd_TM1266; TIGR03959 1231072004121 Histidine Utilizing Protein, the hut operon positive regulatory protein; Region: HutP; cd11640 1231072004122 hexamer interface [polypeptide binding]; other site 1231072004123 RNA binding site [nucleotide binding]; other site 1231072004124 Histidine-zinc binding site [chemical binding]; other site 1231072004125 Putative amidase domain; Region: Amidase_6; pfam12671 1231072004126 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 1231072004127 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 1231072004128 TPP-binding site [chemical binding]; other site 1231072004129 dimer interface [polypeptide binding]; other site 1231072004130 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 1231072004131 PYR/PP interface [polypeptide binding]; other site 1231072004132 dimer interface [polypeptide binding]; other site 1231072004133 TPP binding site [chemical binding]; other site 1231072004134 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1231072004135 Uncharacterized conserved protein [Function unknown]; Region: COG1284 1231072004136 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 1231072004137 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; pfam10035 1231072004138 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3864 1231072004139 Putative metallopeptidase domain; Region: DUF2201_N; pfam13203 1231072004140 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 1231072004141 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 1231072004142 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 1231072004143 Walker A motif; other site 1231072004144 ATP binding site [chemical binding]; other site 1231072004145 Walker B motif; other site 1231072004146 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK08375 1231072004147 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1231072004148 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK08375 1231072004149 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1231072004150 Multicomponent K+:H+antiporter; Region: 2a6301s04; TIGR00944 1231072004151 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1231072004152 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK07375 1231072004153 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 1231072004154 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 1231072004155 Domain of unknown function (DUF4040); Region: DUF4040; pfam13244 1231072004156 Na+/H+ antiporter subunit; Region: PhaG_MnhG_YufB; pfam03334 1231072004157 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK12599 1231072004158 Na+/H+ ion antiporter subunit; Region: MNHE; pfam01899 1231072004159 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 1231072004160 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 1231072004161 dimer interface [polypeptide binding]; other site 1231072004162 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1231072004163 catalytic residue [active] 1231072004164 Predicted transcriptional regulator [Transcription]; Region: COG1959 1231072004165 Transcriptional regulator; Region: Rrf2; pfam02082 1231072004166 putative sporulation protein YtaF; Region: spore_YtaF; TIGR02840 1231072004167 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 1231072004168 dinuclear metal binding motif [ion binding]; other site 1231072004169 Protein of unknown function (DUF1538); Region: DUF1538; pfam07556 1231072004170 Nitrogen regulatory protein P-II; Region: P-II; smart00938 1231072004171 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 1231072004172 MgtE intracellular N domain; Region: MgtE_N; smart00924 1231072004173 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 1231072004174 Divalent cation transporter; Region: MgtE; pfam01769 1231072004175 Uncharacterized conserved protein [Function unknown]; Region: COG1751 1231072004176 Pyruvate kinase, alpha/beta domain; Region: PK_C; pfam02887 1231072004177 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 1231072004178 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 1231072004179 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 1231072004180 dimer interface [polypeptide binding]; other site 1231072004181 conserved gate region; other site 1231072004182 ABC-ATPase subunit interface; other site 1231072004183 ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]; Region: AbcC; COG1135 1231072004184 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 1231072004185 Walker A/P-loop; other site 1231072004186 ATP binding site [chemical binding]; other site 1231072004187 Q-loop/lid; other site 1231072004188 ABC transporter signature motif; other site 1231072004189 Walker B; other site 1231072004190 D-loop; other site 1231072004191 H-loop/switch region; other site 1231072004192 This domain is found at the C-terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins; Region: NIL; smart00930 1231072004193 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 1231072004194 CDP-diacylglycerol--serine O-phosphatidyltransferase; Region: pssA; TIGR00473 1231072004195 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 1231072004196 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1231072004197 Walker A/P-loop; other site 1231072004198 ATP binding site [chemical binding]; other site 1231072004199 Q-loop/lid; other site 1231072004200 ABC transporter signature motif; other site 1231072004201 Walker B; other site 1231072004202 D-loop; other site 1231072004203 H-loop/switch region; other site 1231072004204 Tropomyosin like; Region: Tropomyosin_1; pfam12718 1231072004205 ABC-2 family transporter protein; Region: ABC2_membrane_2; cl17866 1231072004206 ABC-type transport system involved in multi-copper enzyme maturation, permease component [General function prediction only]; Region: NosY; COG1277 1231072004207 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 1231072004208 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 1231072004209 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1231072004210 catalytic residue [active] 1231072004211 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 1231072004212 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 1231072004213 putative FPP binding hydrophobic cleft; other site 1231072004214 dimer interface [polypeptide binding]; other site 1231072004215 putative IPP diphosphate binding site; other site 1231072004216 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 1231072004217 catalytic residue [active] 1231072004218 putative FPP diphosphate binding site; other site 1231072004219 Small, acid-soluble spore proteins, alpha/beta type; Region: SASP; pfam00269 1231072004220 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 1231072004221 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 1231072004222 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1231072004223 Beta-xylosidase [Carbohydrate transport and metabolism]; Region: XynB; COG3664 1231072004224 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 1231072004225 putative efflux protein, MATE family; Region: matE; TIGR00797 1231072004226 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072004227 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072004228 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072004229 Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]; Region: ComEC; COG2333 1231072004230 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1231072004231 bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional; Region: PRK13805 1231072004232 Coenzyme A acylating aldehyde dehydrogenase (ACDH), ALDH family 20-like; Region: ALDH_F20_ACDH; cd07122 1231072004233 putative catalytic cysteine [active] 1231072004234 C-terminal alcohol dehydrogenase domain of the acetaldehyde dehydrogenase-alcohol dehydrogenase bifunctional two-domain protein (AAD); Region: AAD_C; cd08178 1231072004235 putative active site [active] 1231072004236 metal binding site [ion binding]; metal-binding site 1231072004237 Protein of unknown function (DUF3298); Region: DUF3298; pfam11738 1231072004238 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 1231072004239 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 1231072004240 ATP binding site [chemical binding]; other site 1231072004241 putative Mg++ binding site [ion binding]; other site 1231072004242 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 1231072004243 nucleotide binding region [chemical binding]; other site 1231072004244 ATP-binding site [chemical binding]; other site 1231072004245 Mitochondrial degradasome RNA helicase subunit C terminal; Region: SUV3_C; pfam12513 1231072004246 short chain dehydrogenase; Provisional; Region: PRK06701 1231072004247 classical (c) SDR, subgroup 1; Region: SDR_c1; cd05355 1231072004248 NAD binding site [chemical binding]; other site 1231072004249 metal binding site [ion binding]; metal-binding site 1231072004250 active site 1231072004251 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 1231072004252 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 1231072004253 Walker A/P-loop; other site 1231072004254 ATP binding site [chemical binding]; other site 1231072004255 Q-loop/lid; other site 1231072004256 ABC transporter signature motif; other site 1231072004257 Walker B; other site 1231072004258 D-loop; other site 1231072004259 H-loop/switch region; other site 1231072004260 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 1231072004261 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 1231072004262 ABC-ATPase subunit interface; other site 1231072004263 dimer interface [polypeptide binding]; other site 1231072004264 putative PBP binding regions; other site 1231072004265 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 1231072004266 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 1231072004267 intersubunit interface [polypeptide binding]; other site 1231072004268 Predicted DNA-binding proteins [General function prediction only]; Region: COG1342 1231072004269 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 1231072004270 EamA-like transporter family; Region: EamA; pfam00892 1231072004271 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 1231072004272 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 1231072004273 Walker A/P-loop; other site 1231072004274 ATP binding site [chemical binding]; other site 1231072004275 Q-loop/lid; other site 1231072004276 ABC transporter signature motif; other site 1231072004277 Walker B; other site 1231072004278 D-loop; other site 1231072004279 H-loop/switch region; other site 1231072004280 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 1231072004281 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 1231072004282 Walker A/P-loop; other site 1231072004283 ATP binding site [chemical binding]; other site 1231072004284 Q-loop/lid; other site 1231072004285 ABC transporter signature motif; other site 1231072004286 Walker B; other site 1231072004287 D-loop; other site 1231072004288 H-loop/switch region; other site 1231072004289 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 1231072004290 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 1231072004291 dimer interface [polypeptide binding]; other site 1231072004292 conserved gate region; other site 1231072004293 putative PBP binding loops; other site 1231072004294 ABC-ATPase subunit interface; other site 1231072004295 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 1231072004296 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 1231072004297 dimer interface [polypeptide binding]; other site 1231072004298 conserved gate region; other site 1231072004299 putative PBP binding loops; other site 1231072004300 ABC-ATPase subunit interface; other site 1231072004301 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 1231072004302 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_3; cd08490 1231072004303 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 1231072004304 non-specific DNA binding site [nucleotide binding]; other site 1231072004305 salt bridge; other site 1231072004306 sequence-specific DNA binding site [nucleotide binding]; other site 1231072004307 VanZ like family; Region: VanZ; pfam04892 1231072004308 RDD family; Region: RDD; pfam06271 1231072004309 hypothetical protein; Provisional; Region: PRK05802 1231072004310 FAD/NAD binding domain (electron transfer subunit) of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate...; Region: DHOD_e_trans_like; cd06192 1231072004311 FAD binding pocket [chemical binding]; other site 1231072004312 FAD binding motif [chemical binding]; other site 1231072004313 phosphate binding motif [ion binding]; other site 1231072004314 beta-alpha-beta structure motif; other site 1231072004315 NAD binding pocket [chemical binding]; other site 1231072004316 Iron coordination center [ion binding]; other site 1231072004317 Glucose inhibited division protein A; Region: GIDA; pfam01134 1231072004318 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 1231072004319 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cd09725 1231072004320 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-B; cd09722 1231072004321 Domain of unknown function DUF83; Region: Cas_Cas4; pfam01930 1231072004322 CRISPR/Cas system-associated protein Cas3'' Region: Cas3''_I; cd09641 1231072004323 CRISPR-associated helicase Cas3; Region: cas3_core; TIGR01587 1231072004324 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 1231072004325 CRISPR-associated protein Cas5, N-terminal domain; Region: CRISPR_cas5; TIGR02593 1231072004326 CRISPR/Cas system-associated RAMP superfamily protein Cas5; Region: Cas5_I; cl12040 1231072004327 CRISPR-associated autoregulator DevR family; Region: cas_MJ0381; TIGR01875 1231072004328 CRISPR/Cas system-associated RAMP superfamily protein Cas7; Region: Cas7_I; cl00803 1231072004329 CRISPR/Cas system-associated protein Cas8a1; Region: Cas8a1_I-A; cd09744 1231072004330 CRISPR-associated protein Csx8 (Cas_Csx8); Region: Cas_Csx8; pfam09657 1231072004331 CRISPR/Cas system-associated RAMP superfamily protein Cas6; Region: Cas6-I-III; cd09652 1231072004332 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 1231072004333 Ferric reductase like transmembrane component; Region: Ferric_reduct; cl01043 1231072004334 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 1231072004335 Spo0E like sporulation regulatory protein; Region: SpoOE-like; pfam09388 1231072004336 Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); Region: DUF2082; pfam09855 1231072004337 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 1231072004338 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1231072004339 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 1231072004340 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1231072004341 Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA dehydrogenases; Region: SCAD_SBCAD; cd01158 1231072004342 FAD binding site [chemical binding]; other site 1231072004343 homotetramer interface [polypeptide binding]; other site 1231072004344 substrate binding pocket [chemical binding]; other site 1231072004345 catalytic base [active] 1231072004346 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 1231072004347 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 1231072004348 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 1231072004349 Rubredoxin; Region: Rubredoxin; pfam00301 1231072004350 iron binding site [ion binding]; other site 1231072004351 purine nucleoside phosphorylase; Reviewed; Region: deoD; PRK05819 1231072004352 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 1231072004353 phosphopentomutase; Provisional; Region: PRK05362 1231072004354 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 1231072004355 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 1231072004356 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 1231072004357 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 1231072004358 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 1231072004359 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1231072004360 DNA-binding site [nucleotide binding]; DNA binding site 1231072004361 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 1231072004362 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 1231072004363 dimer interface [polypeptide binding]; other site 1231072004364 conserved gate region; other site 1231072004365 putative PBP binding loops; other site 1231072004366 ABC-ATPase subunit interface; other site 1231072004367 ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: TauA; COG4521 1231072004368 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1231072004369 substrate binding pocket [chemical binding]; other site 1231072004370 membrane-bound complex binding site; other site 1231072004371 hinge residues; other site 1231072004372 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 1231072004373 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 1231072004374 Walker A/P-loop; other site 1231072004375 ATP binding site [chemical binding]; other site 1231072004376 Q-loop/lid; other site 1231072004377 ABC transporter signature motif; other site 1231072004378 Walker B; other site 1231072004379 D-loop; other site 1231072004380 H-loop/switch region; other site 1231072004381 CAAX protease self-immunity; Region: Abi; pfam02517 1231072004382 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 1231072004383 putative ADP-ribose binding site [chemical binding]; other site 1231072004384 putative active site [active] 1231072004385 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cd00995 1231072004386 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 1231072004387 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 1231072004388 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 1231072004389 dimer interface [polypeptide binding]; other site 1231072004390 conserved gate region; other site 1231072004391 putative PBP binding loops; other site 1231072004392 ABC-ATPase subunit interface; other site 1231072004393 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 1231072004394 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 1231072004395 dimer interface [polypeptide binding]; other site 1231072004396 conserved gate region; other site 1231072004397 putative PBP binding loops; other site 1231072004398 ABC-ATPase subunit interface; other site 1231072004399 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 1231072004400 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 1231072004401 Walker A/P-loop; other site 1231072004402 ATP binding site [chemical binding]; other site 1231072004403 Q-loop/lid; other site 1231072004404 ABC transporter signature motif; other site 1231072004405 Walker B; other site 1231072004406 D-loop; other site 1231072004407 H-loop/switch region; other site 1231072004408 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 1231072004409 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 1231072004410 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 1231072004411 Walker A/P-loop; other site 1231072004412 ATP binding site [chemical binding]; other site 1231072004413 Q-loop/lid; other site 1231072004414 ABC transporter signature motif; other site 1231072004415 Walker B; other site 1231072004416 D-loop; other site 1231072004417 H-loop/switch region; other site 1231072004418 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; cl17173 1231072004419 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; cl17173 1231072004420 S-adenosylmethionine binding site [chemical binding]; other site 1231072004421 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1231072004422 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1231072004423 ATP-binding cassette domain of a mitochondrial protein MTABC3 and related proteins; Region: ABC_MTABC3_MDL1_MDL2; cd03249 1231072004424 Walker A/P-loop; other site 1231072004425 ATP binding site [chemical binding]; other site 1231072004426 Q-loop/lid; other site 1231072004427 ABC transporter signature motif; other site 1231072004428 Walker B; other site 1231072004429 D-loop; other site 1231072004430 H-loop/switch region; other site 1231072004431 thiol reductant ABC exporter, CydD subunit; Region: CydD; TIGR02857 1231072004432 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1231072004433 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1231072004434 Walker A/P-loop; other site 1231072004435 ATP binding site [chemical binding]; other site 1231072004436 Q-loop/lid; other site 1231072004437 ABC transporter signature motif; other site 1231072004438 Walker B; other site 1231072004439 D-loop; other site 1231072004440 H-loop/switch region; other site 1231072004441 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1231072004442 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1231072004443 VanZ like family; Region: VanZ; pfam04892 1231072004444 methylated-DNA--protein-cysteine methyltransferase; Provisional; Region: PRK00901 1231072004445 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 1231072004446 The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases...; Region: ATase; cd06445 1231072004447 DNA binding site [nucleotide binding] 1231072004448 active site 1231072004449 DNA alkylation repair enzyme; Region: DNA_alkylation; pfam08713 1231072004450 A new structural DNA glycosylase; Region: AlkD_like; cd06561 1231072004451 active site 1231072004452 small acid-soluble spore protein Tlp; Provisional; Region: PRK03830 1231072004453 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 1231072004454 active site 1231072004455 NTP binding site [chemical binding]; other site 1231072004456 metal binding triad [ion binding]; metal-binding site 1231072004457 antibiotic binding site [chemical binding]; other site 1231072004458 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; pfam08780 1231072004459 VanZ like family; Region: VanZ; pfam04892 1231072004460 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 1231072004461 FtsX-like permease family; Region: FtsX; pfam02687 1231072004462 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 1231072004463 FtsX-like permease family; Region: FtsX; pfam02687 1231072004464 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1231072004465 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1231072004466 Walker A/P-loop; other site 1231072004467 ATP binding site [chemical binding]; other site 1231072004468 Q-loop/lid; other site 1231072004469 ABC transporter signature motif; other site 1231072004470 Walker B; other site 1231072004471 D-loop; other site 1231072004472 H-loop/switch region; other site 1231072004473 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1231072004474 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 1231072004475 dimerization interface [polypeptide binding]; other site 1231072004476 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cl00080 1231072004477 dimer interface [polypeptide binding]; other site 1231072004478 phosphorylation site [posttranslational modification] 1231072004479 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 1231072004480 ATP binding site [chemical binding]; other site 1231072004481 Mg2+ binding site [ion binding]; other site 1231072004482 G-X-G motif; other site 1231072004483 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1231072004484 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 1231072004485 active site 1231072004486 phosphorylation site [posttranslational modification] 1231072004487 intermolecular recognition site; other site 1231072004488 dimerization interface [polypeptide binding]; other site 1231072004489 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 1231072004490 DNA binding site [nucleotide binding] 1231072004491 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 1231072004492 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 1231072004493 BlaR1 peptidase M56; Region: Peptidase_M56; pfam05569 1231072004494 Penicillinase repressor; Region: Pencillinase_R; pfam03965 1231072004495 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 1231072004496 putative transporter; Provisional; Region: PRK11660 1231072004497 Sulfate transporter family; Region: Sulfate_transp; pfam00916 1231072004498 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 1231072004499 Chloramphenicol O-acetyltransferase [Defense mechanisms]; Region: COG4845 1231072004500 Chloramphenicol acetyltransferase; Region: CAT; smart01059 1231072004501 Protein of unknown function; Region: DUF3658; pfam12395 1231072004502 Protein of unknown function (DUF1102); Region: DUF1102; pfam06510 1231072004503 HD domain; Region: HD_3; pfam13023 1231072004504 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 1231072004505 non-specific DNA binding site [nucleotide binding]; other site 1231072004506 salt bridge; other site 1231072004507 sequence-specific DNA binding site [nucleotide binding]; other site 1231072004508 Domain of unknown function (DUF3784); Region: DUF3784; pfam12650 1231072004509 Protein of unknown function (DUF2922); Region: DUF2922; pfam11148 1231072004510 Protein of unknown function (DUF1659); Region: DUF1659; pfam07872 1231072004511 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1231072004512 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1231072004513 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1231072004514 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3708 1231072004515 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 1231072004516 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1231072004517 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 1231072004518 DNA binding residues [nucleotide binding] 1231072004519 Ku-core domain; includes the central DNA-binding beta-barrels, polypeptide rings, and the C-terminal arm of Ku proteins. The Ku protein consists of two tightly associated homologous subunits, Ku70 and Ku80, and was originally identified as an autoantigen...; Region: KU; cl02666 1231072004520 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1231072004521 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 1231072004522 active site 1231072004523 phosphorylation site [posttranslational modification] 1231072004524 intermolecular recognition site; other site 1231072004525 dimerization interface [polypeptide binding]; other site 1231072004526 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 1231072004527 DNA binding site [nucleotide binding] 1231072004528 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 1231072004529 dimer interface [polypeptide binding]; other site 1231072004530 phosphorylation site [posttranslational modification] 1231072004531 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 1231072004532 ATP binding site [chemical binding]; other site 1231072004533 Mg2+ binding site [ion binding]; other site 1231072004534 G-X-G motif; other site 1231072004535 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1231072004536 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1231072004537 Walker A/P-loop; other site 1231072004538 ATP binding site [chemical binding]; other site 1231072004539 Q-loop/lid; other site 1231072004540 ABC transporter signature motif; other site 1231072004541 Walker B; other site 1231072004542 D-loop; other site 1231072004543 H-loop/switch region; other site 1231072004544 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 1231072004545 FtsX-like permease family; Region: FtsX; pfam02687 1231072004546 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 1231072004547 FtsX-like permease family; Region: FtsX; pfam02687 1231072004548 YvrJ protein family; Region: YvrJ; pfam12841 1231072004549 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 1231072004550 Replication initiation and membrane attachment; Region: DnaB_2; cl12121 1231072004551 phage replicative helicase, DnaB family, HK022 subfamily; Region: phage_DnaB; TIGR03600 1231072004552 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 1231072004553 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 1231072004554 Walker A motif; other site 1231072004555 ATP binding site [chemical binding]; other site 1231072004556 Walker B motif; other site 1231072004557 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 1231072004558 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 1231072004559 non-specific DNA binding site [nucleotide binding]; other site 1231072004560 salt bridge; other site 1231072004561 sequence-specific DNA binding site [nucleotide binding]; other site 1231072004562 hypothetical protein; Provisional; Region: PHA02965 1231072004563 Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]; Region: ComEC; COG2333 1231072004564 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1231072004565 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 1231072004566 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 1231072004567 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 1231072004568 non-specific DNA binding site [nucleotide binding]; other site 1231072004569 salt bridge; other site 1231072004570 sequence-specific DNA binding site [nucleotide binding]; other site 1231072004571 Cupin domain; Region: Cupin_2; cl17218 1231072004572 Carbon dioxide concentrating mechanism/carboxysome shell protein [Secondary metabolites biosynthesis, transport, and catabolism / Energy production and conversion]; Region: CcmK; COG4577 1231072004573 1,2-propanediol utilization protein A (PduA), Bacterial Micro-Compartment (BMC) domain; Region: BMC_PduA; cd07059 1231072004574 Hexamer interface [polypeptide binding]; other site 1231072004575 Putative hexagonal pore residue; other site 1231072004576 propanediol utilization phosphotransacylase; Provisional; Region: PRK15070 1231072004577 Propanediol utilisation protein PduL; Region: PduL; pfam06130 1231072004578 Ubiquitin-like proteins; Region: UBQ; cl00155 1231072004579 charged pocket; other site 1231072004580 Propanediol utilisation protein PduL; Region: PduL; pfam06130 1231072004581 NAD-dependent aldehyde dehydrogenases [Energy production and conversion]; Region: PutA; COG1012 1231072004582 Coenzyme A acylating aldehyde dehydrogenase (ACDH), ALDH family 20-like; Region: ALDH_F20_ACDH; cd07122 1231072004583 putative catalytic cysteine [active] 1231072004584 Carbon dioxide concentrating mechanism/carboxysome shell protein [Secondary metabolites biosynthesis, transport, and catabolism / Energy production and conversion]; Region: CcmK; COG4577 1231072004585 Carbon dioxide concentrating mechanism K (CcmK)-like proteins, Bacterial Micro-Compartment (BMC) domain; Region: BMC_CcmK_like; cd07045 1231072004586 Hexamer interface [polypeptide binding]; other site 1231072004587 Hexagonal pore residue; other site 1231072004588 ethanolamine utilization protein EutQ; Provisional; Region: PRK15457 1231072004589 Ethanolamine utilisation protein EutQ; Region: EutQ; pfam06249 1231072004590 Ethanolamine utilisation protein and carboxysome structural protein domain family; Region: EutN_CcmL; cd01614 1231072004591 Hexamer/Pentamer interface [polypeptide binding]; other site 1231072004592 central pore; other site 1231072004593 Bacterial Micro-Compartment (BMC) domain; Region: BMC; cl01982 1231072004594 Hexamer interface [polypeptide binding]; other site 1231072004595 Hexagonal pore residue; other site 1231072004596 ethanolamine utilization protein EutJ; Provisional; Region: PRK15080 1231072004597 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 1231072004598 nucleotide binding site [chemical binding]; other site 1231072004599 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 1231072004600 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; cl00920 1231072004601 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 1231072004602 G1 box; other site 1231072004603 GTP/Mg2+ binding site [chemical binding]; other site 1231072004604 G2 box; other site 1231072004605 G3 box; other site 1231072004606 Switch II region; other site 1231072004607 G4 box; other site 1231072004608 G5 box; other site 1231072004609 1,2-propanediol utilization protein U (PduU)/ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain; Region: BMC_PduU-EutS; cd07046 1231072004610 putative hexamer interface [polypeptide binding]; other site 1231072004611 putative hexagonal pore; other site 1231072004612 glycyl-radical enzyme activating protein family; Region: PFLE_PFLC; TIGR02494 1231072004613 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 1231072004614 glycyl radical enzyme, PFL2/glycerol dehydratase family; Region: PFL2-3; TIGR01774 1231072004615 Pyruvate formate lyase 2 and related enzymes; Region: PFL2_DhaB_BssA; cd01677 1231072004616 dimer interface [polypeptide binding]; other site 1231072004617 active site 1231072004618 glycine loop; other site 1231072004619 Carbon dioxide concentrating mechanism/carboxysome shell protein [Secondary metabolites biosynthesis, transport, and catabolism / Energy production and conversion]; Region: CcmK; COG4577 1231072004620 Carbon dioxide concentrating mechanism K (CcmK)-like proteins, Bacterial Micro-Compartment (BMC) domain; Region: BMC_CcmK_like; cd07045 1231072004621 Hexamer interface [polypeptide binding]; other site 1231072004622 Hexagonal pore residue; other site 1231072004623 Carbon dioxide concentrating mechanism/carboxysome shell protein [Secondary metabolites biosynthesis, transport, and catabolism / Energy production and conversion]; Region: CcmK; COG4577 1231072004624 Carbon dioxide concentrating mechanism K (CcmK)-like proteins, Bacterial Micro-Compartment (BMC) domain; Region: BMC_CcmK_like; cd07045 1231072004625 Hexamer interface [polypeptide binding]; other site 1231072004626 Hexagonal pore residue; other site 1231072004627 Multidrug resistance efflux transporter; Region: EmrE; pfam13536 1231072004628 Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Region: HTH_BmrR; cd01107 1231072004629 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 1231072004630 DNA binding residues [nucleotide binding] 1231072004631 drug binding residues [chemical binding]; other site 1231072004632 dimer interface [polypeptide binding]; other site 1231072004633 GyrI-like small molecule binding domain; Region: GyrI-like; cl01368 1231072004634 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 1231072004635 1,3-propanediol dehydrogenase (PPD) catalyzes the reduction of 3-hydroxypropionaldehyde (3-HPA) to 1,3-propanediol in glycerol metabolism; Region: PDD; cd08180 1231072004636 putative active site [active] 1231072004637 metal binding site [ion binding]; metal-binding site 1231072004638 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 1231072004639 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 1231072004640 Ligand Binding Site [chemical binding]; other site 1231072004641 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 1231072004642 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 1231072004643 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1231072004644 catalytic residue [active] 1231072004645 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 1231072004646 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cd09725 1231072004647 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-B; cd09722 1231072004648 Domain of unknown function DUF83; Region: Cas_Cas4; pfam01930 1231072004649 CRISPR/Cas system-associated protein Cas3'' Region: Cas3''_I; cd09641 1231072004650 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 1231072004651 CRISPR-associated protein Cas5, subtype I-B/HMARI; Region: cas_Cas5h; TIGR02592 1231072004652 CRISPR/Cas system-associated RAMP superfamily protein Cas5; Region: Cas5_I-B; cd09692 1231072004653 CRISPR/Cas system-associated RAMP superfamily protein Cas7; Region: Cas7_I-C; cl01465 1231072004654 CRISPR/Cas system-associated protein Cas8b; Region: Cas8b_I-B; cd09691 1231072004655 CRISPR/Cas system-associated RAMP superfamily protein Cas6; Region: Cas6-I-III; cd09652 1231072004656 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 1231072004657 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-II-III; cl00656 1231072004658 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-II-III; cl00656 1231072004659 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 1231072004660 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 1231072004661 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; cl02713 1231072004662 Uncharacterized protein conserved in bacteria (DUF2262); Region: DUF2262; pfam10020 1231072004663 Putative amidase domain; Region: Amidase_6; pfam12671 1231072004664 Peptidase family S41; Region: Peptidase_S41; pfam03572 1231072004665 Active site serine [active] 1231072004666 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 1231072004667 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1231072004668 catalytic residue [active] 1231072004669 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 1231072004670 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 1231072004671 catalytic residues [active] 1231072004672 4Fe-4S binding domain; Region: Fer4_5; pfam12801 1231072004673 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 1231072004674 4Fe-4S dicluster domain; Region: Fer4_9; pfam13187 1231072004675 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1231072004676 HAMP domain; Region: HAMP; pfam00672 1231072004677 dimerization interface [polypeptide binding]; other site 1231072004678 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 1231072004679 dimer interface [polypeptide binding]; other site 1231072004680 phosphorylation site [posttranslational modification] 1231072004681 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 1231072004682 ATP binding site [chemical binding]; other site 1231072004683 Mg2+ binding site [ion binding]; other site 1231072004684 G-X-G motif; other site 1231072004685 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1231072004686 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 1231072004687 active site 1231072004688 phosphorylation site [posttranslational modification] 1231072004689 intermolecular recognition site; other site 1231072004690 dimerization interface [polypeptide binding]; other site 1231072004691 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 1231072004692 DNA binding site [nucleotide binding] 1231072004693 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 1231072004694 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 1231072004695 ABC-2 family transporter protein; Region: ABC2_membrane_2; pfam12679 1231072004696 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: COG3638 1231072004697 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1231072004698 Walker A/P-loop; other site 1231072004699 ATP binding site [chemical binding]; other site 1231072004700 Q-loop/lid; other site 1231072004701 ABC transporter signature motif; other site 1231072004702 Walker B; other site 1231072004703 D-loop; other site 1231072004704 H-loop/switch region; other site 1231072004705 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1231072004706 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1231072004707 dimer interface [polypeptide binding]; other site 1231072004708 putative CheW interface [polypeptide binding]; other site 1231072004709 FMN-binding domain; Region: FMN_bind; cl01081 1231072004710 L-aspartate oxidase; Provisional; Region: PRK06175 1231072004711 flavocytochrome c; Region: flavo_cyto_c; TIGR01813 1231072004712 heat shock protein 90; Provisional; Region: PRK05218 1231072004713 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 1231072004714 ATP binding site [chemical binding]; other site 1231072004715 Mg2+ binding site [ion binding]; other site 1231072004716 G-X-G motif; other site 1231072004717 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1231072004718 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 1231072004719 active site 1231072004720 phosphorylation site [posttranslational modification] 1231072004721 intermolecular recognition site; other site 1231072004722 dimerization interface [polypeptide binding]; other site 1231072004723 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 1231072004724 DNA binding site [nucleotide binding] 1231072004725 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 1231072004726 dimerization interface [polypeptide binding]; other site 1231072004727 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 1231072004728 dimer interface [polypeptide binding]; other site 1231072004729 phosphorylation site [posttranslational modification] 1231072004730 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 1231072004731 ATP binding site [chemical binding]; other site 1231072004732 Mg2+ binding site [ion binding]; other site 1231072004733 G-X-G motif; other site 1231072004734 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1231072004735 gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit; Region: galliderm_ABC; TIGR03740 1231072004736 Walker A/P-loop; other site 1231072004737 ATP binding site [chemical binding]; other site 1231072004738 Q-loop/lid; other site 1231072004739 ABC transporter signature motif; other site 1231072004740 Walker B; other site 1231072004741 D-loop; other site 1231072004742 H-loop/switch region; other site 1231072004743 Protein of unknown function (DUF1266); Region: DUF1266; pfam06889 1231072004744 Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; Region: E_set; cl09101 1231072004745 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 1231072004746 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 1231072004747 ATP binding site [chemical binding]; other site 1231072004748 Mg++ binding site [ion binding]; other site 1231072004749 motif III; other site 1231072004750 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 1231072004751 nucleotide binding region [chemical binding]; other site 1231072004752 ATP-binding site [chemical binding]; other site 1231072004753 RNA recognition motif in Bacillus subtilis ATP-dependent RNA helicase YxiN and similar proteins; Region: RRM_BsYxiN_like; cd12500 1231072004754 RNA binding site [nucleotide binding]; other site 1231072004755 Putative heavy-metal-binding; Region: YbjQ_1; cl00426 1231072004756 Predicted secreted protein [Function unknown]; Region: COG4086 1231072004757 Protein of unknown function (DUF1002); Region: DUF1002; pfam06207 1231072004758 EamA-like transporter family; Region: EamA; pfam00892 1231072004759 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 1231072004760 EamA-like transporter family; Region: EamA; pfam00892 1231072004761 NnaC (CMP-NeuNAc synthetase) _like subfamily of SGNH_hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its...; Region: NnaC_like; cd01841 1231072004762 active site 1231072004763 catalytic triad [active] 1231072004764 oxyanion hole [active] 1231072004765 Protein of unknown function DUF45; Region: DUF45; pfam01863 1231072004766 Esterase/lipase [Lipid metabolism]; Region: Aes; COG0657 1231072004767 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 1231072004768 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1231072004769 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 1231072004770 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 1231072004771 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1231072004772 dimer interface [polypeptide binding]; other site 1231072004773 putative CheW interface [polypeptide binding]; other site 1231072004774 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 1231072004775 Na2 binding site [ion binding]; other site 1231072004776 putative substrate binding site 1 [chemical binding]; other site 1231072004777 Na binding site 1 [ion binding]; other site 1231072004778 putative substrate binding site 2 [chemical binding]; other site 1231072004779 tryptophanase/L-cysteine desulfhydrase, PLP-dependent; Provisional; Region: tnaA; PRK13238 1231072004780 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 1231072004781 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1231072004782 catalytic residue [active] 1231072004783 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 1231072004784 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 1231072004785 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1231072004786 dimer interface [polypeptide binding]; other site 1231072004787 putative CheW interface [polypeptide binding]; other site 1231072004788 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 1231072004789 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 1231072004790 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 1231072004791 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06676 1231072004792 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 1231072004793 RNA binding site [nucleotide binding]; other site 1231072004794 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 1231072004795 RNA binding site [nucleotide binding]; other site 1231072004796 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec3; cd05688 1231072004797 RNA binding site [nucleotide binding]; other site 1231072004798 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 1231072004799 RNA binding site [nucleotide binding]; other site 1231072004800 domain interface; other site 1231072004801 Sporulation protein YtfJ (Spore_YtfJ); Region: Spore_YtfJ; pfam09579 1231072004802 Major membrane immunogen, membrane-anchored lipoprotein [Function unknown]; Region: COG4939 1231072004803 FMN-binding domain; Region: FMN_bind; pfam04205 1231072004804 flavocytochrome c; Region: flavo_cyto_c; TIGR01813 1231072004805 L-aspartate oxidase; Provisional; Region: PRK06175 1231072004806 Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]; Region: CitB; COG4565 1231072004807 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 1231072004808 active site 1231072004809 phosphorylation site [posttranslational modification] 1231072004810 intermolecular recognition site; other site 1231072004811 dimerization interface [polypeptide binding]; other site 1231072004812 Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]; Region: CitA; COG3290 1231072004813 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 1231072004814 putative active site [active] 1231072004815 heme pocket [chemical binding]; other site 1231072004816 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 1231072004817 ATP binding site [chemical binding]; other site 1231072004818 Mg2+ binding site [ion binding]; other site 1231072004819 G-X-G motif; other site 1231072004820 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 1231072004821 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 1231072004822 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; pfam07943 1231072004823 Protein of unknown function (DUF2953); Region: DUF2953; pfam11167 1231072004824 sporulation protein YtfJ; Region: spore_ytfJ; TIGR02874 1231072004825 segregation and condensation protein B; Reviewed; Region: scpB; PRK00135 1231072004826 segregation and condensation protein A; Reviewed; Region: scpA; PRK00104 1231072004827 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 1231072004828 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 1231072004829 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; pfam07943 1231072004830 purine nucleoside phosphorylase; Provisional; Region: PRK08202 1231072004831 XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination...; Region: INT_XerDC; cd00798 1231072004832 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 1231072004833 active site 1231072004834 Int/Topo IB signature motif; other site 1231072004835 stage II sporulation protein M; Region: spo_II_M; TIGR02831 1231072004836 sporulation lipoprotein, YhcN/YlaJ family; Region: spore_YhcN_YlaJ; TIGR02898 1231072004837 Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ); Region: Spore_YhcN_YlaJ; pfam09580 1231072004838 Cache domain; Region: Cache_1; pfam02743 1231072004839 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 1231072004840 dimerization interface [polypeptide binding]; other site 1231072004841 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1231072004842 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1231072004843 dimer interface [polypeptide binding]; other site 1231072004844 putative CheW interface [polypeptide binding]; other site 1231072004845 sporulation transcription factor Spo0A; Region: spore_0_A; TIGR02875 1231072004846 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 1231072004847 active site 1231072004848 phosphorylation site [posttranslational modification] 1231072004849 intermolecular recognition site; other site 1231072004850 dimerization interface [polypeptide binding]; other site 1231072004851 Sporulation initiation factor Spo0A C terminal; Region: Spo0A_C; pfam08769 1231072004852 stage IV sporulation protein B; Region: spore_IV_B; TIGR02860 1231072004853 SpoIVB peptidase S55; Region: Peptidase_S55; pfam05580 1231072004854 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 1231072004855 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 1231072004856 ABC transporter signature motif; other site 1231072004857 Walker B; other site 1231072004858 D-loop; other site 1231072004859 H-loop/switch region; other site 1231072004860 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 1231072004861 Walker A/P-loop; other site 1231072004862 ATP binding site [chemical binding]; other site 1231072004863 Q-loop/lid; other site 1231072004864 arginine repressor; Provisional; Region: argR; PRK00441 1231072004865 Arginine repressor, DNA binding domain; Region: Arg_repressor; pfam01316 1231072004866 Arginine repressor, C-terminal domain; Region: Arg_repressor_C; pfam02863 1231072004867 NAD kinase [Coenzyme metabolism]; Region: nadF; COG0061 1231072004868 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 1231072004869 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 1231072004870 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 1231072004871 RNA binding surface [nucleotide binding]; other site 1231072004872 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 1231072004873 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 1231072004874 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 1231072004875 TPP-binding site; other site 1231072004876 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 1231072004877 PYR/PP interface [polypeptide binding]; other site 1231072004878 dimer interface [polypeptide binding]; other site 1231072004879 TPP binding site [chemical binding]; other site 1231072004880 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1231072004881 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 1231072004882 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 1231072004883 substrate binding pocket [chemical binding]; other site 1231072004884 chain length determination region; other site 1231072004885 substrate-Mg2+ binding site; other site 1231072004886 catalytic residues [active] 1231072004887 aspartate-rich region 1; other site 1231072004888 active site lid residues [active] 1231072004889 aspartate-rich region 2; other site 1231072004890 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 1231072004891 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 1231072004892 ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a...; Region: ExoVII_LU_OBF; cd04489 1231072004893 generic binding surface I; other site 1231072004894 generic binding surface II; other site 1231072004895 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14172 1231072004896 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 1231072004897 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 1231072004898 homodimer interface [polypeptide binding]; other site 1231072004899 NADP binding site [chemical binding]; other site 1231072004900 substrate binding site [chemical binding]; other site 1231072004901 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 1231072004902 Asp23 family; Region: Asp23; pfam03780 1231072004903 SpoIIIAH-like protein; Region: SpoIIIAH; pfam12685 1231072004904 stage III sporulation protein AG; Region: spore_III_AG; TIGR02830 1231072004905 stage III sporulation protein AF; Region: spore_III_AF; TIGR02896 1231072004906 stage III sporulation protein AE; Region: spore_III_AE; TIGR02829 1231072004907 stage III sporulation protein AB; Region: spore_III_AB; TIGR02833 1231072004908 stage III sporulation protein AA; Region: spore_III_AA; TIGR02858 1231072004909 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; cl17189 1231072004910 Walker A motif; other site 1231072004911 ATP binding site [chemical binding]; other site 1231072004912 Walker B motif; other site 1231072004913 ribosomal protein S27; Provisional; Region: PLN00209 1231072004914 elongation factor P; Validated; Region: PRK00529 1231072004915 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 1231072004916 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 1231072004917 RNA binding site [nucleotide binding]; other site 1231072004918 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 1231072004919 RNA binding site [nucleotide binding]; other site 1231072004920 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 1231072004921 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 1231072004922 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 1231072004923 active site 1231072004924 Dehydroquinase (DHQase), type II. Dehydroquinase (or 3-dehydroquinate dehydratase) catalyzes the reversible dehydration of 3-dehydroquinate to form 3-dehydroshikimate. This reaction is part of two metabolic pathways: the biosynthetic shikimate pathway...; Region: DHQase_II; cd00466 1231072004925 Dehydroquinase class II; Region: DHquinase_II; pfam01220 1231072004926 active site 1231072004927 trimer interface [polypeptide binding]; other site 1231072004928 dimer interface [polypeptide binding]; other site 1231072004929 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 1231072004930 Shikimate kinase; Region: SKI; pfam01202 1231072004931 ADP binding site [chemical binding]; other site 1231072004932 magnesium binding site [ion binding]; other site 1231072004933 putative shikimate binding site; other site 1231072004934 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 1231072004935 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 1231072004936 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 1231072004937 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 1231072004938 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 1231072004939 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 1231072004940 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 1231072004941 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 1231072004942 Walker A motif; other site 1231072004943 ATP binding site [chemical binding]; other site 1231072004944 Walker B motif; other site 1231072004945 Fibronectin-binding protein A N-terminus (FbpA); Region: FbpA; pfam05833 1231072004946 Domain of unknown function (DUF814); Region: DUF814; pfam05670 1231072004947 Hemerythrin-like domain; Region: Hr-like; cd12108 1231072004948 Fe binding site [ion binding]; other site 1231072004949 Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Mth212-like_AP-endo; cd09085 1231072004950 active site 1231072004951 putative catalytic site [active] 1231072004952 phosphate binding site A [ion binding]; other site 1231072004953 DNA binding site [nucleotide binding] 1231072004954 metal binding site A [ion binding]; metal-binding site 1231072004955 putative AP binding site [nucleotide binding]; other site 1231072004956 putative metal binding site B [ion binding]; other site 1231072004957 phosphate binding site B [ion binding]; other site 1231072004958 uracil transporter; Provisional; Region: PRK10720 1231072004959 Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase [Nucleotide transport and metabolism]; Region: PyrR; COG2065 1231072004960 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1231072004961 active site 1231072004962 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1231072004963 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 1231072004964 RNA binding surface [nucleotide binding]; other site 1231072004965 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1231072004966 active site 1231072004967 lipoprotein signal peptidase; Provisional; Region: PRK14791 1231072004968 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 1231072004969 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 1231072004970 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 1231072004971 hinge; other site 1231072004972 active site 1231072004973 3-deoxy-7-phosphoheptulonate synthase; Provisional; Region: PRK13398 1231072004974 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 1231072004975 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 1231072004976 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 1231072004977 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 1231072004978 active site 1231072004979 dimer interface [polypeptide binding]; other site 1231072004980 metal binding site [ion binding]; metal-binding site 1231072004981 DivIVA protein; Region: DivIVA; pfam05103 1231072004982 DivIVA domain; Region: DivI1A_domain; TIGR03544 1231072004983 Uncharacterized conserved protein, contains S4-like domain [Function unknown]; Region: COG2302 1231072004984 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 1231072004985 RNA binding surface [nucleotide binding]; other site 1231072004986 YGGT family; Region: YGGT; cl00508 1231072004987 Protein of unknown function (DUF552); Region: DUF552; pfam04472 1231072004988 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 1231072004989 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1231072004990 catalytic residue [active] 1231072004991 Bacterial protein of unknown function (DUF881); Region: DUF881; pfam05949 1231072004992 Protein of unknown function (DUF1290); Region: DUF1290; pfam06947 1231072004993 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3879 1231072004994 Bacterial protein of unknown function (DUF881); Region: DUF881; pfam05949 1231072004995 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 1231072004996 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 1231072004997 stage V sporulation protein E; Region: spoVE; TIGR02615 1231072004998 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 1231072004999 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 1231072005000 Mg++ binding site [ion binding]; other site 1231072005001 putative catalytic motif [active] 1231072005002 putative substrate binding site [chemical binding]; other site 1231072005003 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 1231072005004 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1231072005005 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1231072005006 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1231072005007 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 1231072005008 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1231072005009 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1231072005010 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1231072005011 stage V sporulation protein D; Region: spoVD_pbp; TIGR02214 1231072005012 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1231072005013 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1231072005014 PASTA domain of PBP2x-like proteins, first repeat. Penicillin-binding proteins (PBPs) are the major targets for beta-lactam antibiotics, like penicillins and cephalosporins. Beta-lactam antibiotics specifically inhibit transpeptidase activity by...; Region: PASTA_Pbp2x-like_1; cd06576 1231072005015 PASTA domain of PBP2x-like proteins, second repeat. Penicillin-binding proteins (PBPs) are the major targets for beta-lactam antibiotics, like penicillins and cephalosporins. Beta-lactam antibiotics specifically inhibit transpeptidase activity by...; Region: PASTA_Pbp2x-like_2; cd06575 1231072005016 Cell division protein FtsL; Region: FtsL; cl11433 1231072005017 MraW methylase family; Region: Methyltransf_5; pfam01795 1231072005018 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 1231072005019 cell division protein MraZ; Reviewed; Region: PRK00326 1231072005020 MraZ protein; Region: MraZ; pfam02381 1231072005021 MraZ protein; Region: MraZ; pfam02381 1231072005022 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 1231072005023 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 1231072005024 TrkA-C domain; Region: TrkA_C; pfam02080 1231072005025 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 1231072005026 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 1231072005027 inhibitor-cofactor binding pocket; inhibition site 1231072005028 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1231072005029 catalytic residue [active] 1231072005030 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 1231072005031 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 1231072005032 inhibitor-cofactor binding pocket; inhibition site 1231072005033 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1231072005034 catalytic residue [active] 1231072005035 Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; Region: HTH_TipAL-Mta; cd01106 1231072005036 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 1231072005037 DNA binding residues [nucleotide binding] 1231072005038 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1231072005039 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 1231072005040 S-adenosylmethionine binding site [chemical binding]; other site 1231072005041 GTP-binding protein YchF; Reviewed; Region: PRK09601 1231072005042 YchF GTPase; Region: YchF; cd01900 1231072005043 G1 box; other site 1231072005044 GTP/Mg2+ binding site [chemical binding]; other site 1231072005045 Switch I region; other site 1231072005046 G2 box; other site 1231072005047 Switch II region; other site 1231072005048 G3 box; other site 1231072005049 G4 box; other site 1231072005050 G5 box; other site 1231072005051 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 1231072005052 Bacterial cell division membrane protein [Cell division and chromosome partitioning]; Region: FtsW; COG0772 1231072005053 Predicted transcriptional regulators [Transcription]; Region: COG1695 1231072005054 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 1231072005055 AAA domain; Region: AAA_32; pfam13654 1231072005056 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 1231072005057 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; smart00831 1231072005058 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 1231072005059 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 1231072005060 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 1231072005061 Soluble P-type ATPase [General function prediction only]; Region: COG4087 1231072005062 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 1231072005063 putative manganese-dependent inorganic pyrophosphatase; Provisional; Region: PRK14869 1231072005064 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 1231072005065 DRTGG domain; Region: DRTGG; pfam07085 1231072005066 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 1231072005067 DHHA2 domain; Region: DHHA2; pfam02833 1231072005068 flagellar basal body rod protein FlgG; Reviewed; Region: flgG; PRK12817 1231072005069 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 1231072005070 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 1231072005071 flagellar basal body rod protein FlgG; Reviewed; Region: flgG; PRK12818 1231072005072 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 1231072005073 RNA polymerase sigma factor, FliA/WhiG family; Region: FliA_WhiG; TIGR02479 1231072005074 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1231072005075 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 1231072005076 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 1231072005077 DNA binding residues [nucleotide binding] 1231072005078 Flagellar protein YcgR; Region: YcgR_2; pfam12945 1231072005079 PilZ domain; Region: PilZ; pfam07238 1231072005080 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 1231072005081 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 1231072005082 P-loop; other site 1231072005083 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 1231072005084 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 1231072005085 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 1231072005086 FHIPEP family; Region: FHIPEP; pfam00771 1231072005087 bifunctional flagellar biosynthesis protein FliR/FlhB; Provisional; Region: PRK12772 1231072005088 Flagellar biosynthesis pathway, component FliR [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FliR; COG1684 1231072005089 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 1231072005090 Flagellar biosynthesis pathway, component FliQ [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FliQ; COG1987 1231072005091 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 1231072005092 flagellar biosynthetic protein FliO; Region: FliO_TIGR; TIGR03500 1231072005093 Flagellar basal body-associated protein FliL; Region: FliL; pfam03748 1231072005094 flagellar motor protein MotS; Reviewed; Region: PRK06925 1231072005095 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 1231072005096 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1231072005097 ligand binding site [chemical binding]; other site 1231072005098 flagellar motor protein MotP; Reviewed; Region: PRK06926 1231072005099 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 1231072005100 Flagellar protein (FlbD); Region: FlbD; pfam06289 1231072005101 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12636 1231072005102 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 1231072005103 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 1231072005104 flagellar operon protein; Region: flg_new; TIGR02530 1231072005105 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 1231072005106 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 1231072005107 Flagellar FliJ protein; Region: FliJ; pfam02050 1231072005108 flagellar protein export ATPase FliI; Region: FliI_clade2; TIGR03497 1231072005109 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1231072005110 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 1231072005111 Walker A motif/ATP binding site; other site 1231072005112 Walker B motif; other site 1231072005113 flagellar assembly protein H; Validated; Region: fliH; PRK06669 1231072005114 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 1231072005115 FliG C-terminal domain; Region: FliG_C; pfam01706 1231072005116 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 1231072005117 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 1231072005118 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 1231072005119 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 1231072005120 flagellar basal body rod protein FlgC; Provisional; Region: flgC; PRK12630 1231072005121 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 1231072005122 flagellar basal body rod protein FlgB; Provisional; Region: flgB; PRK12623 1231072005123 flagellin; Provisional; Region: PRK12804 1231072005124 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 1231072005125 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 1231072005126 EDD domain protein, DegV family; Region: DegV; TIGR00762 1231072005127 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 1231072005128 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 1231072005129 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 1231072005130 dimer interface [polypeptide binding]; other site 1231072005131 ssDNA binding site [nucleotide binding]; other site 1231072005132 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1231072005133 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 1231072005134 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 1231072005135 trimer interface [polypeptide binding]; other site 1231072005136 putative metal binding site [ion binding]; other site 1231072005137 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 1231072005138 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 1231072005139 Walker A/P-loop; other site 1231072005140 ATP binding site [chemical binding]; other site 1231072005141 Q-loop/lid; other site 1231072005142 ABC transporter signature motif; other site 1231072005143 Walker B; other site 1231072005144 D-loop; other site 1231072005145 H-loop/switch region; other site 1231072005146 Predicted transcriptional regulators [Transcription]; Region: COG1725 1231072005147 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1231072005148 DNA-binding site [nucleotide binding]; DNA binding site 1231072005149 ECF-type riboflavin transporter, S component; Region: ECF-ribofla_trS; pfam07155 1231072005150 Protein of unknown function (DUF3816); Region: DUF3816; pfam12822 1231072005151 Bacterial protein of unknown function (DUF896); Region: DUF896; pfam05979 1231072005152 flagellin; Provisional; Region: PRK12804 1231072005153 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 1231072005154 HDOD domain; Region: HDOD; pfam08668 1231072005155 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1231072005156 Zn2+ binding site [ion binding]; other site 1231072005157 Mg2+ binding site [ion binding]; other site 1231072005158 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 1231072005159 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 1231072005160 active site 1231072005161 phosphorylation site [posttranslational modification] 1231072005162 intermolecular recognition site; other site 1231072005163 dimerization interface [polypeptide binding]; other site 1231072005164 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2604 1231072005165 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 1231072005166 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 1231072005167 putative active site [active] 1231072005168 putative NTP binding site [chemical binding]; other site 1231072005169 putative nucleic acid binding site [nucleotide binding]; other site 1231072005170 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 1231072005171 RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons; Region: RT_like; cl02808 1231072005172 Putative zinc binding domain; Region: Methyltransf_13; pfam08421 1231072005173 Methyltransferase domain; Region: Methyltransf_23; pfam13489 1231072005174 Methyltransferase domain; Region: Methyltransf_11; pfam08241 1231072005175 C-methyltransferase C-terminal domain; Region: Methyltransf_14; pfam08484 1231072005176 cytidylyltransferase; Region: cytidylyltransferase; cd02170 1231072005177 active site 1231072005178 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 1231072005179 tetramer interface [polypeptide binding]; other site 1231072005180 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 1231072005181 active site 1231072005182 Mg2+/Mn2+ binding site [ion binding]; other site 1231072005183 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 1231072005184 phosphonopyruvate decarboxylase; Region: Ppyr-DeCO2ase; TIGR03297 1231072005185 PYR/PP interface [polypeptide binding]; other site 1231072005186 dimer interface [polypeptide binding]; other site 1231072005187 TPP binding site [chemical binding]; other site 1231072005188 Thiamine pyrophosphate (TPP) family, PpyrDC subfamily, TPP-binding module; composed of proteins similar to phosphonopyruvate decarboxylase (PpyrDC) proteins. PpyrDC is a homotrimeric enzyme which functions in the biosynthesis of C-P compounds such as...; Region: TPP_PpyrDC; cd03371 1231072005189 TPP-binding site; other site 1231072005190 Saccharopine dehydrogenase; Region: Saccharop_dh; pfam03435 1231072005191 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 1231072005192 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 1231072005193 active site 1231072005194 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 1231072005195 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1231072005196 NAD(P) binding site [chemical binding]; other site 1231072005197 active site 1231072005198 Calcineurin-like phosphoesterase superfamily domain; Region: Metallophos_2; pfam12850 1231072005199 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 1231072005200 active site 1231072005201 metal binding site [ion binding]; metal-binding site 1231072005202 Uncharacterized conserved protein [Function unknown]; Region: COG4198 1231072005203 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 1231072005204 TPR motif; other site 1231072005205 binding surface 1231072005206 Tetratricopeptide repeat; Region: TPR_16; pfam13432 1231072005207 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 1231072005208 Sulfatase; Region: Sulfatase; cl17466 1231072005209 pseudaminic acid biosynthesis-associated protein PseG; Region: PseG; TIGR03590 1231072005210 GlcNAc-PI de-N-acetylase; Region: PIG-L; cl00929 1231072005211 Formyl transferase catalytic core domain found in a group of proteins with unknown functions; Region: FMT_core_like_1; cd08821 1231072005212 putative active site [active] 1231072005213 putative substrate binding site [chemical binding]; other site 1231072005214 putative cosubstrate binding site; other site 1231072005215 catalytic site [active] 1231072005216 pseudaminic acid synthase; Region: PseI; TIGR03586 1231072005217 NeuB family; Region: NeuB; pfam03102 1231072005218 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 1231072005219 NeuB binding interface [polypeptide binding]; other site 1231072005220 putative substrate binding site [chemical binding]; other site 1231072005221 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 1231072005222 Acetyltransferase (GNAT) domain; Region: Acetyltransf_7; pfam13508 1231072005223 SpsF is a glycosyltrnasferase implicated in the synthesis of the spore coat; Region: GT2_SpsF; cd02518 1231072005224 ligand binding site; other site 1231072005225 UDP-N-acetylglucosamine 4,6-dehydratase; Region: PseB; TIGR03589 1231072005226 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 1231072005227 NAD(P) binding site [chemical binding]; other site 1231072005228 homodimer interface [polypeptide binding]; other site 1231072005229 substrate binding site [chemical binding]; other site 1231072005230 active site 1231072005231 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2604 1231072005232 flagellin; Provisional; Region: PRK12804 1231072005233 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 1231072005234 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 1231072005235 flagellar capping protein; Validated; Region: fliD; PRK07737 1231072005236 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 1231072005237 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 1231072005238 Flagellar protein FliS; Region: FliS; cl00654 1231072005239 FlaG protein; Region: FlaG; pfam03646 1231072005240 carbon storage regulator; Provisional; Region: PRK01712 1231072005241 flagellar assembly protein FliW; Provisional; Region: PRK13285 1231072005242 flagellar hook-associated protein 3; Region: flagell_flgL; TIGR02550 1231072005243 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 1231072005244 Flagellar hook-associated protein [Cell motility and secretion]; Region: FlgK; COG1256 1231072005245 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 1231072005246 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 1231072005247 FlgN protein; Region: FlgN; pfam05130 1231072005248 flagellar biosynthesis anti-sigma factor FlgM; Region: FlgM_jcvi; TIGR03824 1231072005249 flagellar motor switch protein; Validated; Region: PRK08119 1231072005250 CheC-like family; Region: CheC; pfam04509 1231072005251 CheC-like family; Region: CheC; pfam04509 1231072005252 Flagellar motor switch/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FliN; COG1886 1231072005253 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 1231072005254 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 1231072005255 CheW-like domain; Region: CheW; pfam01584 1231072005256 Response regulator receiver domain; Region: Response_reg; pfam00072 1231072005257 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 1231072005258 active site 1231072005259 phosphorylation site [posttranslational modification] 1231072005260 intermolecular recognition site; other site 1231072005261 dimerization interface [polypeptide binding]; other site 1231072005262 Chemotaxis protein CheC, inhibitor of MCP methylation [Cell motility and secretion / Signal transduction mechanisms]; Region: CheC; COG1776 1231072005263 CheC-like family; Region: CheC; pfam04509 1231072005264 CheC-like family; Region: CheC; pfam04509 1231072005265 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 1231072005266 putative binding surface; other site 1231072005267 active site 1231072005268 P2 response regulator binding domain; Region: P2; pfam07194 1231072005269 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 1231072005270 P2 response regulator binding domain; Region: P2; pfam07194 1231072005271 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 1231072005272 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 1231072005273 ATP binding site [chemical binding]; other site 1231072005274 Mg2+ binding site [ion binding]; other site 1231072005275 G-X-G motif; other site 1231072005276 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 1231072005277 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 1231072005278 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 1231072005279 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 1231072005280 S-adenosylmethionine binding site [chemical binding]; other site 1231072005281 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 1231072005282 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 1231072005283 active site 1231072005284 phosphorylation site [posttranslational modification] 1231072005285 intermolecular recognition site; other site 1231072005286 dimerization interface [polypeptide binding]; other site 1231072005287 CheB methylesterase; Region: CheB_methylest; pfam01339 1231072005288 chemoreceptor glutamine deamidase CheD; Provisional; Region: PRK13490 1231072005289 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 1231072005290 Uncharacterized conserved protein [Function unknown]; Region: COG1315 1231072005291 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 1231072005292 substrate-cofactor binding pocket; other site 1231072005293 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1231072005294 catalytic residue [active] 1231072005295 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 1231072005296 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 1231072005297 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 1231072005298 motif II; other site 1231072005299 Protein of unknown function (DUF1292); Region: DUF1292; pfam06949 1231072005300 pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric; Region: pyruv_ox_red; TIGR02176 1231072005301 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 1231072005302 dimer interface [polypeptide binding]; other site 1231072005303 PYR/PP interface [polypeptide binding]; other site 1231072005304 TPP binding site [chemical binding]; other site 1231072005305 substrate binding site [chemical binding]; other site 1231072005306 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 1231072005307 Domain of unknown function; Region: EKR; smart00890 1231072005308 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 1231072005309 Thiamine pyrophosphate (TPP family), PFOR_PNO subfamily, TPP-binding module; composed of proteins similar to the single subunit pyruvate ferredoxin oxidoreductase (PFOR) of Desulfovibrio Africanus, present in bacteria and amitochondriate eukaryotes. This...; Region: TPP_PFOR_PNO; cd03377 1231072005310 TPP-binding site [chemical binding]; other site 1231072005311 dimer interface [polypeptide binding]; other site 1231072005312 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 1231072005313 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 1231072005314 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 1231072005315 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 1231072005316 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 1231072005317 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 1231072005318 homodimer interface [polypeptide binding]; other site 1231072005319 Small, acid-soluble spore proteins, alpha/beta type; Region: SASP; pfam00269 1231072005320 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 1231072005321 DHH family; Region: DHH; pfam01368 1231072005322 DHHA1 domain; Region: DHHA1; pfam02272 1231072005323 Endonuclease IV [DNA replication, recombination, and repair]; Region: Nfo; COG0648 1231072005324 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 1231072005325 AP (apurinic/apyrimidinic) site pocket; other site 1231072005326 DNA interaction; other site 1231072005327 Metal-binding active site; metal-binding site 1231072005328 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 1231072005329 thiamine phosphate binding site [chemical binding]; other site 1231072005330 active site 1231072005331 pyrophosphate binding site [ion binding]; other site 1231072005332 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09240 1231072005333 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 1231072005334 FeS/SAM binding site; other site 1231072005335 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 1231072005336 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 1231072005337 ThiS interaction site; other site 1231072005338 putative active site [active] 1231072005339 tetramer interface [polypeptide binding]; other site 1231072005340 ThiS-like ubiquitin; Region: ThiS-like; pfam14453 1231072005341 thiamine biosynthesis protein ThiF, family 2; Region: thiF_fam2; TIGR02354 1231072005342 Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common...; Region: E1_enzyme_family; cl17196 1231072005343 ATP binding site [chemical binding]; other site 1231072005344 substrate interface [chemical binding]; other site 1231072005345 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 1231072005346 thiamine phosphate binding site [chemical binding]; other site 1231072005347 active site 1231072005348 pyrophosphate binding site [ion binding]; other site 1231072005349 4-methyl-5-beta-hydroxyethylthiazole (Thz) kinase catalyzes the phosphorylation of the hydroxylgroup of Thz. A reaction that allows cells to recycle Thz into the thiamine biosynthesis pathway, as an alternative to its synthesis from cysteine, tyrosine...; Region: THZ_kinase; cd01170 1231072005350 substrate binding site [chemical binding]; other site 1231072005351 multimerization interface [polypeptide binding]; other site 1231072005352 ATP binding site [chemical binding]; other site 1231072005353 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 1231072005354 dimer interface [polypeptide binding]; other site 1231072005355 substrate binding site [chemical binding]; other site 1231072005356 ATP binding site [chemical binding]; other site 1231072005357 Thiamine-precursor transporter protein (ThiW); Region: ThiW; pfam09512 1231072005358 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 1231072005359 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 1231072005360 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 1231072005361 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 1231072005362 Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1; Region: GATase1_DJ-1; cd03135 1231072005363 conserved cys residue [active] 1231072005364 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; pfam04246 1231072005365 glycerol kinase; Provisional; Region: glpK; PRK00047 1231072005366 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 1231072005367 N- and C-terminal domain interface [polypeptide binding]; other site 1231072005368 active site 1231072005369 MgATP binding site [chemical binding]; other site 1231072005370 catalytic site [active] 1231072005371 metal binding site [ion binding]; metal-binding site 1231072005372 glycerol binding site [chemical binding]; other site 1231072005373 homotetramer interface [polypeptide binding]; other site 1231072005374 homodimer interface [polypeptide binding]; other site 1231072005375 FBP binding site [chemical binding]; other site 1231072005376 protein IIAGlc interface [polypeptide binding]; other site 1231072005377 Glycerol-3-phosphate responsive antiterminator; Region: G3P_antiterm; cl00852 1231072005378 phosphotransferase mannnose-specific family component IIA; Provisional; Region: PRK14484 1231072005379 dihydroxyacetone kinase, phosphoprotein-dependent, L subunit; Region: dha_L_ycgS; TIGR02365 1231072005380 dihydroxyacetone kinase subunit DhaK; Provisional; Region: PRK14481 1231072005381 Dihydroxyacetone kinase [Carbohydrate transport and metabolism]; Region: DAK1; COG2376 1231072005382 Arginase family; Region: Arginase; cd09989 1231072005383 active site 1231072005384 Mn binding site [ion binding]; other site 1231072005385 oligomer interface [polypeptide binding]; other site 1231072005386 PAS domain S-box; Region: sensory_box; TIGR00229 1231072005387 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1231072005388 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1231072005389 metal binding site [ion binding]; metal-binding site 1231072005390 active site 1231072005391 I-site; other site 1231072005392 DNA topoisomerase IV subunit A; Provisional; Region: PRK13979 1231072005393 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 1231072005394 CAP-like domain; other site 1231072005395 active site 1231072005396 primary dimer interface [polypeptide binding]; other site 1231072005397 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1231072005398 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1231072005399 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 1231072005400 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 1231072005401 ATP binding site [chemical binding]; other site 1231072005402 Mg2+ binding site [ion binding]; other site 1231072005403 G-X-G motif; other site 1231072005404 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 1231072005405 anchoring element; other site 1231072005406 dimer interface [polypeptide binding]; other site 1231072005407 ATP binding site [chemical binding]; other site 1231072005408 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 1231072005409 active site 1231072005410 metal binding site [ion binding]; metal-binding site 1231072005411 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1231072005412 Uncharacterized conserved protein [Function unknown]; Region: COG0398 1231072005413 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 1231072005414 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 1231072005415 binding surface 1231072005416 TPR motif; other site 1231072005417 TPR repeat; Region: TPR_11; pfam13414 1231072005418 TPR repeat; Region: TPR_11; pfam13414 1231072005419 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 1231072005420 binding surface 1231072005421 TPR motif; other site 1231072005422 TPR repeat; Region: TPR_11; pfam13414 1231072005423 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 1231072005424 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 1231072005425 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 1231072005426 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 1231072005427 Putative peptidoglycan binding domain; Region: PG_binding_4; pfam12229 1231072005428 VanW like protein; Region: VanW; pfam04294 1231072005429 G5 domain; Region: G5; pfam07501 1231072005430 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 1231072005431 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 1231072005432 Bacillus/Clostridium GerA spore germination protein; Region: GerA; pfam03323 1231072005433 germination protein, Ger(x)C family; Region: spore_ger_x_C; TIGR02887 1231072005434 Spore germination B3/ GerAC like, C-terminal; Region: Spore_GerAC; pfam05504 1231072005435 Spore germination protein; Region: Spore_permease; cl17796 1231072005436 Protein of unknown function (DUF1097); Region: DUF1097; pfam06496 1231072005437 D-hydantoinases (D-HYD) also called dihydropyrimidases (DHPase) and related proteins; DHPases are a family of enzymes that catalyze the reversible hydrolytic ring opening of the amide bond in five- or six-membered cyclic diamides, like dihydropyrimidine...; Region: D-HYD; cd01314 1231072005438 phenylhydantoinase; Validated; Region: PRK08323 1231072005439 tetramer interface [polypeptide binding]; other site 1231072005440 active site 1231072005441 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 1231072005442 PAS domain; Region: PAS_9; pfam13426 1231072005443 putative active site [active] 1231072005444 heme pocket [chemical binding]; other site 1231072005445 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1231072005446 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1231072005447 metal binding site [ion binding]; metal-binding site 1231072005448 active site 1231072005449 I-site; other site 1231072005450 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 1231072005451 Domain of unknown function (DUF4179); Region: DUF4179; pfam13786 1231072005452 RNA polymerase factor sigma-70; Validated; Region: PRK06811 1231072005453 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1231072005454 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; cl17257 1231072005455 Domain of unknown function (DUF4179); Region: DUF4179; pfam13786 1231072005456 RNA polymerase factor sigma-70; Validated; Region: PRK06811 1231072005457 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1231072005458 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 1231072005459 DNA binding residues [nucleotide binding] 1231072005460 RNA polymerase sigma-70 factor, TIGR02954 family; Region: Sig70_famx3 1231072005461 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1231072005462 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 1231072005463 DNA binding residues [nucleotide binding] 1231072005464 MORN repeat; Region: MORN; cl14787 1231072005465 TIM-barrel signal transduction protein; Region: TIM-br_sig_trns; pfam09370 1231072005466 hypothetical protein; Provisional; Region: PRK02399 1231072005467 Uncharacterized protein family (UPF0261); Region: UPF0261; pfam06792 1231072005468 TIM-barrel signal transduction protein; Region: TIM-br_sig_trns; pfam09370 1231072005469 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 1231072005470 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 1231072005471 Walker A motif; other site 1231072005472 ATP binding site [chemical binding]; other site 1231072005473 Walker B motif; other site 1231072005474 arginine finger; other site 1231072005475 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1231072005476 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 1231072005477 putative active site [active] 1231072005478 putative metal binding site [ion binding]; other site 1231072005479 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 1231072005480 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Thermotoga marina NorM; Region: MATE_NorM_like; cd13137 1231072005481 Peptidase family S41; Region: Peptidase_S41; pfam03572 1231072005482 Active site serine [active] 1231072005483 ABC-type transport system involved in multi-copper enzyme maturation, permease component [General function prediction only]; Region: NosY; COG1277 1231072005484 ABC-2 family transporter protein; Region: ABC2_membrane_4; pfam12730 1231072005485 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 1231072005486 ATP-binding cassette domain of the bacitracin-resistance transporter; Region: ABC_BcrA_bacitracin_resist; cd03268 1231072005487 Walker A/P-loop; other site 1231072005488 ATP binding site [chemical binding]; other site 1231072005489 Q-loop/lid; other site 1231072005490 ABC transporter signature motif; other site 1231072005491 Walker B; other site 1231072005492 D-loop; other site 1231072005493 H-loop/switch region; other site 1231072005494 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1231072005495 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 1231072005496 dimer interface [polypeptide binding]; other site 1231072005497 phosphorylation site [posttranslational modification] 1231072005498 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 1231072005499 ATP binding site [chemical binding]; other site 1231072005500 Mg2+ binding site [ion binding]; other site 1231072005501 G-X-G motif; other site 1231072005502 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1231072005503 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 1231072005504 active site 1231072005505 phosphorylation site [posttranslational modification] 1231072005506 intermolecular recognition site; other site 1231072005507 dimerization interface [polypeptide binding]; other site 1231072005508 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 1231072005509 DNA binding site [nucleotide binding] 1231072005510 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 1231072005511 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 1231072005512 Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a...; Region: Pterin_binding; cl00219 1231072005513 substrate binding pocket [chemical binding]; other site 1231072005514 dihydropteroate synthase; Region: DHPS; TIGR01496 1231072005515 dimer interface [polypeptide binding]; other site 1231072005516 inhibitor binding site; inhibition site 1231072005517 methyltransferase cognate corrinoid proteins, Methanosarcina family; Region: pyl_corrinoid; TIGR02370 1231072005518 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 1231072005519 B12 binding site [chemical binding]; other site 1231072005520 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 1231072005521 Predicted dehydrogenase [General function prediction only]; Region: COG0579 1231072005522 hydroxyglutarate oxidase; Provisional; Region: PRK11728 1231072005523 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 1231072005524 Protein of unknown function (DUF1292); Region: DUF1292; cl01608 1231072005525 Membrane protein of unknown function; Region: DUF360; pfam04020 1231072005526 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 1231072005527 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 1231072005528 Walker A/P-loop; other site 1231072005529 ATP binding site [chemical binding]; other site 1231072005530 Q-loop/lid; other site 1231072005531 ABC transporter signature motif; other site 1231072005532 Walker B; other site 1231072005533 D-loop; other site 1231072005534 H-loop/switch region; other site 1231072005535 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1231072005536 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1231072005537 formimidoylglutamase; Provisional; Region: PRK13775 1231072005538 Formimidoylglutamase or HutE; Region: Formimidoylglutamase; cd09988 1231072005539 putative active site [active] 1231072005540 putative metal binding site [ion binding]; other site 1231072005541 EamA-like transporter family; Region: EamA; pfam00892 1231072005542 EamA-like transporter family; Region: EamA; pfam00892 1231072005543 Protein of unknown function (DUF541); Region: SIMPL; pfam04402 1231072005544 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 1231072005545 active site 1231072005546 metal binding site [ion binding]; metal-binding site 1231072005547 homotetramer interface [polypeptide binding]; other site 1231072005548 Domain of unknown function (DUF4179); Region: DUF4179; pfam13786 1231072005549 RNA polymerase factor sigma-70; Validated; Region: PRK06811 1231072005550 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1231072005551 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 1231072005552 DNA binding residues [nucleotide binding] 1231072005553 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 1231072005554 metal binding triad [ion binding]; metal-binding site 1231072005555 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 1231072005556 dimer interface [polypeptide binding]; other site 1231072005557 phosphorylation site [posttranslational modification] 1231072005558 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 1231072005559 ATP binding site [chemical binding]; other site 1231072005560 Mg2+ binding site [ion binding]; other site 1231072005561 G-X-G motif; other site 1231072005562 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 1231072005563 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1231072005564 active site 1231072005565 phosphorylation site [posttranslational modification] 1231072005566 intermolecular recognition site; other site 1231072005567 dimerization interface [polypeptide binding]; other site 1231072005568 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 1231072005569 DNA binding site [nucleotide binding] 1231072005570 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 1231072005571 FtsX-like permease family; Region: FtsX; pfam02687 1231072005572 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 1231072005573 FtsX-like permease family; Region: FtsX; pfam02687 1231072005574 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1231072005575 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1231072005576 Walker A/P-loop; other site 1231072005577 ATP binding site [chemical binding]; other site 1231072005578 Q-loop/lid; other site 1231072005579 ABC transporter signature motif; other site 1231072005580 Walker B; other site 1231072005581 D-loop; other site 1231072005582 H-loop/switch region; other site 1231072005583 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1231072005584 Coenzyme A binding pocket [chemical binding]; other site 1231072005585 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 1231072005586 binding surface 1231072005587 TPR motif; other site 1231072005588 TPR repeat; Region: TPR_11; pfam13414 1231072005589 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 1231072005590 binding surface 1231072005591 TPR motif; other site 1231072005592 TPR repeat; Region: TPR_11; pfam13414 1231072005593 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 1231072005594 binding surface 1231072005595 TPR repeat; Region: TPR_11; pfam13414 1231072005596 TPR motif; other site 1231072005597 LrgA family; Region: LrgA; pfam03788 1231072005598 LrgB-like family; Region: LrgB; pfam04172 1231072005599 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 1231072005600 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1231072005601 catalytic residue [active] 1231072005602 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 1231072005603 ApbE family; Region: ApbE; pfam02424 1231072005604 Kynurenine formamidase [Amino acid transport and metabolism]; Region: COG1878 1231072005605 Cache domain; Region: Cache_2; pfam08269 1231072005606 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 1231072005607 dimerization interface [polypeptide binding]; other site 1231072005608 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1231072005609 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1231072005610 dimer interface [polypeptide binding]; other site 1231072005611 putative CheW interface [polypeptide binding]; other site 1231072005612 DNA topoisomerase III; Provisional; Region: PRK07726 1231072005613 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 1231072005614 active site 1231072005615 putative interdomain interaction site [polypeptide binding]; other site 1231072005616 putative metal-binding site [ion binding]; other site 1231072005617 putative nucleotide binding site [chemical binding]; other site 1231072005618 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; cl11986 1231072005619 domain I; other site 1231072005620 DNA binding groove [nucleotide binding] 1231072005621 phosphate binding site [ion binding]; other site 1231072005622 domain II; other site 1231072005623 domain III; other site 1231072005624 nucleotide binding site [chemical binding]; other site 1231072005625 catalytic site [active] 1231072005626 domain IV; other site 1231072005627 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 1231072005628 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 1231072005629 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1231072005630 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1231072005631 metal binding site [ion binding]; metal-binding site 1231072005632 active site 1231072005633 I-site; other site 1231072005634 Cache domain; Region: Cache_1; pfam02743 1231072005635 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 1231072005636 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 1231072005637 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1231072005638 dimer interface [polypeptide binding]; other site 1231072005639 putative CheW interface [polypeptide binding]; other site 1231072005640 metallo-beta-lactamase/flavodoxin domain-containing protein; Provisional; Region: PRK11921 1231072005641 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1231072005642 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 1231072005643 Predicted membrane protein [Function unknown]; Region: COG2855 1231072005644 Domain of unknown function (DUF4163); Region: DUF4163; pfam13739 1231072005645 Protein of unknown function (DUF3298); Region: DUF3298; pfam11738 1231072005646 TIGR04076 family protein; Region: TIGR04076 1231072005647 FMN-binding domain; Region: FMN_bind; pfam04205 1231072005648 flavocytochrome c; Region: flavo_cyto_c; TIGR01813 1231072005649 L-aspartate oxidase; Provisional; Region: PRK06175 1231072005650 Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]; Region: COG2972 1231072005651 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 1231072005652 dimerization interface [polypeptide binding]; other site 1231072005653 Histidine kinase; Region: His_kinase; pfam06580 1231072005654 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 1231072005655 ATP binding site [chemical binding]; other site 1231072005656 Mg2+ binding site [ion binding]; other site 1231072005657 G-X-G motif; other site 1231072005658 Response regulator receiver domain; Region: Response_reg; pfam00072 1231072005659 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 1231072005660 active site 1231072005661 phosphorylation site [posttranslational modification] 1231072005662 intermolecular recognition site; other site 1231072005663 dimerization interface [polypeptide binding]; other site 1231072005664 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1231072005665 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1231072005666 Rubrerythrin [Energy production and conversion]; Region: COG1592 1231072005667 rubrerythrin-like, diiron-binding domain; Region: Rubrerythrin_like; cd01046 1231072005668 diiron binding motif [ion binding]; other site 1231072005669 SWIM zinc finger; Region: SWIM; pfam04434 1231072005670 Bacterial SNF2 helicase associated; Region: SNF2_assoc; pfam08455 1231072005671 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 1231072005672 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 1231072005673 ATP binding site [chemical binding]; other site 1231072005674 putative Mg++ binding site [ion binding]; other site 1231072005675 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 1231072005676 nucleotide binding region [chemical binding]; other site 1231072005677 ATP-binding site [chemical binding]; other site 1231072005678 tRNA pseudouridine synthase A; Reviewed; Region: PRK12434 1231072005679 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 1231072005680 dimerization interface 3.5A [polypeptide binding]; other site 1231072005681 active site 1231072005682 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 1231072005683 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 1231072005684 TrkA-C domain; Region: TrkA_C; pfam02080 1231072005685 probable dihydroxyacetone kinase regulator; Region: DHAK_reg; TIGR02366 1231072005686 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1231072005687 myosin-cross-reactive antigen; Provisional; Region: PRK13977 1231072005688 helicase 45; Provisional; Region: PTZ00424 1231072005689 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 1231072005690 ATP binding site [chemical binding]; other site 1231072005691 putative Mg++ binding site [ion binding]; other site 1231072005692 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 1231072005693 nucleotide binding region [chemical binding]; other site 1231072005694 ATP-binding site [chemical binding]; other site 1231072005695 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1231072005696 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1231072005697 Walker A/P-loop; other site 1231072005698 ATP binding site [chemical binding]; other site 1231072005699 Q-loop/lid; other site 1231072005700 ABC transporter signature motif; other site 1231072005701 Walker B; other site 1231072005702 D-loop; other site 1231072005703 H-loop/switch region; other site 1231072005704 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 1231072005705 FtsX-like permease family; Region: FtsX; pfam02687 1231072005706 Cache domain; Region: Cache_1; pfam02743 1231072005707 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 1231072005708 HAMP domain; Region: HAMP; pfam00672 1231072005709 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1231072005710 dimer interface [polypeptide binding]; other site 1231072005711 putative CheW interface [polypeptide binding]; other site 1231072005712 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 1231072005713 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 1231072005714 non-specific DNA binding site [nucleotide binding]; other site 1231072005715 salt bridge; other site 1231072005716 sequence-specific DNA binding site [nucleotide binding]; other site 1231072005717 Domain of unknown function (DUF955); Region: DUF955; pfam06114 1231072005718 AAA domain; Region: AAA_26; pfam13500 1231072005719 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 1231072005720 Uncharacterized conserved protein [General function prediction only]; Region: BioY; COG1268 1231072005721 Kynurenine formamidase [Amino acid transport and metabolism]; Region: COG1878 1231072005722 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 1231072005723 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 1231072005724 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 1231072005725 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 1231072005726 6-phosphogluconate dehydrogenase; Validated; Region: PRK09287 1231072005727 6-phosphogluconate dehydrogenase, C-terminal domain; Region: 6PGD; pfam00393 1231072005728 multifunctional aminopeptidase A; Provisional; Region: PRK00913 1231072005729 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 1231072005730 interface (dimer of trimers) [polypeptide binding]; other site 1231072005731 Substrate-binding/catalytic site; other site 1231072005732 Zn-binding sites [ion binding]; other site 1231072005733 Branched-chain amino acid transport protein; Region: Branch_AA_trans; pfam05525 1231072005734 Protein of unknown function (DUF1533); Region: DUF1533; pfam07550 1231072005735 Protein of unknown function (DUF1533); Region: DUF1533; pfam07550 1231072005736 Protein of unknown function (DUF1533); Region: DUF1533; pfam07550 1231072005737 Protein of unknown function (DUF1533); Region: DUF1533; pfam07550 1231072005738 Protein of unknown function (DUF1533); Region: DUF1533; pfam07550 1231072005739 Protein of unknown function (DUF1533); Region: DUF1533; pfam07550 1231072005740 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072005741 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072005742 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072005743 Family of unknown function (DUF438); Region: DUF438; pfam04282 1231072005744 Hemerythrin HHE cation binding domain; Region: Hemerythrin; pfam01814 1231072005745 Domain of Unknown function (DUF542); Region: ScdA_N; pfam04405 1231072005746 iron-sulfur cluster repair di-iron protein; Region: FeS_repair_RIC; TIGR03652 1231072005747 Hemerythrin HHE cation binding domain; Region: Hemerythrin; pfam01814 1231072005748 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 1231072005749 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1231072005750 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 1231072005751 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 1231072005752 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 1231072005753 ligand binding site [chemical binding]; other site 1231072005754 flexible hinge region; other site 1231072005755 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 1231072005756 putative switch regulator; other site 1231072005757 non-specific DNA interactions [nucleotide binding]; other site 1231072005758 DNA binding site [nucleotide binding] 1231072005759 sequence specific DNA binding site [nucleotide binding]; other site 1231072005760 putative cAMP binding site [chemical binding]; other site 1231072005761 Type I (cytosolic) bacterial L-asparaginase; Region: L-asparaginase_I; cd08963 1231072005762 active site 1231072005763 homodimer interface [polypeptide binding]; other site 1231072005764 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]; Region: COG4260 1231072005765 A subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual...; Region: Band_7_5; cd03408 1231072005766 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 1231072005767 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]; Region: COG1512 1231072005768 Repair protein; Region: Repair_PSII; pfam04536 1231072005769 TFIIB zinc-binding; Region: TF_Zn_Ribbon; pfam08271 1231072005770 Phage shock protein A (IM30), suppresses sigma54-dependent transcription [Transcription / Signal transduction mechanisms]; Region: PspA; COG1842 1231072005771 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 1231072005772 XdhC Rossmann domain; Region: XdhC_C; pfam13478 1231072005773 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 1231072005774 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 1231072005775 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 1231072005776 dimerization interface [polypeptide binding]; other site 1231072005777 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1231072005778 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1231072005779 dimer interface [polypeptide binding]; other site 1231072005780 putative CheW interface [polypeptide binding]; other site 1231072005781 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 1231072005782 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 1231072005783 dimerization interface [polypeptide binding]; other site 1231072005784 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1231072005785 dimer interface [polypeptide binding]; other site 1231072005786 putative CheW interface [polypeptide binding]; other site 1231072005787 cytosine deaminase; Provisional; Region: PRK09230 1231072005788 Bacterial cytosine deaminase and related metal-dependent hydrolases. Cytosine deaminases (CDs) catalyze the deamination of cytosine, producing uracil and ammonia. They play an important role in pyrimidine salvage. CDs are present in prokaryotes and fungi; Region: Bact_CD; cd01293 1231072005789 active site 1231072005790 Creatinine amidohydrolase; Region: Creatininase; pfam02633 1231072005791 EamA-like transporter family; Region: EamA; pfam00892 1231072005792 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 1231072005793 EamA-like transporter family; Region: EamA; pfam00892 1231072005794 Purine catabolism regulatory protein-like family; Region: PucR; pfam07905 1231072005795 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 1231072005796 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 1231072005797 Thiol-activated cytolysin; Region: Thiol_cytolysin; pfam01289 1231072005798 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 1231072005799 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 1231072005800 S-adenosylmethionine binding site [chemical binding]; other site 1231072005801 ABC-2 family transporter protein; Region: ABC2_membrane_5; pfam13346 1231072005802 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 1231072005803 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 1231072005804 Walker A/P-loop; other site 1231072005805 ATP binding site [chemical binding]; other site 1231072005806 Q-loop/lid; other site 1231072005807 ABC transporter signature motif; other site 1231072005808 Walker B; other site 1231072005809 D-loop; other site 1231072005810 H-loop/switch region; other site 1231072005811 Predicted transcriptional regulators [Transcription]; Region: COG1725 1231072005812 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1231072005813 DNA-binding site [nucleotide binding]; DNA binding site 1231072005814 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1231072005815 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1231072005816 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 1231072005817 dimerization interface [polypeptide binding]; other site 1231072005818 putative DNA binding site [nucleotide binding]; other site 1231072005819 putative Zn2+ binding site [ion binding]; other site 1231072005820 Arsenical resistance operon trans-acting repressor ArsD; Region: ArsD; pfam06953 1231072005821 arsenical pump-driving ATPase; Region: arsen_driv_ArsA; TIGR04291 1231072005822 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 1231072005823 P loop; other site 1231072005824 Nucleotide binding site [chemical binding]; other site 1231072005825 DTAP/Switch II; other site 1231072005826 Switch I; other site 1231072005827 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 1231072005828 P loop; other site 1231072005829 Nucleotide binding site [chemical binding]; other site 1231072005830 DTAP/Switch II; other site 1231072005831 Switch I; other site 1231072005832 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1231072005833 Mor transcription activator family; Region: Mor; cl02360 1231072005834 Putative cyclase; Region: Cyclase; pfam04199 1231072005835 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 1231072005836 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 1231072005837 putative DNA binding site [nucleotide binding]; other site 1231072005838 putative Zn2+ binding site [ion binding]; other site 1231072005839 allantoate amidohydrolase; Reviewed; Region: PRK09290 1231072005840 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 1231072005841 active site 1231072005842 metal binding site [ion binding]; metal-binding site 1231072005843 dimer interface [polypeptide binding]; other site 1231072005844 Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]; Region: {ManC}; COG0662 1231072005845 ABC-2 type transporter; Region: ABC2_membrane; cl17235 1231072005846 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 1231072005847 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1231072005848 Walker A/P-loop; other site 1231072005849 ATP binding site [chemical binding]; other site 1231072005850 Q-loop/lid; other site 1231072005851 ABC transporter signature motif; other site 1231072005852 Walker B; other site 1231072005853 D-loop; other site 1231072005854 H-loop/switch region; other site 1231072005855 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; smart00871 1231072005856 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1231072005857 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3708 1231072005858 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_19; cd08518 1231072005859 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 1231072005860 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 1231072005861 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 1231072005862 dimer interface [polypeptide binding]; other site 1231072005863 conserved gate region; other site 1231072005864 putative PBP binding loops; other site 1231072005865 ABC-ATPase subunit interface; other site 1231072005866 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 1231072005867 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 1231072005868 dimer interface [polypeptide binding]; other site 1231072005869 conserved gate region; other site 1231072005870 putative PBP binding loops; other site 1231072005871 ABC-ATPase subunit interface; other site 1231072005872 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 1231072005873 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 1231072005874 Walker A/P-loop; other site 1231072005875 ATP binding site [chemical binding]; other site 1231072005876 Q-loop/lid; other site 1231072005877 ABC transporter signature motif; other site 1231072005878 Walker B; other site 1231072005879 D-loop; other site 1231072005880 H-loop/switch region; other site 1231072005881 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1231072005882 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 1231072005883 Walker A/P-loop; other site 1231072005884 ATP binding site [chemical binding]; other site 1231072005885 Q-loop/lid; other site 1231072005886 ABC transporter signature motif; other site 1231072005887 Walker B; other site 1231072005888 D-loop; other site 1231072005889 H-loop/switch region; other site 1231072005890 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1231072005891 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 1231072005892 dimerization interface [polypeptide binding]; other site 1231072005893 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 1231072005894 dimer interface [polypeptide binding]; other site 1231072005895 phosphorylation site [posttranslational modification] 1231072005896 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 1231072005897 ATP binding site [chemical binding]; other site 1231072005898 Mg2+ binding site [ion binding]; other site 1231072005899 G-X-G motif; other site 1231072005900 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 1231072005901 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 1231072005902 active site 1231072005903 phosphorylation site [posttranslational modification] 1231072005904 intermolecular recognition site; other site 1231072005905 dimerization interface [polypeptide binding]; other site 1231072005906 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 1231072005907 DNA binding site [nucleotide binding] 1231072005908 Radical SAM superfamily; Region: Radical_SAM; pfam04055 1231072005909 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 1231072005910 FeS/SAM binding site; other site 1231072005911 Protein of unknown function (DUF2089); Region: DUF2089; pfam09862 1231072005912 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 1231072005913 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 1231072005914 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 1231072005915 The MutT pyrophosphohydrolase is a prototypical Nudix hydrolase that catalyzes the hydrolysis of nucleoside and deoxynucleoside triphosphates (NTPs and dNTPs) by substitution at a beta-phosphorus to yield a nucleotide monophosphate (NMP) and inorganic...; Region: MutT_pyrophosphohydrolase; cd03425 1231072005916 active site 1231072005917 8-oxo-dGMP binding site [chemical binding]; other site 1231072005918 nudix motif; other site 1231072005919 metal binding site [ion binding]; metal-binding site 1231072005920 Domain of unknown function (DUF3427); Region: DUF3427; pfam11907 1231072005921 N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; Region: PLDc_N_DEXD_b2; cd09204 1231072005922 PLD-like domain; Region: PLDc_2; pfam13091 1231072005923 putative homodimer interface [polypeptide binding]; other site 1231072005924 putative active site [active] 1231072005925 catalytic site [active] 1231072005926 DNA phosphorothioation system restriction enzyme; Region: dnd_restrict_1; TIGR04095 1231072005927 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 1231072005928 ATP binding site [chemical binding]; other site 1231072005929 putative Mg++ binding site [ion binding]; other site 1231072005930 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 1231072005931 nucleotide binding region [chemical binding]; other site 1231072005932 ATP-binding site [chemical binding]; other site 1231072005933 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 1231072005934 RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA...; Region: RT_Bac_retron_II; cd03487 1231072005935 putative active site [active] 1231072005936 putative NTP binding site [chemical binding]; other site 1231072005937 putative nucleic acid binding site [nucleotide binding]; other site 1231072005938 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4185 1231072005939 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 1231072005940 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 1231072005941 ligand binding site [chemical binding]; other site 1231072005942 flexible hinge region; other site 1231072005943 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 1231072005944 Predicted membrane protein [Function unknown]; Region: COG2364 1231072005945 HAD superfamily (subfamily IA) hydrolase, TIGR02254; Region: YjjG/YfnB 1231072005946 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 1231072005947 motif II; other site 1231072005948 Protein of unknown function DUF91; Region: DUF91; cl00709 1231072005949 Helix-turn-helix domain; Region: HTH_17; pfam12728 1231072005950 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1231072005951 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 1231072005952 active site 1231072005953 phosphorylation site [posttranslational modification] 1231072005954 intermolecular recognition site; other site 1231072005955 dimerization interface [polypeptide binding]; other site 1231072005956 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 1231072005957 DNA binding site [nucleotide binding] 1231072005958 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1231072005959 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 1231072005960 dimer interface [polypeptide binding]; other site 1231072005961 phosphorylation site [posttranslational modification] 1231072005962 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 1231072005963 ATP binding site [chemical binding]; other site 1231072005964 Mg2+ binding site [ion binding]; other site 1231072005965 G-X-G motif; other site 1231072005966 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1231072005967 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1231072005968 Walker A/P-loop; other site 1231072005969 ATP binding site [chemical binding]; other site 1231072005970 Q-loop/lid; other site 1231072005971 ABC transporter signature motif; other site 1231072005972 Walker B; other site 1231072005973 D-loop; other site 1231072005974 H-loop/switch region; other site 1231072005975 FtsX-like permease family; Region: FtsX; pfam02687 1231072005976 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 1231072005977 FtsX-like permease family; Region: FtsX; pfam02687 1231072005978 Homeodomain-like domain; Region: HTH_23; pfam13384 1231072005979 Domain of unknown function (DUF4351); Region: DUF4351; pfam14261 1231072005980 Phage-related protein [Function unknown]; Region: COG4722 1231072005981 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 1231072005982 non-specific DNA binding site [nucleotide binding]; other site 1231072005983 salt bridge; other site 1231072005984 sequence-specific DNA binding site [nucleotide binding]; other site 1231072005985 Phage terminase, small subunit; Region: Terminase_4; pfam05119 1231072005986 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 1231072005987 dimerization interface [polypeptide binding]; other site 1231072005988 putative active site pocket [active] 1231072005989 putative catalytic residue [active] 1231072005990 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 1231072005991 ParB-like nuclease domain; Region: ParBc; pfam02195 1231072005992 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]; Region: COG0856 1231072005993 Predicted nuclease of the RecB family [DNA replication, recombination, and repair]; Region: COG1637 1231072005994 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 1231072005995 active site 1231072005996 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 1231072005997 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 1231072005998 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 1231072005999 non-specific DNA binding site [nucleotide binding]; other site 1231072006000 salt bridge; other site 1231072006001 sequence-specific DNA binding site [nucleotide binding]; other site 1231072006002 Domain of unknown function (DUF955); Region: DUF955; cl01076 1231072006003 Type IV secretory system Conjugative DNA transfer; Region: T4SS-DNA_transf; pfam02534 1231072006004 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 1231072006005 Walker A motif; other site 1231072006006 ATP binding site [chemical binding]; other site 1231072006007 Walker B motif; other site 1231072006008 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cl00083 1231072006009 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 1231072006010 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 1231072006011 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 1231072006012 TRAM domain; Region: TRAM; cl01282 1231072006013 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 1231072006014 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 1231072006015 S-adenosylmethionine binding site [chemical binding]; other site 1231072006016 RDD family; Region: RDD; cl00746 1231072006017 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 1231072006018 Sulfatase; Region: Sulfatase; pfam00884 1231072006019 hypothetical protein; Provisional; Region: PRK10621 1231072006020 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 1231072006021 dipeptidase PepV; Reviewed; Region: PRK07318 1231072006022 M20 Peptidase Xaa-His dipeptidase (PepV) degrades hydrophobic dipeptides; Region: M20_PepV; cd03888 1231072006023 active site 1231072006024 metal binding site [ion binding]; metal-binding site 1231072006025 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1231072006026 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1231072006027 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 1231072006028 dimerization interface [polypeptide binding]; other site 1231072006029 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 1231072006030 dimer interface [polypeptide binding]; other site 1231072006031 phosphorylation site [posttranslational modification] 1231072006032 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 1231072006033 ATP binding site [chemical binding]; other site 1231072006034 Mg2+ binding site [ion binding]; other site 1231072006035 G-X-G motif; other site 1231072006036 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1231072006037 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 1231072006038 active site 1231072006039 phosphorylation site [posttranslational modification] 1231072006040 intermolecular recognition site; other site 1231072006041 dimerization interface [polypeptide binding]; other site 1231072006042 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 1231072006043 DNA binding site [nucleotide binding] 1231072006044 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 1231072006045 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 1231072006046 metal-binding site [ion binding] 1231072006047 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 1231072006048 Soluble P-type ATPase [General function prediction only]; Region: COG4087 1231072006049 oligoendopeptidase F; Region: pepF; TIGR00181 1231072006050 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_3; cd09608 1231072006051 active site 1231072006052 Zn binding site [ion binding]; other site 1231072006053 histidyl-tRNA synthetase; Region: hisS; TIGR00442 1231072006054 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 1231072006055 dimer interface [polypeptide binding]; other site 1231072006056 motif 1; other site 1231072006057 active site 1231072006058 motif 2; other site 1231072006059 motif 3; other site 1231072006060 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 1231072006061 anticodon binding site; other site 1231072006062 Protein of unknown function (DUF3829); Region: DUF3829; pfam12889 1231072006063 Protein of unknown function (DUF3829); Region: DUF3829; pfam12889 1231072006064 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 1231072006065 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 1231072006066 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 1231072006067 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 1231072006068 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 1231072006069 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 1231072006070 purine monophosphate binding site [chemical binding]; other site 1231072006071 dimer interface [polypeptide binding]; other site 1231072006072 putative catalytic residues [active] 1231072006073 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 1231072006074 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 1231072006075 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 1231072006076 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 1231072006077 active site 1231072006078 substrate binding site [chemical binding]; other site 1231072006079 cosubstrate binding site; other site 1231072006080 catalytic site [active] 1231072006081 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 1231072006082 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 1231072006083 dimerization interface [polypeptide binding]; other site 1231072006084 putative ATP binding site [chemical binding]; other site 1231072006085 amidophosphoribosyltransferase; Provisional; Region: PRK05793 1231072006086 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 1231072006087 active site 1231072006088 tetramer interface [polypeptide binding]; other site 1231072006089 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1231072006090 active site 1231072006091 AIR carboxylase; Region: AIRC; pfam00731 1231072006092 Uncharacterized conserved protein [Function unknown]; Region: COG1434 1231072006093 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 1231072006094 putative active site [active] 1231072006095 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 1231072006096 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 1231072006097 ligand binding site [chemical binding]; other site 1231072006098 flexible hinge region; other site 1231072006099 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 1231072006100 Sporulation protein YtfJ (Spore_YtfJ); Region: Spore_YtfJ; cl01596 1231072006101 Ferredoxin [Energy production and conversion]; Region: COG1146 1231072006102 4Fe-4S binding domain; Region: Fer4_6; pfam12837 1231072006103 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 1231072006104 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 1231072006105 amino acid carrier protein; Region: agcS; TIGR00835 1231072006106 ECF-type riboflavin transporter, S component; Region: ECF-ribofla_trS; pfam07155 1231072006107 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 1231072006108 Carbon starvation protein CstA; Region: CstA; pfam02554 1231072006109 Carbon starvation protein CstA; Region: CstA; pfam02554 1231072006110 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 1231072006111 5TMR of 5TMR-LYT; Region: 5TM-5TMR_LYT; pfam07694 1231072006112 Putative regulator of cell autolysis [Signal transduction mechanisms]; Region: LytS; COG3275 1231072006113 Histidine kinase; Region: His_kinase; pfam06580 1231072006114 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 1231072006115 ATP binding site [chemical binding]; other site 1231072006116 Mg2+ binding site [ion binding]; other site 1231072006117 G-X-G motif; other site 1231072006118 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 1231072006119 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 1231072006120 active site 1231072006121 phosphorylation site [posttranslational modification] 1231072006122 intermolecular recognition site; other site 1231072006123 dimerization interface [polypeptide binding]; other site 1231072006124 LytTr DNA-binding domain; Region: LytTR; pfam04397 1231072006125 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072006126 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072006127 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072006128 L-serine dehydratase, iron-sulfur-dependent, beta subunit; Region: sda_beta; TIGR00719 1231072006129 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 1231072006130 C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit; Region: ACT_LSD; cd04903 1231072006131 putative L-serine binding site [chemical binding]; other site 1231072006132 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 1231072006133 L-serine deaminase [Amino acid transport and metabolism]; Region: SdaA; COG1760 1231072006134 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1231072006135 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1231072006136 metal binding site [ion binding]; metal-binding site 1231072006137 active site 1231072006138 I-site; other site 1231072006139 Predicted transcriptional regulators [Transcription]; Region: COG1725 1231072006140 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1231072006141 DNA-binding site [nucleotide binding]; DNA binding site 1231072006142 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 1231072006143 Walker A/P-loop; other site 1231072006144 ATP binding site [chemical binding]; other site 1231072006145 ABC transporter; Region: ABC_tran; pfam00005 1231072006146 Q-loop/lid; other site 1231072006147 ABC transporter signature motif; other site 1231072006148 Walker B; other site 1231072006149 D-loop; other site 1231072006150 H-loop/switch region; other site 1231072006151 gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit; Region: galliderm_ABC; TIGR03740 1231072006152 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 1231072006153 Walker A/P-loop; other site 1231072006154 ATP binding site [chemical binding]; other site 1231072006155 Q-loop/lid; other site 1231072006156 ABC transporter signature motif; other site 1231072006157 Walker B; other site 1231072006158 D-loop; other site 1231072006159 H-loop/switch region; other site 1231072006160 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 1231072006161 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 1231072006162 active site 1231072006163 metal binding site [ion binding]; metal-binding site 1231072006164 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 1231072006165 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 1231072006166 pyrimidine-nucleoside phosphorylase; Reviewed; Region: PRK06078 1231072006167 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 1231072006168 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 1231072006169 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; pfam07831 1231072006170 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 1231072006171 intersubunit interface [polypeptide binding]; other site 1231072006172 active site 1231072006173 catalytic residue [active] 1231072006174 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 1231072006175 Escherichia coli UshA-like family, N-terminal metallophosphatase domain; Region: MPP_UshA_N_like; cd00845 1231072006176 active site 1231072006177 metal binding site [ion binding]; metal-binding site 1231072006178 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 1231072006179 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 1231072006180 Glycerol uptake facilitator and related permeases (Major Intrinsic Protein Family) [Carbohydrate transport and metabolism]; Region: GlpF; COG0580 1231072006181 amphipathic channel; other site 1231072006182 Asn-Pro-Ala signature motifs; other site 1231072006183 Leucyl aminopeptidase (aminopeptidase T) [Amino acid transport and metabolism]; Region: AmpS; COG2309 1231072006184 Thermophilic metalloprotease (M29); Region: Peptidase_M29; pfam02073 1231072006185 A subgroup of L-lactate dehydrogenases; Region: LDH_2; cd05292 1231072006186 L-lactate dehydrogenase; Reviewed; Region: ldh; PRK00066 1231072006187 NAD binding site [chemical binding]; other site 1231072006188 dimer interface [polypeptide binding]; other site 1231072006189 substrate binding site [chemical binding]; other site 1231072006190 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1231072006191 Probable zinc-binding domain; Region: zf-trcl; pfam13451 1231072006192 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 1231072006193 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 1231072006194 ATP binding site [chemical binding]; other site 1231072006195 Mg++ binding site [ion binding]; other site 1231072006196 motif III; other site 1231072006197 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 1231072006198 nucleotide binding region [chemical binding]; other site 1231072006199 ATP-binding site [chemical binding]; other site 1231072006200 RNA recognition motif in the DbpA subfamily of prokaryotic DEAD-box rRNA helicases; Region: RRM_DbpA; cd12252 1231072006201 RNA binding site [nucleotide binding]; other site 1231072006202 ClC chloride channel EriC. This domain is found in the EriC chloride transporters that mediate the extreme acid resistance response in eubacteria and archaea. This response allows bacteria to survive in the acidic environments by decarboxylation-linked...; Region: EriC; cd01031 1231072006203 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 1231072006204 Cl- selectivity filter; other site 1231072006205 Cl- binding residues [ion binding]; other site 1231072006206 pore gating glutamate residue; other site 1231072006207 dimer interface [polypeptide binding]; other site 1231072006208 H+/Cl- coupling transport residue; other site 1231072006209 TrkA-C domain; Region: TrkA_C; pfam02080 1231072006210 EDD domain protein, DegV family; Region: DegV; TIGR00762 1231072006211 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 1231072006212 Predicted membrane protein [Function unknown]; Region: COG4129 1231072006213 Bacterial protein of unknown function (DUF939); Region: DUF939; pfam06081 1231072006214 DUF939 C-terminal domain; Region: DUF939_C; pfam11728 1231072006215 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]; Region: COG1579 1231072006216 Putative zinc ribbon domain; Region: DUF164; pfam02591 1231072006217 Uncharacterized conserved protein [Function unknown]; Region: COG0327 1231072006218 NIF3 (NGG1p interacting factor 3); Region: NIF3; pfam01784 1231072006219 Predicted SAM-dependent methyltransferase [General function prediction only]; Region: COG2384 1231072006220 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 1231072006221 S-adenosylmethionine binding site [chemical binding]; other site 1231072006222 Protein of unknown function (DUF2679); Region: DUF2679; pfam10882 1231072006223 RNA polymerase sigma factor RpoD; Validated; Region: PRK09210 1231072006224 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 1231072006225 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1231072006226 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1231072006227 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 1231072006228 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 1231072006229 DNA binding residues [nucleotide binding] 1231072006230 DNA primase; Validated; Region: dnaG; PRK05667 1231072006231 CHC2 zinc finger; Region: zf-CHC2; pfam01807 1231072006232 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 1231072006233 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 1231072006234 active site 1231072006235 metal binding site [ion binding]; metal-binding site 1231072006236 interdomain interaction site; other site 1231072006237 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 1231072006238 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 1231072006239 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1231072006240 Zn2+ binding site [ion binding]; other site 1231072006241 Mg2+ binding site [ion binding]; other site 1231072006242 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 1231072006243 spore coat protein, CotS family; Region: spore_CotS; TIGR02906 1231072006244 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 1231072006245 substrate binding site [chemical binding]; other site 1231072006246 pyruvate phosphate dikinase; Provisional; Region: PRK09279 1231072006247 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 1231072006248 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 1231072006249 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 1231072006250 HTH domain; Region: HTH_11; pfam08279 1231072006251 FOG: CBS domain [General function prediction only]; Region: COG0517 1231072006252 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_4; cd04617 1231072006253 Domain of unknown function (DUF4342); Region: DUF4342; pfam14242 1231072006254 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 1231072006255 Recombination protein O C terminal; Region: RecO_C; pfam02565 1231072006256 GTPase Era; Reviewed; Region: era; PRK00089 1231072006257 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 1231072006258 G1 box; other site 1231072006259 GTP/Mg2+ binding site [chemical binding]; other site 1231072006260 Switch I region; other site 1231072006261 G2 box; other site 1231072006262 Switch II region; other site 1231072006263 G3 box; other site 1231072006264 G4 box; other site 1231072006265 G5 box; other site 1231072006266 KH domain; Region: KH_2; pfam07650 1231072006267 Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on...; Region: cytidine_deaminase; cd01283 1231072006268 active site 1231072006269 catalytic motif [active] 1231072006270 Zn binding site [ion binding]; other site 1231072006271 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; pfam01219 1231072006272 PAP2_like proteins, diacylglycerol_kinase like sub-family. In some prokaryotes, PAP2_like phosphatase domains appear fused to E. coli DAGK-like trans-membrane diacylglycerol kinase domains. The cellular function of these architectures remains to be...; Region: PAP2_diacylglycerolkinase; cd03383 1231072006273 active site 1231072006274 metal-binding heat shock protein; Provisional; Region: PRK00016 1231072006275 Predicted membrane-associated HD superfamily hydrolase [General function prediction only]; Region: COG1480 1231072006276 7TM receptor with intracellular HD hydrolase; Region: 7TM-7TMR_HD; pfam07698 1231072006277 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1231072006278 Zn2+ binding site [ion binding]; other site 1231072006279 Mg2+ binding site [ion binding]; other site 1231072006280 Putative stage IV sporulation protein YqfD; Region: YqfD; pfam06898 1231072006281 sporulation protein YqfD; Region: spore_yqfD; TIGR02876 1231072006282 YabP family; Region: YabP; cl06766 1231072006283 Yqey-like protein; Region: YqeY; pfam09424 1231072006284 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 1231072006285 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 1231072006286 nucleotide binding site/active site [active] 1231072006287 HIT family signature motif; other site 1231072006288 catalytic residue [active] 1231072006289 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 1231072006290 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1231072006291 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 1231072006292 RNA methyltransferase, RsmE family; Region: TIGR00046 1231072006293 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 1231072006294 DNA methylase; Region: N6_N4_Mtase; cl17433 1231072006295 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 1231072006296 S-adenosylmethionine binding site [chemical binding]; other site 1231072006297 chaperone protein DnaJ; Provisional; Region: PRK14297 1231072006298 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 1231072006299 HSP70 interaction site [polypeptide binding]; other site 1231072006300 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 1231072006301 substrate binding site [polypeptide binding]; other site 1231072006302 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 1231072006303 Zn binding sites [ion binding]; other site 1231072006304 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 1231072006305 dimer interface [polypeptide binding]; other site 1231072006306 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 1231072006307 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 1231072006308 nucleotide binding site [chemical binding]; other site 1231072006309 NEF interaction site [polypeptide binding]; other site 1231072006310 SBD interface [polypeptide binding]; other site 1231072006311 GrpE; Region: GrpE; pfam01025 1231072006312 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 1231072006313 dimer interface [polypeptide binding]; other site 1231072006314 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 1231072006315 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 1231072006316 Winged helix-turn-helix transcription repressor, HrcA DNA-binding; Region: HrcA_DNA-bdg; pfam03444 1231072006317 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 1231072006318 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 1231072006319 FeS/SAM binding site; other site 1231072006320 HemN C-terminal domain; Region: HemN_C; pfam06969 1231072006321 GTP-binding protein LepA; Provisional; Region: PRK05433 1231072006322 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 1231072006323 G1 box; other site 1231072006324 putative GEF interaction site [polypeptide binding]; other site 1231072006325 GTP/Mg2+ binding site [chemical binding]; other site 1231072006326 Switch I region; other site 1231072006327 G2 box; other site 1231072006328 G3 box; other site 1231072006329 Switch II region; other site 1231072006330 G4 box; other site 1231072006331 G5 box; other site 1231072006332 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 1231072006333 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 1231072006334 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 1231072006335 Stage II sporulation protein P (SpoIIP); Region: SpoIIP; pfam07454 1231072006336 stage II sporulation protein P; Region: spore_II_P; TIGR02867 1231072006337 Stage II sporulation protein P (SpoIIP); Region: SpoIIP; pfam07454 1231072006338 stage II sporulation protein P; Region: spore_II_P; TIGR02867 1231072006339 germination protease; Provisional; Region: PRK12362 1231072006340 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 1231072006341 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 1231072006342 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 1231072006343 Predicted membrane metal-binding protein [General function prediction only]; Region: ComEC; COG0658 1231072006344 Competence protein; Region: Competence; pfam03772 1231072006345 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 1231072006346 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; smart00831 1231072006347 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 1231072006348 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 1231072006349 Protein of unknown function (DUF503); Region: DUF503; pfam04456 1231072006350 PAP2_like proteins, Aur1_like subfamily. Yeast Aur1p or Ipc1p is necessary for the addition of inositol phosphate to ceramide, an essential step in yeast sphingolipid synthesis, and is the target of several antifungal compounds such as aureobasidin; Region: PAP2_Aur1_like; cd03386 1231072006351 active site 1231072006352 lipoyltransferase and lipoate-protein ligase; Region: lipoyltrans; TIGR00545 1231072006353 Lipoate-protein ligase A [Coenzyme metabolism]; Region: LplA; COG0095 1231072006354 Bacterial lipoate protein ligase C-terminus; Region: Lip_prot_lig_C; pfam10437 1231072006355 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 1231072006356 E3 interaction surface; other site 1231072006357 lipoyl attachment site [posttranslational modification]; other site 1231072006358 dihydrolipoamide dehydrogenase; Region: lipoamide_DH; TIGR01350 1231072006359 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1231072006360 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1231072006361 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1231072006362 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 1231072006363 MarR family; Region: MarR_2; pfam12802 1231072006364 MarR family; Region: MarR_2; cl17246 1231072006365 SLBB domain; Region: SLBB; pfam10531 1231072006366 comEA protein; Region: comE; TIGR01259 1231072006367 Helix-hairpin-helix motif; Region: HHH; pfam00633 1231072006368 H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination; Region: H3TH_StructSpec-5'-nucleases; cl14815 1231072006369 DNA binding site [nucleotide binding] 1231072006370 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 1231072006371 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 1231072006372 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; cl06814 1231072006373 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1231072006374 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1231072006375 active site 1231072006376 Transcriptional regulator [Transcription]; Region: LytR; COG1316 1231072006377 LytR cell envelope-related transcriptional attenuator; Region: LytR_C; pfam13399 1231072006378 Predicted HD superfamily hydrolase involved in NAD metabolism [Coenzyme metabolism]; Region: COG1713 1231072006379 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1231072006380 Zn2+ binding site [ion binding]; other site 1231072006381 Mg2+ binding site [ion binding]; other site 1231072006382 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 1231072006383 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 1231072006384 active site 1231072006385 (T/H)XGH motif; other site 1231072006386 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]; Region: COG1534 1231072006387 GTPase CgtA; Reviewed; Region: obgE; PRK12297 1231072006388 GTP1/OBG; Region: GTP1_OBG; pfam01018 1231072006389 Obg GTPase; Region: Obg; cd01898 1231072006390 G1 box; other site 1231072006391 GTP/Mg2+ binding site [chemical binding]; other site 1231072006392 Switch I region; other site 1231072006393 G2 box; other site 1231072006394 G3 box; other site 1231072006395 Switch II region; other site 1231072006396 G4 box; other site 1231072006397 G5 box; other site 1231072006398 Domain of unknown function (DUF1967); Region: DUF1967; pfam09269 1231072006399 Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]; Region: CitA; COG3290 1231072006400 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 1231072006401 hypothetical protein; Provisional; Region: PRK14553 1231072006402 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 1231072006403 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 1231072006404 homodimer interface [polypeptide binding]; other site 1231072006405 oligonucleotide binding site [chemical binding]; other site 1231072006406 Ribonuclease E/G family; Region: RNase_E_G; pfam10150 1231072006407 radical SAM-linked protein; Region: sam_1_link_chp; TIGR03936 1231072006408 Uncharacterized protein conserved in bacteria (DUF2344); Region: DUF2344; pfam10105 1231072006409 radical SAM family uncharacterized protein; Region: rSAM_fuse_unch; TIGR03960 1231072006410 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 1231072006411 FeS/SAM binding site; other site 1231072006412 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. SpoIVFB (sporulation protein, stage IV cell wall formation, F...; Region: S2P-M50_SpoIVFB; cd06161 1231072006413 Peptidase family M50; Region: Peptidase_M50; pfam02163 1231072006414 active site 1231072006415 putative substrate binding region [chemical binding]; other site 1231072006416 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1231072006417 Peptidase family M23; Region: Peptidase_M23; pfam01551 1231072006418 Integrase core domain; Region: rve; pfam00665 1231072006419 Integrase core domain; Region: rve_2; pfam13333 1231072006420 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 1231072006421 Septum formation topological specificity factor MinE; Region: MinE; cl00538 1231072006422 septum site-determining protein MinD; Region: minD_bact; TIGR01968 1231072006423 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 1231072006424 Switch I; other site 1231072006425 Switch II; other site 1231072006426 septum formation inhibitor; Reviewed; Region: minC; PRK00513 1231072006427 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 1231072006428 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1231072006429 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1231072006430 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 1231072006431 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 1231072006432 rod shape-determining protein MreD; Region: shape_MreD; TIGR03426 1231072006433 rod shape-determining protein MreC; Provisional; Region: PRK13922 1231072006434 rod shape-determining protein MreC; Region: MreC; pfam04085 1231072006435 rod shape-determining protein MreB; Provisional; Region: PRK13927 1231072006436 MreB and similar proteins; Region: MreB_like; cd10225 1231072006437 nucleotide binding site [chemical binding]; other site 1231072006438 Mg binding site [ion binding]; other site 1231072006439 putative protofilament interaction site [polypeptide binding]; other site 1231072006440 RodZ interaction site [polypeptide binding]; other site 1231072006441 hypothetical protein; Reviewed; Region: PRK00024 1231072006442 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 1231072006443 helix-hairpin-helix signature motif; other site 1231072006444 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 1231072006445 MPN+ (JAMM) motif; other site 1231072006446 Zinc-binding site [ion binding]; other site 1231072006447 Maf-like protein; Reviewed; Region: PRK00078 1231072006448 Nucleotide binding protein Maf. Maf has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea, but homologs in B.subtilis and S.cerevisiae are nonessential for cell division. Maf has been predicted to be a nucleotide- or...; Region: Maf; cd00555 1231072006449 active site 1231072006450 dimer interface [polypeptide binding]; other site 1231072006451 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 1231072006452 NlpC/P60 family; Region: NLPC_P60; pfam00877 1231072006453 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 1231072006454 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 1231072006455 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1231072006456 Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA dehydrogenases; Region: SCAD_SBCAD; cd01158 1231072006457 FAD binding site [chemical binding]; other site 1231072006458 homotetramer interface [polypeptide binding]; other site 1231072006459 substrate binding pocket [chemical binding]; other site 1231072006460 catalytic base [active] 1231072006461 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 1231072006462 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_alpha; cd01715 1231072006463 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 1231072006464 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_beta; cd01714 1231072006465 Ligand binding site [chemical binding]; other site 1231072006466 Electron transfer flavoprotein domain; Region: ETF; pfam01012 1231072006467 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1231072006468 Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA dehydrogenases; Region: SCAD_SBCAD; cd01158 1231072006469 FAD binding site [chemical binding]; other site 1231072006470 homotetramer interface [polypeptide binding]; other site 1231072006471 substrate binding pocket [chemical binding]; other site 1231072006472 catalytic base [active] 1231072006473 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 1231072006474 active site 2 [active] 1231072006475 active site 1 [active] 1231072006476 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 1231072006477 active site 2 [active] 1231072006478 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 1231072006479 CoA-transferase family III; Region: CoA_transf_3; pfam02515 1231072006480 Branched-chain amino acid transport protein; Region: Branch_AA_trans; cl00547 1231072006481 Peptidase family S41; Region: Peptidase_S41; pfam03572 1231072006482 Active site serine [active] 1231072006483 DEAD/DEAH box helicase; Region: DEAD; pfam00270 1231072006484 putative Mg++ binding site [ion binding]; other site 1231072006485 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 1231072006486 nucleotide binding region [chemical binding]; other site 1231072006487 ATP-binding site [chemical binding]; other site 1231072006488 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 1231072006489 HRDC domain; Region: HRDC; pfam00570 1231072006490 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 1231072006491 ATP binding site [chemical binding]; other site 1231072006492 BioY family; Region: BioY; pfam02632 1231072006493 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072006494 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072006495 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072006496 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 1231072006497 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 1231072006498 active site 1231072006499 metal binding site [ion binding]; metal-binding site 1231072006500 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 1231072006501 Predicted periplasmic protein [Function unknown]; Region: COG3698 1231072006502 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072006503 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072006504 Putative cell wall binding repeat 2; Region: CW_binding_2; pfam04122 1231072006505 spore germination protein (amino acid permease); Region: 2A0309; TIGR00912 1231072006506 germination protein, Ger(x)C family; Region: spore_ger_x_C; TIGR02887 1231072006507 Spore germination B3/ GerAC like, C-terminal; Region: Spore_GerAC; pfam05504 1231072006508 Bacillus/Clostridium GerA spore germination protein; Region: GerA; pfam03323 1231072006509 bacteriocin-associated integral membrane (putative immunity) protein; Region: bact_immun_7tm; TIGR01654 1231072006510 Protein of unknown function (DUF1430); Region: DUF1430; pfam07242 1231072006511 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1231072006512 putative bacteriocin export ABC transporter, lactococcin 972 group; Region: L_ocin_972_ABC; TIGR03608 1231072006513 Walker A/P-loop; other site 1231072006514 ATP binding site [chemical binding]; other site 1231072006515 Q-loop/lid; other site 1231072006516 ABC transporter signature motif; other site 1231072006517 Walker B; other site 1231072006518 D-loop; other site 1231072006519 H-loop/switch region; other site 1231072006520 bacteriocin-associated integral membrane (putative immunity) protein; Region: bact_immun_7tm; TIGR01654 1231072006521 Protein of unknown function (DUF1430); Region: DUF1430; pfam07242 1231072006522 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1231072006523 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 1231072006524 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1231072006525 catalytic residue [active] 1231072006526 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 1231072006527 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 1231072006528 CoA-binding site [chemical binding]; other site 1231072006529 ATP-binding [chemical binding]; other site 1231072006530 DNA polymerase I; Provisional; Region: PRK05755 1231072006531 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 1231072006532 active site 1231072006533 metal binding site 1 [ion binding]; metal-binding site 1231072006534 putative 5' ssDNA interaction site; other site 1231072006535 metal binding site 3; metal-binding site 1231072006536 metal binding site 2 [ion binding]; metal-binding site 1231072006537 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 1231072006538 putative DNA binding site [nucleotide binding]; other site 1231072006539 putative metal binding site [ion binding]; other site 1231072006540 inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases; Region: DNA_polA_I_Bacillus_like_exo; cd06140 1231072006541 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 1231072006542 active site 1231072006543 DNA binding site [nucleotide binding] 1231072006544 catalytic site [active] 1231072006545 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 1231072006546 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 1231072006547 Tetramer interface [polypeptide binding]; other site 1231072006548 active site 1231072006549 FMN-binding site [chemical binding]; other site 1231072006550 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 1231072006551 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1231072006552 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 1231072006553 DNA binding residues [nucleotide binding] 1231072006554 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; cl17393 1231072006555 Protein of unknown function (DUF3782); Region: DUF3782; pfam12644 1231072006556 Replicative DNA helicase [DNA replication, recombination, and repair]; Region: DnaB; COG0305 1231072006557 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 1231072006558 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 1231072006559 Walker A motif; other site 1231072006560 ATP binding site [chemical binding]; other site 1231072006561 Walker B motif; other site 1231072006562 Conserved phage C-terminus (Phg_2220_C); Region: Phg_2220_C; cl09752 1231072006563 Helix-turn-helix domain; Region: HTH_17; pfam12728 1231072006564 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 1231072006565 non-specific DNA binding site [nucleotide binding]; other site 1231072006566 salt bridge; other site 1231072006567 sequence-specific DNA binding site [nucleotide binding]; other site 1231072006568 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 1231072006569 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 1231072006570 non-specific DNA binding site [nucleotide binding]; other site 1231072006571 salt bridge; other site 1231072006572 sequence-specific DNA binding site [nucleotide binding]; other site 1231072006573 integron integrase; Region: integrase_gron; TIGR02249 1231072006574 phiLC3 phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial (mainly gram positive) and phage integrases, including those similar to Lactococcus...; Region: INT_phiLC3_C; cd01189 1231072006575 Int/Topo IB signature motif; other site 1231072006576 Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus; Region: RNase_HI_bacteria_HBD; cd09277 1231072006577 RNA/DNA hybrid binding site [nucleotide binding]; other site 1231072006578 active site 1231072006579 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1231072006580 Walker A/P-loop; other site 1231072006581 ATP binding site [chemical binding]; other site 1231072006582 Q-loop/lid; other site 1231072006583 ABC transporter signature motif; other site 1231072006584 Walker B; other site 1231072006585 D-loop; other site 1231072006586 H-loop/switch region; other site 1231072006587 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1231072006588 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 1231072006589 dimerization interface [polypeptide binding]; other site 1231072006590 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 1231072006591 dimer interface [polypeptide binding]; other site 1231072006592 phosphorylation site [posttranslational modification] 1231072006593 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 1231072006594 ATP binding site [chemical binding]; other site 1231072006595 Mg2+ binding site [ion binding]; other site 1231072006596 G-X-G motif; other site 1231072006597 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1231072006598 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 1231072006599 active site 1231072006600 phosphorylation site [posttranslational modification] 1231072006601 intermolecular recognition site; other site 1231072006602 dimerization interface [polypeptide binding]; other site 1231072006603 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 1231072006604 DNA binding site [nucleotide binding] 1231072006605 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 1231072006606 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 1231072006607 Protein of unknown function DUF86; Region: DUF86; pfam01934 1231072006608 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 1231072006609 active site 1231072006610 NTP binding site [chemical binding]; other site 1231072006611 metal binding triad [ion binding]; metal-binding site 1231072006612 antibiotic binding site [chemical binding]; other site 1231072006613 YoaP-like; Region: YoaP; pfam14268 1231072006614 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 1231072006615 YmaF family; Region: YmaF; pfam12788 1231072006616 Metal-dependent hydrolases of the beta-lactamase superfamily II [General function prediction only]; Region: COG1237 1231072006617 Ethanolamine utilisation protein EutQ; Region: EutQ; pfam06249 1231072006618 ethanolamine utilization protein EutQ; Provisional; Region: PRK15457 1231072006619 Ethanolamine utilisation protein, EutH; Region: EutH; pfam04346 1231072006620 PduT-like ethanolamine utilization protein; Region: eut_PduT; TIGR02526 1231072006621 1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat 1; Region: BMC_PduT_repeat1; cd07053 1231072006622 putative hexamer interface [polypeptide binding]; other site 1231072006623 putative hexagonal pore; other site 1231072006624 1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat 2; Region: BMC_PduT_repeat2; cd07054 1231072006625 putative hexamer interface [polypeptide binding]; other site 1231072006626 putative hexagonal pore; other site 1231072006627 Ethanolamine utilisation protein and carboxysome structural protein domain family; Region: EutN_CcmL; cd01614 1231072006628 Hexamer/Pentamer interface [polypeptide binding]; other site 1231072006629 central pore; other site 1231072006630 ethanolamine utilization protein; Region: eut_hyp; TIGR02536 1231072006631 ethanolamine utilization protein EutJ; Provisional; Region: PRK15080 1231072006632 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 1231072006633 nucleotide binding site [chemical binding]; other site 1231072006634 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 1231072006635 propanediol utilization phosphotransacylase; Provisional; Region: PRK15070 1231072006636 Propanediol utilisation protein PduL; Region: PduL; pfam06130 1231072006637 Propanediol utilisation protein PduL; Region: PduL; pfam06130 1231072006638 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; cl00920 1231072006639 Carbon dioxide concentrating mechanism/carboxysome shell protein [Secondary metabolites biosynthesis, transport, and catabolism / Energy production and conversion]; Region: CcmK; COG4577 1231072006640 1,2-propanediol utilization protein A (PduA), Bacterial Micro-Compartment (BMC) domain; Region: BMC_PduA; cd07059 1231072006641 Hexamer interface [polypeptide binding]; other site 1231072006642 Putative hexagonal pore residue; other site 1231072006643 Coenzyme A acylating aldehyde dehydrogenase (ACDH), ALDH family 20-like; Region: ALDH_F20_ACDH; cd07122 1231072006644 putative catalytic cysteine [active] 1231072006645 Carbon dioxide concentrating mechanism/carboxysome shell protein [Secondary metabolites biosynthesis, transport, and catabolism / Energy production and conversion]; Region: CcmK; COG4577 1231072006646 Carbon dioxide concentrating mechanism K (CcmK)-like proteins, Bacterial Micro-Compartment (BMC) domain; Region: BMC_CcmK_like; cd07045 1231072006647 Hexamer interface [polypeptide binding]; other site 1231072006648 Hexagonal pore residue; other site 1231072006649 ethanolamine utilization protein EutL; Provisional; Region: PRK15405 1231072006650 ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain repeat 1; Region: BMC_EutL_repeat1; cd07049 1231072006651 putative hexamer interface [polypeptide binding]; other site 1231072006652 putative hexagonal pore; other site 1231072006653 Bacterial Micro-Compartment (BMC) domain; Region: BMC; cl01982 1231072006654 Hexamer interface [polypeptide binding]; other site 1231072006655 Hexagonal pore residue; other site 1231072006656 ethanolamine ammonia-lyase small subunit; Provisional; Region: PRK05465 1231072006657 ethanolamine ammonia lyase large subunit; Provisional; Region: PRK15067 1231072006658 Ethanolamine ammonia lyase large subunit (EutB); Region: EutB; pfam06751 1231072006659 Ethanolamine utilisation protein EutA; Region: EutA; pfam06277 1231072006660 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 1231072006661 Signal transduction histidine kinase; Region: H_kinase_N; pfam12282 1231072006662 PAS domain S-box; Region: sensory_box; TIGR00229 1231072006663 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 1231072006664 Histidine kinase; Region: HisKA_2; pfam07568 1231072006665 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 1231072006666 ATP binding site [chemical binding]; other site 1231072006667 Mg2+ binding site [ion binding]; other site 1231072006668 G-X-G motif; other site 1231072006669 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 1231072006670 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 1231072006671 active site 1231072006672 phosphorylation site [posttranslational modification] 1231072006673 intermolecular recognition site; other site 1231072006674 dimerization interface [polypeptide binding]; other site 1231072006675 ANTAR domain; Region: ANTAR; pfam03861 1231072006676 Ethanolamine utilisation - propanediol utilisation; Region: PduV-EutP; pfam10662 1231072006677 G1 box; other site 1231072006678 GTP/Mg2+ binding site [chemical binding]; other site 1231072006679 G3 box; other site 1231072006680 Switch II region; other site 1231072006681 G4 box; other site 1231072006682 G5 box; other site 1231072006683 1,2-propanediol utilization protein U (PduU)/ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain; Region: BMC_PduU-EutS; cd07046 1231072006684 putative hexamer interface [polypeptide binding]; other site 1231072006685 putative hexagonal pore; other site 1231072006686 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 1231072006687 1,3-propanediol dehydrogenase (PPD) catalyzes the reduction of 3-hydroxypropionaldehyde (3-HPA) to 1,3-propanediol in glycerol metabolism; Region: PDD; cd08180 1231072006688 putative active site [active] 1231072006689 metal binding site [ion binding]; metal-binding site 1231072006690 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1231072006691 helicase 45; Provisional; Region: PTZ00424 1231072006692 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 1231072006693 ATP binding site [chemical binding]; other site 1231072006694 Mg++ binding site [ion binding]; other site 1231072006695 motif III; other site 1231072006696 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 1231072006697 nucleotide binding region [chemical binding]; other site 1231072006698 ATP-binding site [chemical binding]; other site 1231072006699 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 1231072006700 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 1231072006701 active site 1231072006702 metal binding site [ion binding]; metal-binding site 1231072006703 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 1231072006704 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 1231072006705 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 1231072006706 S-adenosylmethionine binding site [chemical binding]; other site 1231072006707 Domain of unknown function (DUF2935); Region: DUF2935; pfam11155 1231072006708 Domain of unknown function (DUF2935); Region: DUF2935; pfam11155 1231072006709 ribonuclease Z; Region: RNase_Z; TIGR02651 1231072006710 Branched-chain amino acid transport protein; Region: Branch_AA_trans; cl00547 1231072006711 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 1231072006712 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 1231072006713 dimer interface [polypeptide binding]; other site 1231072006714 anticodon binding site; other site 1231072006715 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 1231072006716 homodimer interface [polypeptide binding]; other site 1231072006717 motif 1; other site 1231072006718 active site 1231072006719 motif 2; other site 1231072006720 GAD domain; Region: GAD; pfam02938 1231072006721 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 1231072006722 motif 3; other site 1231072006723 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 1231072006724 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 1231072006725 FeS/SAM binding site; other site 1231072006726 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 1231072006727 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 1231072006728 dimerization interface [polypeptide binding]; other site 1231072006729 putative tRNAtyr binding site [nucleotide binding]; other site 1231072006730 putative active site [active] 1231072006731 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1231072006732 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1231072006733 Zn2+ binding site [ion binding]; other site 1231072006734 Mg2+ binding site [ion binding]; other site 1231072006735 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 1231072006736 synthetase active site [active] 1231072006737 NTP binding site [chemical binding]; other site 1231072006738 metal binding site [ion binding]; metal-binding site 1231072006739 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 1231072006740 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 1231072006741 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1231072006742 active site 1231072006743 DHH family; Region: DHH; pfam01368 1231072006744 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 1231072006745 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 1231072006746 Protein export membrane protein; Region: SecD_SecF; pfam02355 1231072006747 protein-export membrane protein SecD; Region: secD; TIGR01129 1231072006748 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 1231072006749 SCIFF radical SAM maturase; Region: rSAM_six_Cys; TIGR03974 1231072006750 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 1231072006751 FeS/SAM binding site; other site 1231072006752 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 1231072006753 Protein of unknown function (DUF4001); Region: DUF4001; pfam13165 1231072006754 putative membrane protein, TIGR04086 family; Region: TIGR04086_membr 1231072006755 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 1231072006756 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 1231072006757 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 1231072006758 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 1231072006759 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 1231072006760 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 1231072006761 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 1231072006762 Walker A motif; other site 1231072006763 ATP binding site [chemical binding]; other site 1231072006764 Walker B motif; other site 1231072006765 arginine finger; other site 1231072006766 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 1231072006767 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 1231072006768 RuvA N terminal domain; Region: RuvA_N; pfam01330 1231072006769 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 1231072006770 Bacterial Ig-like domain (group 2); Region: Big_2; cl02708 1231072006771 Phage portal protein, SPP1 Gp6-like; Region: Phage_prot_Gp6; pfam05133 1231072006772 large terminase protein; Provisional; Region: 17; PHA02533 1231072006773 Helix-turn-helix domain; Region: HTH_36; pfam13730 1231072006774 Helix-turn-helix XRE-family like proteins; Region: HTH_XRE; smart00530 1231072006775 non-specific DNA binding site [nucleotide binding]; other site 1231072006776 salt bridge; other site 1231072006777 sequence-specific DNA binding site [nucleotide binding]; other site 1231072006778 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 1231072006779 non-specific DNA binding site [nucleotide binding]; other site 1231072006780 salt bridge; other site 1231072006781 sequence-specific DNA binding site [nucleotide binding]; other site 1231072006782 Cro/C1-type HTH DNA-binding domain; Region: HTH_26; pfam13443 1231072006783 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 1231072006784 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 1231072006785 active site 1231072006786 Int/Topo IB signature motif; other site 1231072006787 DNA binding site [nucleotide binding] 1231072006788 hypothetical protein; Validated; Region: PRK00110 1231072006789 Uncharacterized conserved protein [Function unknown]; Region: COG1739 1231072006790 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 1231072006791 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 1231072006792 HEAT-like repeat; Region: HEAT_EZ; pfam13513 1231072006793 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 1231072006794 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1231072006795 DNA-binding site [nucleotide binding]; DNA binding site 1231072006796 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 1231072006797 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1231072006798 homodimer interface [polypeptide binding]; other site 1231072006799 catalytic residue [active] 1231072006800 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 1231072006801 active site 1231072006802 NTP binding site [chemical binding]; other site 1231072006803 metal binding triad [ion binding]; metal-binding site 1231072006804 antibiotic binding site [chemical binding]; other site 1231072006805 chaperone protein DnaJ; Provisional; Region: PRK14293 1231072006806 pyruvate carboxylase; Reviewed; Region: PRK12999 1231072006807 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1231072006808 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 1231072006809 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 1231072006810 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 1231072006811 active site 1231072006812 catalytic residues [active] 1231072006813 metal binding site [ion binding]; metal-binding site 1231072006814 homodimer binding site [polypeptide binding]; other site 1231072006815 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 1231072006816 carboxyltransferase (CT) interaction site; other site 1231072006817 biotinylation site [posttranslational modification]; other site 1231072006818 Rubredoxin [Energy production and conversion]; Region: COG1773 1231072006819 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 1231072006820 iron binding site [ion binding]; other site 1231072006821 N-ethylammeline chlorohydrolase; Provisional; Region: PRK06038 1231072006822 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 1231072006823 active site 1231072006824 putative substrate binding pocket [chemical binding]; other site 1231072006825 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 1231072006826 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 1231072006827 HflX GTPase family; Region: HflX; cd01878 1231072006828 G1 box; other site 1231072006829 GTP/Mg2+ binding site [chemical binding]; other site 1231072006830 Switch I region; other site 1231072006831 G2 box; other site 1231072006832 G3 box; other site 1231072006833 Switch II region; other site 1231072006834 G4 box; other site 1231072006835 G5 box; other site 1231072006836 Uncharacterized proteins involved in stress response, homologs of TerZ and putative cAMP-binding protein CABP1 [Signal transduction mechanisms]; Region: TerZ; COG2310 1231072006837 Uncharacterized proteins involved in stress response, similar to tellurium resistance terD; Region: TerD_like; cd06974 1231072006838 putative metal binding site [ion binding]; other site 1231072006839 Mitochondrial biogenesis AIM24; Region: AIM24; pfam01987 1231072006840 Domain of unknown function (DUF4356); Region: DUF4356; pfam14266 1231072006841 Toxic anion resistance protein (TelA); Region: TelA; pfam05816 1231072006842 Toxic anion resistance protein (TelA); Region: TelA; pfam05816 1231072006843 Uncharacterized proteins involved in stress response, homologs of TerZ and putative cAMP-binding protein CABP1 [Signal transduction mechanisms]; Region: TerZ; COG2310 1231072006844 Uncharacterized proteins involved in stress response, similar to tellurium resistance terD; Region: TerD_like; cd06974 1231072006845 putative metal binding site [ion binding]; other site 1231072006846 Uncharacterized proteins involved in stress response, homologs of TerZ and putative cAMP-binding protein CABP1 [Signal transduction mechanisms]; Region: TerZ; COG2310 1231072006847 Uncharacterized proteins involved in stress response, similar to tellurium resistance terD; Region: TerD_like; cd06974 1231072006848 putative metal binding site [ion binding]; other site 1231072006849 Uncharacterized proteins involved in stress response, homologs of TerZ and putative cAMP-binding protein CABP1 [Signal transduction mechanisms]; Region: TerZ; COG2310 1231072006850 Uncharacterized proteins involved in stress response, similar to tellurium resistance terD; Region: TerD_like; cd06974 1231072006851 putative metal binding site [ion binding]; other site 1231072006852 HAD-superfamily hydrolase, subfamily IIB; Region: HAD-SF-IIB; TIGR01484 1231072006853 Protein of unknown function (DUF2983); Region: DUF2983; pfam11202 1231072006854 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1231072006855 active site 1231072006856 Protein of unknown function (DUF3706); Region: DUF3706; pfam12500 1231072006857 HpcH/HpaI aldolase/citrate lyase family; Region: HpcH_HpaI; cl17231 1231072006858 K+-dependent Na+/Ca+ exchanger related-protein; Region: TIGR00367 1231072006859 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 1231072006860 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 1231072006861 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1231072006862 active site 1231072006863 Sporulation protein YunB (Spo_YunB); Region: Spore_YunB; cl09783 1231072006864 Transglycosylase; Region: Transgly; pfam00912 1231072006865 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 1231072006866 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 1231072006867 stage V sporulation protein AE; Region: spore_V_AE; TIGR02839 1231072006868 stage V sporulation protein AD; Validated; Region: PRK08304 1231072006869 stage V sporulation protein AD; Provisional; Region: PRK12404 1231072006870 stage V sporulation protein AC; Region: spore_V_AC; TIGR02838 1231072006871 sporulation sigma factor SigF; Validated; Region: PRK05572 1231072006872 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1231072006873 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 1231072006874 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 1231072006875 DNA binding residues [nucleotide binding] 1231072006876 Anti-sigma regulatory factor (Ser/Thr protein kinase) [Signal transduction mechanisms]; Region: RsbW; COG2172 1231072006877 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 1231072006878 ATP binding site [chemical binding]; other site 1231072006879 Mg2+ binding site [ion binding]; other site 1231072006880 G-X-G motif; other site 1231072006881 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 1231072006882 anti sigma factor interaction site; other site 1231072006883 regulatory phosphorylation site [posttranslational modification]; other site 1231072006884 spermidine synthase; Provisional; Region: PRK00811 1231072006885 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 1231072006886 TaqI-like C-terminal specificity domain; Region: TaqI_C; pfam12950 1231072006887 Catalytic NodB homology domain of Bacillus subtilis polysaccharide deacetylase PdaA, and its bacterial homologs; Region: CE4_BsPdaA_like; cd10948 1231072006888 delta-lactam-biosynthetic de-N-acetylase; Region: spore_pdaA; TIGR02884 1231072006889 NodB motif; other site 1231072006890 active site 1231072006891 catalytic site [active] 1231072006892 Cd binding site [ion binding]; other site 1231072006893 The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common...; Region: Glyco_transf_WecG_TagA; cd06533 1231072006894 exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase; Region: EPS_sugtrans; TIGR03025 1231072006895 Bacterial sugar transferase; Region: Bac_transf; pfam02397 1231072006896 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 1231072006897 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 1231072006898 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 1231072006899 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 1231072006900 Glycosyltransferase Family 4; Region: Glyco_transf_4; pfam13439 1231072006901 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 1231072006902 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1231072006903 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 1231072006904 O-Antigen ligase; Region: Wzy_C; cl04850 1231072006905 ExoA is involved in the biosynthesis of succinoglycan; Region: Succinoglycan_BP_ExoA; cd02525 1231072006906 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 1231072006907 Ligand binding site; other site 1231072006908 O-Antigen ligase; Region: Wzy_C; cl04850 1231072006909 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 1231072006910 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 1231072006911 integral membrane protein MviN; Region: mviN; TIGR01695 1231072006912 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 1231072006913 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1231072006914 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 1231072006915 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 1231072006916 putative trimer interface [polypeptide binding]; other site 1231072006917 putative CoA binding site [chemical binding]; other site 1231072006918 WcxM-like, Left-handed parallel beta-Helix (LbH) N-terminal domain: This group is composed of Xanthomonas campestris WcxM and proteins with similarity to the WcxM N-terminal domain. WcxM is thought to be bifunctional, catalyzing both the isomerization...; Region: LbH_WxcM_N_like; cd03358 1231072006919 putative trimer interface [polypeptide binding]; other site 1231072006920 putative active site [active] 1231072006921 putative substrate binding site [chemical binding]; other site 1231072006922 putative CoA binding site [chemical binding]; other site 1231072006923 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 1231072006924 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 1231072006925 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 1231072006926 UDP-N-acetyl-D-mannosaminuronate dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: WecC; COG0677 1231072006927 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 1231072006928 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 1231072006929 This family is most closely related to the GT1 family of glycosyltransferases. wlbH in Bordetella parapertussis has been shown to be required for the biosynthesis of a trisaccharide that, when attached to the B. pertussis lipopolysaccharide (LPS) core; Region: GT1_wlbH_like; cd03798 1231072006930 N-acetyl-alpha-D-glucosaminyl L-malate synthase BshA; Region: thiol_BshA; TIGR03999 1231072006931 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 1231072006932 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 1231072006933 NAD(P) binding site [chemical binding]; other site 1231072006934 homodimer interface [polypeptide binding]; other site 1231072006935 substrate binding site [chemical binding]; other site 1231072006936 active site 1231072006937 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 1231072006938 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 1231072006939 active site 1231072006940 tetramer interface; other site 1231072006941 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 1231072006942 binding surface 1231072006943 Tetratricopeptide repeat; Region: TPR_12; pfam13424 1231072006944 TPR motif; other site 1231072006945 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 1231072006946 Ornithine decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to ornithine decarboxylase (ODC), arginine decarboxylase (ADC) and lysine...; Region: Orn_deC_like; cd00615 1231072006947 homodimer interface [polypeptide binding]; other site 1231072006948 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1231072006949 catalytic residue [active] 1231072006950 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 1231072006951 Protein of unknown function (DUF523); Region: DUF523; pfam04463 1231072006952 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 1231072006953 MutS domain III; Region: MutS_III; pfam05192 1231072006954 ATP-binding cassette domain of MutS2; Region: ABC_MutS2; cd03280 1231072006955 Walker A/P-loop; other site 1231072006956 ATP binding site [chemical binding]; other site 1231072006957 Q-loop/lid; other site 1231072006958 ABC transporter signature motif; other site 1231072006959 Walker B; other site 1231072006960 D-loop; other site 1231072006961 H-loop/switch region; other site 1231072006962 Smr domain; Region: Smr; pfam01713 1231072006963 Peptidase family U32; Region: Peptidase_U32; cl03113 1231072006964 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 1231072006965 Peptidase family U32; Region: Peptidase_U32; pfam01136 1231072006966 Collagenase; Region: DUF3656; pfam12392 1231072006967 Cell division protein ZapA; Region: ZapA; pfam05164 1231072006968 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 1231072006969 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 1231072006970 putative tRNA-binding site [nucleotide binding]; other site 1231072006971 B3/4 domain; Region: B3_4; pfam03483 1231072006972 tRNA synthetase B5 domain; Region: B5; smart00874 1231072006973 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 1231072006974 dimer interface [polypeptide binding]; other site 1231072006975 motif 1; other site 1231072006976 motif 3; other site 1231072006977 motif 2; other site 1231072006978 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; smart00896 1231072006979 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 1231072006980 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 1231072006981 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 1231072006982 dimer interface [polypeptide binding]; other site 1231072006983 motif 1; other site 1231072006984 active site 1231072006985 motif 2; other site 1231072006986 motif 3; other site 1231072006987 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 1231072006988 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 1231072006989 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 1231072006990 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 1231072006991 TrkA-N domain; Region: TrkA_N; pfam02254 1231072006992 TrkA-C domain; Region: TrkA_C; pfam02080 1231072006993 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 1231072006994 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 1231072006995 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 1231072006996 23S rRNA binding site [nucleotide binding]; other site 1231072006997 L21 binding site [polypeptide binding]; other site 1231072006998 L13 binding site [polypeptide binding]; other site 1231072006999 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 1231072007000 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 1231072007001 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 1231072007002 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 1231072007003 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1231072007004 Walker A/P-loop; other site 1231072007005 ATP binding site [chemical binding]; other site 1231072007006 ABC transporter; Region: ABC_tran; pfam00005 1231072007007 Q-loop/lid; other site 1231072007008 ABC transporter signature motif; other site 1231072007009 Walker B; other site 1231072007010 D-loop; other site 1231072007011 H-loop/switch region; other site 1231072007012 FtsX-like permease family; Region: FtsX; pfam02687 1231072007013 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 1231072007014 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 1231072007015 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 1231072007016 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 1231072007017 active site 1231072007018 dimer interface [polypeptide binding]; other site 1231072007019 motif 1; other site 1231072007020 motif 2; other site 1231072007021 motif 3; other site 1231072007022 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 1231072007023 anticodon binding site; other site 1231072007024 putative sporulation protein YtxC; Region: spo_ytxC; TIGR02834 1231072007025 Coenzyme F420-reducing hydrogenase, beta subunit [Energy production and conversion]; Region: FrhB; COG1035 1231072007026 Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus; Region: FrhB_FdhB_C; pfam04432 1231072007027 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 1231072007028 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 1231072007029 putative dimer interface [polypeptide binding]; other site 1231072007030 active site pocket [active] 1231072007031 putative cataytic base [active] 1231072007032 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 1231072007033 Heat shock protein 33 (Hsp33): Cytosolic protein that acts as a molecular chaperone under oxidative conditions. In normal (reducing) cytosolic conditions, four conserved Cys residues are coordinated by a Zn ion. Under oxidative stress (such as heat...; Region: Hsp33; cd00498 1231072007034 dimerization interface [polypeptide binding]; other site 1231072007035 domain crossover interface; other site 1231072007036 redox-dependent activation switch; other site 1231072007037 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1231072007038 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 1231072007039 S-adenosylmethionine binding site [chemical binding]; other site 1231072007040 Small, acid-soluble spore proteins, alpha/beta type; Region: SASP; pfam00269 1231072007041 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 1231072007042 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 1231072007043 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 1231072007044 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 1231072007045 dimer interface [polypeptide binding]; other site 1231072007046 active site 1231072007047 catalytic residue [active] 1231072007048 dihydrodipicolinate reductase; Provisional; Region: PRK00048 1231072007049 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 1231072007050 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 1231072007051 single-stranded DNA-binding protein; Provisional; Region: PRK05813 1231072007052 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 1231072007053 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 1231072007054 dimer interface [polypeptide binding]; other site 1231072007055 ssDNA binding site [nucleotide binding]; other site 1231072007056 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1231072007057 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 1231072007058 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 1231072007059 NodB motif; other site 1231072007060 active site 1231072007061 catalytic site [active] 1231072007062 metal binding site [ion binding]; metal-binding site 1231072007063 Domain of unknown function (DUF4364); Region: DUF4364; pfam14277 1231072007064 Uncharacterized conserved protein [Function unknown]; Region: COG3391 1231072007065 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 1231072007066 TSCPD domain; Region: TSCPD; cl14834 1231072007067 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 1231072007068 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1231072007069 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1231072007070 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 1231072007071 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1231072007072 active site 1231072007073 HIGH motif; other site 1231072007074 nucleotide binding site [chemical binding]; other site 1231072007075 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1231072007076 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 1231072007077 active site 1231072007078 KMSKS motif; other site 1231072007079 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 1231072007080 tRNA binding surface [nucleotide binding]; other site 1231072007081 anticodon binding site; other site 1231072007082 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 1231072007083 Formiminotransferase-cyclodeaminase; Region: FTCD_C; pfam04961 1231072007084 formate--tetrahydrofolate ligase; Provisional; Region: PRK13505 1231072007085 Formyltetrahydrofolate synthetase (FTHFS) catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2...; Region: FTHFS; cd00477 1231072007086 Potassium binding sites [ion binding]; other site 1231072007087 Cesium cation binding sites [ion binding]; other site 1231072007088 glutamate formiminotransferase; Region: FtcD; TIGR02024 1231072007089 Formiminotransferase domain, N-terminal subdomain; Region: FTCD_N; pfam07837 1231072007090 Formiminotransferase domain; Region: FTCD; pfam02971 1231072007091 Na+/glutamate symporter [Amino acid transport and metabolism]; Region: GltS; COG0786 1231072007092 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 1231072007093 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 1231072007094 L-cysteine desulfidase [Amino acid transport and metabolism]; Region: COG3681 1231072007095 Predicted permease [General function prediction only]; Region: COG2056 1231072007096 Na+-H+ antiporter family; Region: Na_H_antiport_2; pfam13726 1231072007097 Predicted permease [General function prediction only]; Region: COG2056 1231072007098 Na+-H+ antiporter family; Region: Na_H_antiport_2; pfam13726 1231072007099 Diaminopimelate epimerase [Amino acid transport and metabolism]; Region: DapF; COG0253 1231072007100 Uncharacterized conserved protein [Function unknown]; Region: COG2966 1231072007101 Protein of unknown function (DUF1212); Region: DUF1212; pfam06738 1231072007102 Protein of unknown function (DUF3815); Region: DUF3815; pfam12821 1231072007103 Putative p-aminobenzoyl-glutamate transporter [Coenzyme metabolism]; Region: AbgT; COG2978 1231072007104 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 1231072007105 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 1231072007106 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 1231072007107 metal binding site [ion binding]; metal-binding site 1231072007108 dimer interface [polypeptide binding]; other site 1231072007109 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 1231072007110 active sites [active] 1231072007111 tetramer interface [polypeptide binding]; other site 1231072007112 DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]; Region: DnrI; COG3629 1231072007113 Predicted ATPase [General function prediction only]; Region: COG3899 1231072007114 AAA ATPase domain; Region: AAA_16; pfam13191 1231072007115 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 1231072007116 binding surface 1231072007117 TPR motif; other site 1231072007118 imidazolonepropionase; Validated; Region: PRK09356 1231072007119 Imidazolonepropionase/imidazolone-5-propionate hydrolase (Imidazolone-5PH) catalyzes the third step in the histidine degradation pathway, the hydrolysis of (S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate to N-formimidoyl-L-glutamate. In bacteria; Region: Imidazolone-5PH; cd01296 1231072007120 active site 1231072007121 urocanate hydratase; Provisional; Region: PRK05414 1231072007122 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1231072007123 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 1231072007124 active site 1231072007125 phosphorylation site [posttranslational modification] 1231072007126 intermolecular recognition site; other site 1231072007127 dimerization interface [polypeptide binding]; other site 1231072007128 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 1231072007129 Walker A motif; other site 1231072007130 ATP binding site [chemical binding]; other site 1231072007131 Walker B motif; other site 1231072007132 arginine finger; other site 1231072007133 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1231072007134 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1231072007135 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1231072007136 substrate binding pocket [chemical binding]; other site 1231072007137 membrane-bound complex binding site; other site 1231072007138 hinge residues; other site 1231072007139 sensory histidine kinase AtoS; Provisional; Region: PRK11360 1231072007140 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 1231072007141 dimer interface [polypeptide binding]; other site 1231072007142 phosphorylation site [posttranslational modification] 1231072007143 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 1231072007144 ATP binding site [chemical binding]; other site 1231072007145 Mg2+ binding site [ion binding]; other site 1231072007146 G-X-G motif; other site 1231072007147 Na+/glutamate symporter [Amino acid transport and metabolism]; Region: GltS; COG0786 1231072007148 Na+/glutamate symporter [Amino acid transport and metabolism]; Region: GltS; COG0786 1231072007149 BadF/BadG/BcrA/BcrD ATPase family; Region: BcrAD_BadFG; cl17271 1231072007150 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3580 1231072007151 2-hydroxyglutaryl-CoA dehydratase, D-component; Region: HGD-D; pfam06050 1231072007152 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3581 1231072007153 BadF/BadG/BcrA/BcrD ATPase family; Region: BcrAD_BadFG; cl17271 1231072007154 BadF/BadG/BcrA/BcrD ATPase family; Region: BcrAD_BadFG; cl17271 1231072007155 ATP synthase subunit D; Region: ATP-synt_D; pfam01813 1231072007156 V-type ATP synthase subunit B; Provisional; Region: PRK04196 1231072007157 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1231072007158 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 1231072007159 Walker A motif homologous position; other site 1231072007160 Walker B motif; other site 1231072007161 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1231072007162 V-type ATP synthase subunit A; Provisional; Region: PRK04192 1231072007163 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 1231072007164 Walker A motif/ATP binding site; other site 1231072007165 Walker B motif; other site 1231072007166 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1231072007167 V-type ATP synthase subunit E; Provisional; Region: PRK03963; cl17074 1231072007168 ATP synthase (F/14-kDa) subunit; Region: ATP-synt_F; pfam01990 1231072007169 ATP synthase subunit C; Region: ATP-synt_C; pfam00137 1231072007170 V-type ATP synthase subunit I; Validated; Region: PRK05771 1231072007171 V-type ATP synthase subunit C; Provisional; Region: PRK01198; cl00660 1231072007172 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 1231072007173 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 1231072007174 binding surface 1231072007175 TPR repeat; Region: TPR_11; pfam13414 1231072007176 TPR motif; other site 1231072007177 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 1231072007178 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 1231072007179 RecX family; Region: RecX; cl00936 1231072007180 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 1231072007181 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 1231072007182 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 1231072007183 QueT transporter; Region: QueT; pfam06177 1231072007184 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 1231072007185 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1231072007186 ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism]; Region: ProX; cl17891 1231072007187 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 1231072007188 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 1231072007189 dimer interface [polypeptide binding]; other site 1231072007190 conserved gate region; other site 1231072007191 putative PBP binding loops; other site 1231072007192 ABC-ATPase subunit interface; other site 1231072007193 ABC-type proline/glycine betaine transport system, ATPase component [Amino acid transport and metabolism]; Region: ProV; COG4175 1231072007194 ATP-binding cassette domain of the osmoprotectant proline/glycine betaine uptake system; Region: ABC_Pro_Gly_Betaine; cd03294 1231072007195 Walker A/P-loop; other site 1231072007196 ATP binding site [chemical binding]; other site 1231072007197 Q-loop/lid; other site 1231072007198 ABC transporter signature motif; other site 1231072007199 Walker B; other site 1231072007200 D-loop; other site 1231072007201 H-loop/switch region; other site 1231072007202 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the ABC transporter OpuCA. OpuCA is the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing...; Region: CBS_pair_ABC_OpuCA_assoc2; cd04583 1231072007203 Putative peptidoglycan-binding domain-containing protein [Cell envelope biogenesis, outer membrane]; Region: COG3409 1231072007204 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 1231072007205 Subtilisin-like serine proteases [Posttranslational modification, protein turnover, chaperones]; Region: AprE; COG1404 1231072007206 Peptidase S8 family domain in CspA-like proteins; Region: Peptidases_S8_CspA-like; cd07478 1231072007207 active site 1231072007208 catalytic triad [active] 1231072007209 Peptidase S8 family domain in CspA-like proteins; Region: Peptidases_S8_CspA-like; cd07478 1231072007210 active site 1231072007211 catalytic triad [active] 1231072007212 Transcriptional regulators [Transcription]; Region: PurR; COG1609 1231072007213 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 1231072007214 DNA binding site [nucleotide binding] 1231072007215 domain linker motif; other site 1231072007216 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 1231072007217 dimerization interface [polypeptide binding]; other site 1231072007218 ligand binding site [chemical binding]; other site 1231072007219 D-ribose transporter subunit RbsB; Provisional; Region: PRK10653 1231072007220 Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs; Region: PBP1_ribose_binding; cd06323 1231072007221 ligand binding site [chemical binding]; other site 1231072007222 dimerization interface [polypeptide binding]; other site 1231072007223 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 1231072007224 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 1231072007225 TM-ABC transporter signature motif; other site 1231072007226 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 1231072007227 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1231072007228 Walker A/P-loop; other site 1231072007229 ATP binding site [chemical binding]; other site 1231072007230 Q-loop/lid; other site 1231072007231 ABC transporter signature motif; other site 1231072007232 Walker B; other site 1231072007233 D-loop; other site 1231072007234 H-loop/switch region; other site 1231072007235 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 1231072007236 D-ribose pyranase; Provisional; Region: PRK11797 1231072007237 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 1231072007238 Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of nucleotides...; Region: ribokinase; cd01174 1231072007239 substrate binding site [chemical binding]; other site 1231072007240 dimer interface [polypeptide binding]; other site 1231072007241 ATP binding site [chemical binding]; other site 1231072007242 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 1231072007243 Uncharacterized protein with SCP/PR1 domains [Function unknown]; Region: COG2340 1231072007244 SCP_bacterial: SCP-like extracellular protein domain, as found in bacteria and archaea. The wider family of SCP containing proteins includes plant pathogenesis-related protein 1 (PR-1), CRISPs, mammalian cysteine-rich secretory proteins, and allergen 5...; Region: SCP_bacterial; cd05379 1231072007245 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 1231072007246 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 1231072007247 metal binding site [ion binding]; metal-binding site 1231072007248 homoserine dehydrogenase; Provisional; Region: PRK06349 1231072007249 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 1231072007250 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 1231072007251 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 1231072007252 homoserine kinase; Provisional; Region: PRK01212 1231072007253 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 1231072007254 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 1231072007255 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants; Region: Thr-synth_2; cd01560 1231072007256 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 1231072007257 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1231072007258 catalytic residue [active] 1231072007259 Hemerythrin; Region: Hemerythrin; cd12107 1231072007260 Fe binding site [ion binding]; other site 1231072007261 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cl00083 1231072007262 active site 1231072007263 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 1231072007264 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 1231072007265 intersubunit interface [polypeptide binding]; other site 1231072007266 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 1231072007267 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1231072007268 Walker A/P-loop; other site 1231072007269 ATP binding site [chemical binding]; other site 1231072007270 Q-loop/lid; other site 1231072007271 ABC transporter signature motif; other site 1231072007272 Walker B; other site 1231072007273 D-loop; other site 1231072007274 H-loop/switch region; other site 1231072007275 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 1231072007276 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 1231072007277 ABC-ATPase subunit interface; other site 1231072007278 dimer interface [polypeptide binding]; other site 1231072007279 putative PBP binding regions; other site 1231072007280 ferric uptake regulator; Provisional; Region: fur; PRK09462 1231072007281 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 1231072007282 metal binding site 2 [ion binding]; metal-binding site 1231072007283 putative DNA binding helix; other site 1231072007284 metal binding site 1 [ion binding]; metal-binding site 1231072007285 dimer interface [polypeptide binding]; other site 1231072007286 structural Zn2+ binding site [ion binding]; other site 1231072007287 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 1231072007288 G1 box; other site 1231072007289 GTP/Mg2+ binding site [chemical binding]; other site 1231072007290 Switch I region; other site 1231072007291 G2 box; other site 1231072007292 G3 box; other site 1231072007293 Switch II region; other site 1231072007294 G4 box; other site 1231072007295 G5 box; other site 1231072007296 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 1231072007297 Found in ATP-dependent protease La (LON); Region: LON; smart00464 1231072007298 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 1231072007299 Walker A motif; other site 1231072007300 ATP binding site [chemical binding]; other site 1231072007301 Walker B motif; other site 1231072007302 arginine finger; other site 1231072007303 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 1231072007304 ATP-dependent protease LonB; Region: spore_lonB; TIGR02902 1231072007305 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 1231072007306 Walker A motif; other site 1231072007307 ATP binding site [chemical binding]; other site 1231072007308 Walker B motif; other site 1231072007309 arginine finger; other site 1231072007310 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 1231072007311 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 1231072007312 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 1231072007313 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 1231072007314 Walker A motif; other site 1231072007315 ATP binding site [chemical binding]; other site 1231072007316 Walker B motif; other site 1231072007317 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1231072007318 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 1231072007319 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 1231072007320 oligomer interface [polypeptide binding]; other site 1231072007321 active site residues [active] 1231072007322 trigger factor; Provisional; Region: tig; PRK01490 1231072007323 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1231072007324 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 1231072007325 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1231072007326 active site 1231072007327 dihydroorotate dehydrogenase (subfamily 1) family protein; Region: pyrD_sub1_fam; TIGR01037 1231072007328 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 1231072007329 heterodimer interface [polypeptide binding]; other site 1231072007330 active site 1231072007331 FMN binding site [chemical binding]; other site 1231072007332 homodimer interface [polypeptide binding]; other site 1231072007333 substrate binding site [chemical binding]; other site 1231072007334 dihydroorotate dehydrogenase electron transfer subunit; Reviewed; Region: PRK00054 1231072007335 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 1231072007336 FAD binding pocket [chemical binding]; other site 1231072007337 FAD binding motif [chemical binding]; other site 1231072007338 phosphate binding motif [ion binding]; other site 1231072007339 beta-alpha-beta structure motif; other site 1231072007340 NAD binding pocket [chemical binding]; other site 1231072007341 Iron coordination center [ion binding]; other site 1231072007342 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 1231072007343 active site 1231072007344 dimer interface [polypeptide binding]; other site 1231072007345 dihydroorotase; Validated; Region: pyrC; PRK09357 1231072007346 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 1231072007347 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 1231072007348 active site 1231072007349 aspartate carbamoyltransferase regulatory subunit; Reviewed; Region: PRK00893 1231072007350 Aspartate carbamoyltransferase regulatory chain, allosteric domain; Region: PyrI; pfam01948 1231072007351 Aspartate carbamoyltransferase regulatory chain, metal binding domain; Region: PyrI_C; pfam02748 1231072007352 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 1231072007353 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 1231072007354 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 1231072007355 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1231072007356 active site 1231072007357 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 1231072007358 active site 1231072007359 metal binding site [ion binding]; metal-binding site 1231072007360 homotetramer interface [polypeptide binding]; other site 1231072007361 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 1231072007362 active site 1231072007363 dimerization interface [polypeptide binding]; other site 1231072007364 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 1231072007365 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 1231072007366 GatB domain; Region: GatB_Yqey; smart00845 1231072007367 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 1231072007368 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 1231072007369 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 1231072007370 NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction...; Region: LIGANc; cl03295 1231072007371 nucleotide binding pocket [chemical binding]; other site 1231072007372 K-X-D-G motif; other site 1231072007373 catalytic site [active] 1231072007374 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 1231072007375 Helix-hairpin-helix motif; Region: HHH_2; pfam12826 1231072007376 Helix-hairpin-helix motif; Region: HHH; pfam00633 1231072007377 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 1231072007378 Dimer interface [polypeptide binding]; other site 1231072007379 BRCT sequence motif; other site 1231072007380 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 1231072007381 UvrD-like helicase C-terminal domain; Region: UvrD_C; pfam13361 1231072007382 Family description; Region: UvrD_C_2; pfam13538 1231072007383 Part of AAA domain; Region: AAA_19; pfam13245 1231072007384 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 1231072007385 M20 Peptidase Aminoacylase 1 family; Region: M20_Acy1; cd03886 1231072007386 metal binding site [ion binding]; metal-binding site 1231072007387 dimer interface [polypeptide binding]; other site 1231072007388 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 1231072007389 M20 Peptidases Aminoacyclase-1 indole-3-acetic-L-aspartic acid hydrolase from bacteria and archaea; Region: M20_Acy1_IAAspH_bact; cd05665 1231072007390 putative metal binding site [ion binding]; other site 1231072007391 dimer interface [polypeptide binding]; other site 1231072007392 Trp repressor protein; Region: Trp_repressor; cl17266 1231072007393 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 1231072007394 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 1231072007395 RNA binding surface [nucleotide binding]; other site 1231072007396 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 1231072007397 active site 1231072007398 uracil binding [chemical binding]; other site 1231072007399 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1231072007400 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 1231072007401 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1231072007402 catalytic residue [active] 1231072007403 triple tyrosine motif-containing protein; Provisional; Region: PRK14081 1231072007404 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 1231072007405 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 1231072007406 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 1231072007407 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 1231072007408 hypothetical protein; Validated; Region: PRK00124 1231072007409 glucose-6-phosphate isomerase; Provisional; Region: pgi; PRK14097 1231072007410 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 1231072007411 active site 1231072007412 dimer interface [polypeptide binding]; other site 1231072007413 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 1231072007414 dimer interface [polypeptide binding]; other site 1231072007415 active site 1231072007416 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 1231072007417 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 1231072007418 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 1231072007419 MarR family; Region: MarR_2; cl17246 1231072007420 type I restriction enzyme EcoKI subunit R; Provisional; Region: hsdR; PRK11448 1231072007421 Superfamily II DNA helicase [DNA replication, recombination, and repair]; Region: RecQ; COG0514 1231072007422 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 1231072007423 ATP binding site [chemical binding]; other site 1231072007424 putative Mg++ binding site [ion binding]; other site 1231072007425 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 1231072007426 nucleotide binding region [chemical binding]; other site 1231072007427 ATP-binding site [chemical binding]; other site 1231072007428 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1231072007429 RNA polymerase sigma factor RpoD, C-terminal domain; Region: RpoD_Cterm; TIGR02393 1231072007430 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 1231072007431 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 1231072007432 DNA binding residues [nucleotide binding] 1231072007433 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 1231072007434 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 1231072007435 Type III restriction enzyme, res subunit; Region: ResIII; pfam04851 1231072007436 ATP binding site [chemical binding]; other site 1231072007437 putative Mg++ binding site [ion binding]; other site 1231072007438 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 1231072007439 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 1231072007440 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 1231072007441 HsdM N-terminal domain; Region: HsdM_N; pfam12161 1231072007442 Methyltransferase domain; Region: Methyltransf_26; pfam13659 1231072007443 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 1231072007444 non-specific DNA binding site [nucleotide binding]; other site 1231072007445 salt bridge; other site 1231072007446 sequence-specific DNA binding site [nucleotide binding]; other site 1231072007447 Virulence-associated protein E; Region: VirE; pfam05272 1231072007448 Uncharacterized conserved protein [Function unknown]; Region: COG4983 1231072007449 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 1231072007450 phiLC3 phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial (mainly gram positive) and phage integrases, including those similar to Lactococcus...; Region: INT_phiLC3_C; cd01189 1231072007451 Int/Topo IB signature motif; other site 1231072007452 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 1231072007453 sequence-specific DNA binding site [nucleotide binding]; other site 1231072007454 salt bridge; other site 1231072007455 KilA-N domain; Region: KilA-N; pfam04383 1231072007456 GMP synthase; Reviewed; Region: guaA; PRK00074 1231072007457 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 1231072007458 AMP/PPi binding site [chemical binding]; other site 1231072007459 candidate oxyanion hole; other site 1231072007460 catalytic triad [active] 1231072007461 potential glutamine specificity residues [chemical binding]; other site 1231072007462 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 1231072007463 ATP Binding subdomain [chemical binding]; other site 1231072007464 Ligand Binding sites [chemical binding]; other site 1231072007465 Dimerization subdomain; other site 1231072007466 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 1231072007467 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 1231072007468 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 1231072007469 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 1231072007470 active site 1231072007471 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 1231072007472 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 1231072007473 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 1231072007474 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 1231072007475 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 1231072007476 ring oligomerisation interface [polypeptide binding]; other site 1231072007477 ATP/Mg binding site [chemical binding]; other site 1231072007478 stacking interactions; other site 1231072007479 hinge regions; other site 1231072007480 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 1231072007481 oligomerisation interface [polypeptide binding]; other site 1231072007482 mobile loop; other site 1231072007483 roof hairpin; other site 1231072007484 Protein of unknown function (DUF1461); Region: DUF1461; pfam07314 1231072007485 Uncharacterized conserved protein [Function unknown]; Region: COG0398 1231072007486 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 1231072007487 [FeFe] hydrogenase, group B1/B3; Region: FeFe_hydrog_B1; TIGR04105 1231072007488 4Fe-4S binding domain; Region: Fer4; pfam00037 1231072007489 4Fe-4S binding domain; Region: Fer4; pfam00037 1231072007490 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 1231072007491 8-oxoguanine DNA glycosylase, N-terminal domain; Region: OGG_N; pfam07934 1231072007492 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]; Region: AlkA; COG0122 1231072007493 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 1231072007494 helix-hairpin-helix signature motif; other site 1231072007495 substrate binding pocket [chemical binding]; other site 1231072007496 active site 1231072007497 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 1231072007498 putative oxidoreductase; Provisional; Region: PRK12831 1231072007499 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1231072007500 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1231072007501 ferredoxin-NADP(+) reductase subunit alpha; Reviewed; Region: PRK06222 1231072007502 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)...; Region: DHOD_e_trans_like1; cd06219 1231072007503 FAD binding pocket [chemical binding]; other site 1231072007504 FAD binding motif [chemical binding]; other site 1231072007505 phosphate binding motif [ion binding]; other site 1231072007506 beta-alpha-beta structure motif; other site 1231072007507 NAD binding pocket [chemical binding]; other site 1231072007508 Iron coordination center [ion binding]; other site 1231072007509 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 1231072007510 NADPH-dependent butanol dehydrogenase involved in the butanol and ethanol formation pathway in bacteria; Region: NADPH_BDH; cd08179 1231072007511 putative active site [active] 1231072007512 metal binding site [ion binding]; metal-binding site 1231072007513 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK05808 1231072007514 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 1231072007515 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 1231072007516 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 1231072007517 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_alpha; cd01715 1231072007518 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 1231072007519 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_beta; cd01714 1231072007520 Ligand binding site [chemical binding]; other site 1231072007521 Electron transfer flavoprotein domain; Region: ETF; pfam01012 1231072007522 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1231072007523 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1231072007524 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1231072007525 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1231072007526 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1231072007527 active site 1231072007528 3-hydroxybutyryl-CoA dehydratase; Validated; Region: PRK05809 1231072007529 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 1231072007530 substrate binding site [chemical binding]; other site 1231072007531 oxyanion hole (OAH) forming residues; other site 1231072007532 trimer interface [polypeptide binding]; other site 1231072007533 redox-sensing transcriptional repressor Rex; Provisional; Region: PRK05472 1231072007534 Putative DNA-binding protein N-terminus; Region: Put_DNA-bind_N; pfam06971 1231072007535 CoA binding domain; Region: CoA_binding; pfam02629 1231072007536 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1231072007537 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1231072007538 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1231072007539 ABC transporter; Region: ABC_tran_2; pfam12848 1231072007540 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1231072007541 EamA-like transporter family; Region: EamA; pfam00892 1231072007542 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 1231072007543 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 1231072007544 UGMP family protein; Validated; Region: PRK09604 1231072007545 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 1231072007546 Endodeoxyribonuclease RusA; Region: RusA; pfam05866 1231072007547 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 1231072007548 Protein of unknown function (DUF1667); Region: DUF1667; pfam07892 1231072007549 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1231072007550 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 1231072007551 Predicted dehydrogenase [General function prediction only]; Region: COG0579 1231072007552 hydroxyglutarate oxidase; Provisional; Region: PRK11728 1231072007553 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 1231072007554 ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]; Region: LraI; COG0803 1231072007555 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 1231072007556 intersubunit interface [polypeptide binding]; other site 1231072007557 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 1231072007558 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 1231072007559 Glycoprotease family; Region: Peptidase_M22; pfam00814 1231072007560 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 1231072007561 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1231072007562 Coenzyme A binding pocket [chemical binding]; other site 1231072007563 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 1231072007564 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 1231072007565 active site 1231072007566 HIGH motif; other site 1231072007567 dimer interface [polypeptide binding]; other site 1231072007568 KMSKS motif; other site 1231072007569 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 1231072007570 RNA binding surface [nucleotide binding]; other site 1231072007571 germination protein, Ger(x)C family; Region: spore_ger_x_C; TIGR02887 1231072007572 Spore germination B3/ GerAC like, C-terminal; Region: Spore_GerAC; pfam05504 1231072007573 Bacillus/Clostridium GerA spore germination protein; Region: GerA; pfam03323 1231072007574 spore germination protein (amino acid permease); Region: 2A0309; TIGR00912 1231072007575 Probable zinc-binding domain; Region: zf-trcl; pfam13451 1231072007576 Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis]; Region: PrfC; COG4108 1231072007577 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 1231072007578 G1 box; other site 1231072007579 putative GEF interaction site [polypeptide binding]; other site 1231072007580 GTP/Mg2+ binding site [chemical binding]; other site 1231072007581 Switch I region; other site 1231072007582 G2 box; other site 1231072007583 G3 box; other site 1231072007584 Switch II region; other site 1231072007585 G4 box; other site 1231072007586 G5 box; other site 1231072007587 RF3_II: this subfamily represents the domain II of bacterial Release Factor 3 (RF3). Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the...; Region: RF3_II; cd03689 1231072007588 sugar phosphate phosphatase; Provisional; Region: PRK10513 1231072007589 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 1231072007590 active site 1231072007591 motif I; other site 1231072007592 motif II; other site 1231072007593 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 1231072007594 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 1231072007595 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 1231072007596 active site 1231072007597 HIGH motif; other site 1231072007598 dimer interface [polypeptide binding]; other site 1231072007599 KMSKS motif; other site 1231072007600 desulfoferrodoxin; Region: dfx_rbo; TIGR00320 1231072007601 Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small; Region: DSRD; cd00974 1231072007602 non-heme iron binding site [ion binding]; other site 1231072007603 dimer interface [polypeptide binding]; other site 1231072007604 Superoxide reductase-like (SORL) domain, class I; SORL-domains are present in a family of mononuclear non-heme iron proteins that includes superoxide reductase and desulfoferrodoxin. Superoxide reductase-like proteins scavenge superoxide anion radicals...; Region: SORL_Dfx_classI; cd03171 1231072007605 non-heme iron binding site [ion binding]; other site 1231072007606 dimer interface [polypeptide binding]; other site 1231072007607 Protein of unknown function (DUF3131); Region: DUF3131; pfam11329 1231072007608 Putative glucoamylase; Region: Glycoamylase; pfam10091 1231072007609 Second GH94N domain of cyclic beta 1-2 glucan synthetase and similar domains; Region: GH94N_ChvB_NdvB_2_like; cd11753 1231072007610 Cellobiose phosphorylase [Carbohydrate transport and metabolism]; Region: COG3459 1231072007611 First GH94N domain of cyclic beta 1-2 glucan synthetase and similar domains; Region: GH94N_ChvB_NdvB_1_like; cd11756 1231072007612 diaminopimelate decarboxylase; Region: lysA; TIGR01048 1231072007613 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 1231072007614 active site 1231072007615 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1231072007616 substrate binding site [chemical binding]; other site 1231072007617 catalytic residues [active] 1231072007618 dimer interface [polypeptide binding]; other site 1231072007619 M18 Peptidase Aspartyl aminopeptidase; Region: M18_DAP; cd05658 1231072007620 Aminopeptidase I zinc metalloprotease (M18); Region: Peptidase_M18; pfam02127 1231072007621 active site 1231072007622 metal binding site [ion binding]; metal-binding site 1231072007623 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 1231072007624 cation diffusion facilitator family transporter; Region: CDF; TIGR01297 1231072007625 hypothetical protein; Provisional; Region: PRK06851 1231072007626 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; cl17189 1231072007627 Walker A motif; other site 1231072007628 ATP binding site [chemical binding]; other site 1231072007629 Superfamily I DNA and RNA helicases [General function prediction only]; Region: COG3973 1231072007630 Part of AAA domain; Region: AAA_19; pfam13245 1231072007631 Family description; Region: UvrD_C_2; pfam13538 1231072007632 FtsH Extracellular; Region: FtsH_ext; pfam06480 1231072007633 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 1231072007634 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 1231072007635 Walker A motif; other site 1231072007636 ATP binding site [chemical binding]; other site 1231072007637 Walker B motif; other site 1231072007638 arginine finger; other site 1231072007639 Peptidase family M41; Region: Peptidase_M41; pfam01434 1231072007640 glycerol kinase; Provisional; Region: glpK; PRK00047 1231072007641 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 1231072007642 N- and C-terminal domain interface [polypeptide binding]; other site 1231072007643 active site 1231072007644 MgATP binding site [chemical binding]; other site 1231072007645 catalytic site [active] 1231072007646 metal binding site [ion binding]; metal-binding site 1231072007647 glycerol binding site [chemical binding]; other site 1231072007648 homotetramer interface [polypeptide binding]; other site 1231072007649 homodimer interface [polypeptide binding]; other site 1231072007650 FBP binding site [chemical binding]; other site 1231072007651 protein IIAGlc interface [polypeptide binding]; other site 1231072007652 Malic enzyme [Energy production and conversion]; Region: SfcA; COG0281 1231072007653 Malic enzyme, N-terminal domain; Region: malic; pfam00390 1231072007654 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 1231072007655 putative NAD(P) binding site [chemical binding]; other site 1231072007656 M20 Peptidase Aminoacylase 1-like protein 2-like, amidohydrolase subfamily; Region: M20_ACY1L2_like; cd05672 1231072007657 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 1231072007658 metal binding site [ion binding]; metal-binding site 1231072007659 Predicted membrane protein [Function unknown]; Region: COG1288 1231072007660 C4-dicarboxylate anaerobic carrier; Region: DcuC; pfam03606 1231072007661 Citrate lyase, alpha subunit [Energy production and conversion]; Region: CitF; COG3051 1231072007662 Coenzyme A transferase; Region: CoA_trans; cl17247 1231072007663 HpcH/HpaI aldolase/citrate lyase family; Region: HpcH_HpaI; cl17231 1231072007664 Malonate decarboxylase delta subunit (MdcD); Region: ACP; cl06082 1231072007665 Transcriptional regulators [Transcription]; Region: GntR; COG1802 1231072007666 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1231072007667 DNA-binding site [nucleotide binding]; DNA binding site 1231072007668 FCD domain; Region: FCD; pfam07729 1231072007669 Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and...; Region: ACD_LpsHSP_like; cd06471 1231072007670 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 1231072007671 putative dimer interface [polypeptide binding]; other site 1231072007672 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1231072007673 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1231072007674 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 1231072007675 Ligand binding site; other site 1231072007676 metal-binding site 1231072007677 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 1231072007678 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 1231072007679 catalytic loop [active] 1231072007680 iron binding site [ion binding]; other site 1231072007681 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 1231072007682 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 1231072007683 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; smart01092 1231072007684 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 1231072007685 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 1231072007686 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 1231072007687 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cd00232 1231072007688 heme binding pocket [chemical binding]; other site 1231072007689 heme ligand [chemical binding]; other site 1231072007690 L-2-amino-thiazoline-4-carboxylic acid hydrolase; Region: ATC_hydrolase; pfam14196 1231072007691 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 1231072007692 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 1231072007693 Ketopantoate reductase [Coenzyme metabolism]; Region: ApbA; COG1893 1231072007694 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1231072007695 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1231072007696 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]; Region: COG3269 1231072007697 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 1231072007698 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 1231072007699 S-adenosylmethionine binding site [chemical binding]; other site 1231072007700 Protein of unknown function (DUF554); Region: DUF554; pfam04474 1231072007701 sulfite reductase, subunit C; Region: sulfite_red_C; TIGR02912 1231072007702 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 1231072007703 4Fe-4S binding domain; Region: Fer4; pfam00037 1231072007704 anaerobic sulfite reductase subunit B; Provisional; Region: PRK08221 1231072007705 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 1231072007706 FAD binding pocket [chemical binding]; other site 1231072007707 FAD binding motif [chemical binding]; other site 1231072007708 phosphate binding motif [ion binding]; other site 1231072007709 beta-alpha-beta structure motif; other site 1231072007710 NAD binding pocket [chemical binding]; other site 1231072007711 Iron coordination center [ion binding]; other site 1231072007712 anaerobic sulfite reductase subunit A; Provisional; Region: PRK15055 1231072007713 Formate/nitrite transporter; Region: Form_Nir_trans; pfam01226 1231072007714 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 1231072007715 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 1231072007716 ligand binding site [chemical binding]; other site 1231072007717 flexible hinge region; other site 1231072007718 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 1231072007719 non-specific DNA interactions [nucleotide binding]; other site 1231072007720 DNA binding site [nucleotide binding] 1231072007721 sequence specific DNA binding site [nucleotide binding]; other site 1231072007722 putative cAMP binding site [chemical binding]; other site 1231072007723 pyruvate kinase; Provisional; Region: PRK06354 1231072007724 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 1231072007725 domain interfaces; other site 1231072007726 active site 1231072007727 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl17700 1231072007728 6-phosphofructokinase; Provisional; Region: PRK03202 1231072007729 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 1231072007730 active site 1231072007731 ADP/pyrophosphate binding site [chemical binding]; other site 1231072007732 dimerization interface [polypeptide binding]; other site 1231072007733 allosteric effector site; other site 1231072007734 fructose-1,6-bisphosphate binding site; other site 1231072007735 DNA polymerase III DnaE; Reviewed; Region: dnaE; PRK06826 1231072007736 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; Region: PHP_PolIIIA_DnaE3; cd12113 1231072007737 active site 1231072007738 PHP Thumb interface [polypeptide binding]; other site 1231072007739 metal binding site [ion binding]; metal-binding site 1231072007740 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 1231072007741 generic binding surface II; other site 1231072007742 generic binding surface I; other site 1231072007743 Predicted transcriptional regulator containing CBS domains [Transcription]; Region: COG4109 1231072007744 DRTGG domain; Region: DRTGG; pfam07085 1231072007745 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 1231072007746 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1481 1231072007747 Sporulation Regulator WhiA N terminal; Region: WhiA_N; pfam10298 1231072007748 conserved hypothetical protein, cofD-related; Region: CofD_related; TIGR01826 1231072007749 family of mostly uncharacterized proteins similar to B.subtilis YvcK; Region: YvcK_like; cd07187 1231072007750 putative substrate binding pocket [chemical binding]; other site 1231072007751 dimer interface [polypeptide binding]; other site 1231072007752 phosphate binding site [ion binding]; other site 1231072007753 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 1231072007754 AAA domain; Region: AAA_18; pfam13238 1231072007755 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 1231072007756 FAD binding domain; Region: FAD_binding_4; pfam01565 1231072007757 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 1231072007758 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 1231072007759 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 1231072007760 GIY-YIG motif/motif A; other site 1231072007761 active site 1231072007762 catalytic site [active] 1231072007763 putative DNA binding site [nucleotide binding]; other site 1231072007764 metal binding site [ion binding]; metal-binding site 1231072007765 UvrB/uvrC motif; Region: UVR; pfam02151 1231072007766 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 1231072007767 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; pfam04307 1231072007768 Predicted HD-superfamily hydrolase [General function prediction only]; Region: COG3481 1231072007769 YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is...; Region: YhaM_OBF_like; cd04492 1231072007770 generic binding surface II; other site 1231072007771 generic binding surface I; other site 1231072007772 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1231072007773 Zn2+ binding site [ion binding]; other site 1231072007774 Mg2+ binding site [ion binding]; other site 1231072007775 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 1231072007776 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1231072007777 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1231072007778 Bacterial cell division membrane protein [Cell division and chromosome partitioning]; Region: FtsW; COG0772 1231072007779 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cd00060 1231072007780 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 1231072007781 phosphopeptide binding site; other site 1231072007782 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 1231072007783 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 1231072007784 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 1231072007785 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 1231072007786 excinuclease ABC subunit B; Provisional; Region: PRK05298 1231072007787 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 1231072007788 ATP binding site [chemical binding]; other site 1231072007789 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 1231072007790 nucleotide binding region [chemical binding]; other site 1231072007791 ATP-binding site [chemical binding]; other site 1231072007792 Ultra-violet resistance protein B; Region: UvrB; pfam12344 1231072007793 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 1231072007794 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 1231072007795 C-terminal peptidase (prc); Region: prc; TIGR00225 1231072007796 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 1231072007797 protein binding site [polypeptide binding]; other site 1231072007798 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 1231072007799 Catalytic dyad [active] 1231072007800 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 1231072007801 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 1231072007802 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 1231072007803 ATP-binding cassette domain of the cell division transporter; Region: ABC_FtsE_transporter; cd03292 1231072007804 Walker A/P-loop; other site 1231072007805 ATP binding site [chemical binding]; other site 1231072007806 Q-loop/lid; other site 1231072007807 ABC transporter signature motif; other site 1231072007808 Walker B; other site 1231072007809 D-loop; other site 1231072007810 H-loop/switch region; other site 1231072007811 Uncharacterized conserved protein [Function unknown]; Region: COG1284 1231072007812 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 1231072007813 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; pfam10035 1231072007814 PemK-like protein; Region: PemK; pfam02452 1231072007815 Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Transcription]; Region: NikR; COG0864 1231072007816 alanine racemase; Reviewed; Region: alr; PRK00053 1231072007817 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 1231072007818 active site 1231072007819 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1231072007820 dimer interface [polypeptide binding]; other site 1231072007821 substrate binding site [chemical binding]; other site 1231072007822 catalytic residues [active] 1231072007823 Outer membrane lipoprotein-sorting protein [Cell envelope biogenesis, outer membrane]; Region: LolA; COG2834 1231072007824 YjeF-related protein N-terminus; Region: YjeF_N; cl00318 1231072007825 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 1231072007826 putative substrate binding site [chemical binding]; other site 1231072007827 putative ATP binding site [chemical binding]; other site 1231072007828 YjeF-related protein N-terminus; Region: YjeF_N; pfam03853 1231072007829 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 1231072007830 Putative small multi-drug export protein; Region: Sm_multidrug_ex; pfam06695 1231072007831 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 1231072007832 Rubredoxin [Energy production and conversion]; Region: COG1773 1231072007833 Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and...; Region: rubredoxin_SM; cd00729 1231072007834 iron binding site [ion binding]; other site 1231072007835 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 1231072007836 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1231072007837 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 1231072007838 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK07111 1231072007839 aldehyde dehydrogenase family protein; Provisional; Region: PTZ00381 1231072007840 Bacillus subtilis aldehyde dehydrogenase ywdH-like; Region: ALDH_YwdH-P39616; cd07136 1231072007841 NAD(P) binding site [chemical binding]; other site 1231072007842 catalytic residues [active] 1231072007843 carbamate kinase-like carbamoyl phosphate synthetase; Reviewed; Region: PRK12454 1231072007844 AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP. Both CK (this CD) and nonhomologous CP synthetase synthesize carbamoyl phosphate, an...; Region: AAK_CK; cd04235 1231072007845 putative substrate binding site [chemical binding]; other site 1231072007846 nucleotide binding site [chemical binding]; other site 1231072007847 nucleotide binding site [chemical binding]; other site 1231072007848 homodimer interface [polypeptide binding]; other site 1231072007849 pyruvate ferredoxin oxidoreductase subunit beta; Provisional; Region: PRK11865 1231072007850 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 1231072007851 TPP-binding site [chemical binding]; other site 1231072007852 putative dimer interface [polypeptide binding]; other site 1231072007853 pyruvate flavodoxin oxidoreductase subunit alpha; Reviewed; Region: porA; PRK09622 1231072007854 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 1231072007855 dimer interface [polypeptide binding]; other site 1231072007856 PYR/PP interface [polypeptide binding]; other site 1231072007857 TPP binding site [chemical binding]; other site 1231072007858 substrate binding site [chemical binding]; other site 1231072007859 2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate family; Region: PorD_KorD; TIGR02179 1231072007860 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 1231072007861 2-oxoacid:acceptor oxidoreductase, gamma subunit, pyruvate/2-ketoisovalerate family; Region: PorC_KorC; TIGR02175 1231072007862 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 1231072007863 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 1231072007864 methionine gamma-lyase; Provisional; Region: PRK06234 1231072007865 CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of...; Region: CGS_like; cd00614 1231072007866 homodimer interface [polypeptide binding]; other site 1231072007867 substrate-cofactor binding pocket; other site 1231072007868 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1231072007869 catalytic residue [active] 1231072007870 Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]; Region: TyrR; COG3283 1231072007871 N-terminal ACT domain of the TyrR protein; Region: ACT_TyrR; cd04877 1231072007872 putative aromatic amino acid binding site; other site 1231072007873 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 1231072007874 Walker A motif; other site 1231072007875 ATP binding site [chemical binding]; other site 1231072007876 Walker B motif; other site 1231072007877 arginine finger; other site 1231072007878 diaminopimelate dehydrogenase; Region: DAP-DH; TIGR01921 1231072007879 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 1231072007880 This uncharacterized conserved protein belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of...; Region: MTH1175; cd00851 1231072007881 Hemerythrin HHE cation binding domain; Region: Hemerythrin; pfam01814 1231072007882 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 1231072007883 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1231072007884 NAD(P) binding site [chemical binding]; other site 1231072007885 active site 1231072007886 Polymerase and Histidinol Phosphatase domain; Region: PHP; cl17102 1231072007887 Histidinol phosphatase and related hydrolases of the PHP family [Amino acid transport and metabolism / General function prediction only]; Region: HIS2; COG1387 1231072007888 active site 1231072007889 coproporphyrinogen III oxidase; Validated; Region: PRK08208 1231072007890 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 1231072007891 FeS/SAM binding site; other site 1231072007892 HemN C-terminal domain; Region: HemN_C; pfam06969 1231072007893 Sulfatase; Region: Sulfatase; cl17466 1231072007894 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 1231072007895 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 1231072007896 glutaminase active site [active] 1231072007897 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 1231072007898 dimer interface [polypeptide binding]; other site 1231072007899 active site 1231072007900 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 1231072007901 dimer interface [polypeptide binding]; other site 1231072007902 active site 1231072007903 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14316 1231072007904 GlmM is a bacterial phosphoglucosamine mutase (PNGM) that belongs to the alpha-D-phosphohexomutase superfamily. It is required for the interconversion of glucosamine-6-phosphate and glucosamine-1-phosphate in the biosynthetic pathway of...; Region: GlmM; cd05802 1231072007905 active site 1231072007906 substrate binding site [chemical binding]; other site 1231072007907 metal binding site [ion binding]; metal-binding site 1231072007908 butyrate kinase; Provisional; Region: PRK03011 1231072007909 phosphate butyryltransferase; Validated; Region: PRK05805 1231072007910 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 1231072007911 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1231072007912 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4856 1231072007913 YbbR-like protein; Region: YbbR; pfam07949 1231072007914 Uncharacterized conserved protein [Function unknown]; Region: COG1624 1231072007915 DisA bacterial checkpoint controller nucleotide-binding; Region: DisA_N; pfam02457 1231072007916 Cell Wall Hydrolase; Region: Hydrolase_2; pfam07486 1231072007917 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 1231072007918 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 1231072007919 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 1231072007920 catalytic residues [active] 1231072007921 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1729 1231072007922 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 1231072007923 binding surface 1231072007924 TPR repeat; Region: TPR_11; pfam13414 1231072007925 TPR motif; other site 1231072007926 ATP:dephospho-CoA triphosphoribosyl transferase; Region: CitG; cl00768 1231072007927 holo-ACP synthase CitX; Region: citrate_citX; TIGR03124 1231072007928 Citrate lyase synthetase [Energy production and conversion]; Region: CitC; COG3053 1231072007929 Citrate lyase ligase; Region: Citrate_lyase_ligase; cd02169 1231072007930 putative active site [active] 1231072007931 (T/H)XGH motif; other site 1231072007932 Citrate lyase, alpha subunit [Energy production and conversion]; Region: CitF; COG3051 1231072007933 Coenzyme A transferase; Region: CoA_trans; cl17247 1231072007934 HpcH/HpaI aldolase/citrate lyase family; Region: HpcH_HpaI; cl17231 1231072007935 citrate lyase subunit gamma; Provisional; Region: PRK13253 1231072007936 fumarate hydratase; Provisional; Region: PRK06842 1231072007937 fumarate hydratase; Provisional; Region: PRK06246 1231072007938 methylaspartate ammonia-lyase; Region: B_methylAsp_ase; TIGR01502 1231072007939 Methylaspartate ammonia lyase (3-methylaspartase, MAL) is a homodimeric enzyme, catalyzing the magnesium-dependent reversible alpha,beta-elimination of ammonia from L-threo-(2S,3S)-3-methylaspartic acid to mesaconic acid. This reaction is part of the...; Region: MAL; cd03314 1231072007940 dimer interface [polypeptide binding]; other site 1231072007941 active site 1231072007942 Coenzyme B12-dependent glutamate mutase epsilon subunit-like family; contains proteins similar to Clostridium cochlearium glutamate mutase (Glm) and Streptomyces tendae Tu901 NikV. Glm catalyzes a carbon-skeleton rearrangement of L-glutamate to...; Region: Glm_e; cd00245 1231072007943 substrate binding site [chemical binding]; other site 1231072007944 B12 cofactor binding site [chemical binding]; other site 1231072007945 heterodimer (sigma-epsilon) interface [polypeptide binding]; other site 1231072007946 homodimer (epsilon-epsilon) interface [polypeptide binding]; other site 1231072007947 conserved hypothetical protein; Region: glmL_fam; TIGR01319 1231072007948 B12 binding domain of glutamate mutase (Glm). Glutamate mutase catalysis the conversion of (S)-glutamate with (2S,3S)-3-methylaspartate. The rearrangement reaction is initiated by the extraction of a hydrogen from the protein-bound substrate by a 5'...; Region: Glm_B12_BD; cd02072 1231072007949 B12 binding site [chemical binding]; other site 1231072007950 heterodimer interface [polypeptide binding]; other site 1231072007951 cobalt ligand [ion binding]; other site 1231072007952 Predicted transcriptional regulators [Transcription]; Region: COG1725 1231072007953 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 1231072007954 DNA-binding site [nucleotide binding]; DNA binding site 1231072007955 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 1231072007956 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 1231072007957 active site 1231072007958 metal binding site [ion binding]; metal-binding site 1231072007959 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 1231072007960 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 1231072007961 23S rRNA interface [nucleotide binding]; other site 1231072007962 L3 interface [polypeptide binding]; other site 1231072007963 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 1231072007964 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 1231072007965 dimerization interface 3.5A [polypeptide binding]; other site 1231072007966 active site 1231072007967 ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]; Region: CbiQ; COG0619 1231072007968 ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]; Region: CbiQ; COG0619 1231072007969 cobalt transporter ATP-binding subunit; Provisional; Region: cbiO; PRK13637 1231072007970 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 1231072007971 Walker A/P-loop; other site 1231072007972 ATP binding site [chemical binding]; other site 1231072007973 Q-loop/lid; other site 1231072007974 ABC transporter signature motif; other site 1231072007975 Walker B; other site 1231072007976 D-loop; other site 1231072007977 H-loop/switch region; other site 1231072007978 cobalt transporter ATP-binding subunit; Provisional; Region: PRK13633 1231072007979 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 1231072007980 Walker A/P-loop; other site 1231072007981 ATP binding site [chemical binding]; other site 1231072007982 Q-loop/lid; other site 1231072007983 ABC transporter signature motif; other site 1231072007984 Walker B; other site 1231072007985 D-loop; other site 1231072007986 H-loop/switch region; other site 1231072007987 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 1231072007988 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 1231072007989 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 1231072007990 alphaNTD - beta interaction site [polypeptide binding]; other site 1231072007991 alphaNTD homodimer interface [polypeptide binding]; other site 1231072007992 alphaNTD - beta' interaction site [polypeptide binding]; other site 1231072007993 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 1231072007994 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 1231072007995 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 1231072007996 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 1231072007997 RNA binding surface [nucleotide binding]; other site 1231072007998 30S ribosomal protein S11; Validated; Region: PRK05309 1231072007999 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 1231072008000 30S ribosomal protein S13; Region: bact_S13; TIGR03631 1231072008001 50S ribosomal protein L36; Reviewed; Region: rpmJ; PRK00465 1231072008002 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 1231072008003 rRNA binding site [nucleotide binding]; other site 1231072008004 predicted 30S ribosome binding site; other site 1231072008005 KOW motif of Ribosomal Protein L14; Region: KOW_RPL14; cd06088 1231072008006 RNA binding site [nucleotide binding]; other site 1231072008007 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 1231072008008 active site 1231072008009 adenylate kinase; Reviewed; Region: adk; PRK00279 1231072008010 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 1231072008011 AMP-binding site [chemical binding]; other site 1231072008012 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 1231072008013 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 1231072008014 SecY translocase; Region: SecY; pfam00344 1231072008015 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 1231072008016 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 1231072008017 23S rRNA binding site [nucleotide binding]; other site 1231072008018 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 1231072008019 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 1231072008020 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 1231072008021 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 1231072008022 23S rRNA interface [nucleotide binding]; other site 1231072008023 L21e interface [polypeptide binding]; other site 1231072008024 5S rRNA interface [nucleotide binding]; other site 1231072008025 L27 interface [polypeptide binding]; other site 1231072008026 L5 interface [polypeptide binding]; other site 1231072008027 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 1231072008028 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1231072008029 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1231072008030 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 1231072008031 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08061 1231072008032 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 1231072008033 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 1231072008034 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 1231072008035 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 1231072008036 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 1231072008037 RNA binding site [nucleotide binding]; other site 1231072008038 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 1231072008039 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 1231072008040 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 1231072008041 23S rRNA interface [nucleotide binding]; other site 1231072008042 putative translocon interaction site; other site 1231072008043 signal recognition particle (SRP54) interaction site; other site 1231072008044 L23 interface [polypeptide binding]; other site 1231072008045 trigger factor interaction site; other site 1231072008046 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 1231072008047 23S rRNA interface [nucleotide binding]; other site 1231072008048 5S rRNA interface [nucleotide binding]; other site 1231072008049 putative antibiotic binding site [chemical binding]; other site 1231072008050 L25 interface [polypeptide binding]; other site 1231072008051 L27 interface [polypeptide binding]; other site 1231072008052 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 1231072008053 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 1231072008054 G-X-X-G motif; other site 1231072008055 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 1231072008056 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 1231072008057 putative translocon binding site; other site 1231072008058 protein-rRNA interface [nucleotide binding]; other site 1231072008059 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 1231072008060 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 1231072008061 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 1231072008062 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 1231072008063 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 1231072008064 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 1231072008065 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 1231072008066 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 1231072008067 elongation factor Tu; Reviewed; Region: PRK00049 1231072008068 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 1231072008069 G1 box; other site 1231072008070 GEF interaction site [polypeptide binding]; other site 1231072008071 GTP/Mg2+ binding site [chemical binding]; other site 1231072008072 Switch I region; other site 1231072008073 G2 box; other site 1231072008074 G3 box; other site 1231072008075 Switch II region; other site 1231072008076 G4 box; other site 1231072008077 G5 box; other site 1231072008078 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 1231072008079 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 1231072008080 Antibiotic Binding Site [chemical binding]; other site 1231072008081 elongation factor G; Reviewed; Region: PRK00007 1231072008082 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 1231072008083 G1 box; other site 1231072008084 putative GEF interaction site [polypeptide binding]; other site 1231072008085 GTP/Mg2+ binding site [chemical binding]; other site 1231072008086 Switch I region; other site 1231072008087 G2 box; other site 1231072008088 G3 box; other site 1231072008089 Switch II region; other site 1231072008090 G4 box; other site 1231072008091 G5 box; other site 1231072008092 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 1231072008093 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 1231072008094 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 1231072008095 30S ribosomal protein S7; Validated; Region: PRK05302 1231072008096 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 1231072008097 S17 interaction site [polypeptide binding]; other site 1231072008098 S8 interaction site; other site 1231072008099 16S rRNA interaction site [nucleotide binding]; other site 1231072008100 streptomycin interaction site [chemical binding]; other site 1231072008101 23S rRNA interaction site [nucleotide binding]; other site 1231072008102 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 1231072008103 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; Region: Ribosomal_L7Ae; cl00600 1231072008104 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 1231072008105 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 1231072008106 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 1231072008107 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 1231072008108 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 1231072008109 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 1231072008110 Rpb1 (beta') - Rpb6 (omega) interaction site [polypeptide binding]; other site 1231072008111 G-loop; other site 1231072008112 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 1231072008113 DNA binding site [nucleotide binding] 1231072008114 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 1231072008115 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 1231072008116 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 1231072008117 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 1231072008118 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 1231072008119 RPB1 interaction site [polypeptide binding]; other site 1231072008120 RPB10 interaction site [polypeptide binding]; other site 1231072008121 RPB11 interaction site [polypeptide binding]; other site 1231072008122 RPB3 interaction site [polypeptide binding]; other site 1231072008123 RPB12 interaction site [polypeptide binding]; other site 1231072008124 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 1231072008125 core dimer interface [polypeptide binding]; other site 1231072008126 peripheral dimer interface [polypeptide binding]; other site 1231072008127 L10 interface [polypeptide binding]; other site 1231072008128 L11 interface [polypeptide binding]; other site 1231072008129 putative EF-Tu interaction site [polypeptide binding]; other site 1231072008130 putative EF-G interaction site [polypeptide binding]; other site 1231072008131 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 1231072008132 23S rRNA interface [nucleotide binding]; other site 1231072008133 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 1231072008134 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 1231072008135 mRNA/rRNA interface [nucleotide binding]; other site 1231072008136 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 1231072008137 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 1231072008138 23S rRNA interface [nucleotide binding]; other site 1231072008139 L7/L12 interface [polypeptide binding]; other site 1231072008140 putative thiostrepton binding site; other site 1231072008141 L25 interface [polypeptide binding]; other site 1231072008142 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 1231072008143 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 1231072008144 putative homodimer interface [polypeptide binding]; other site 1231072008145 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 1231072008146 heterodimer interface [polypeptide binding]; other site 1231072008147 homodimer interface [polypeptide binding]; other site 1231072008148 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK07597 1231072008149 elongation factor Tu; Reviewed; Region: PRK00049 1231072008150 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 1231072008151 G1 box; other site 1231072008152 GEF interaction site [polypeptide binding]; other site 1231072008153 GTP/Mg2+ binding site [chemical binding]; other site 1231072008154 Switch I region; other site 1231072008155 G2 box; other site 1231072008156 G3 box; other site 1231072008157 Switch II region; other site 1231072008158 G4 box; other site 1231072008159 G5 box; other site 1231072008160 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 1231072008161 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 1231072008162 Antibiotic Binding Site [chemical binding]; other site 1231072008163 RNA polymerase sigma-H factor; Region: spore_sigH; TIGR02859 1231072008164 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1231072008165 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 1231072008166 YacP-like NYN domain; Region: NYN_YacP; pfam05991 1231072008167 rRNA methylase, putative, group 3; Region: rRNA_methyl_3; TIGR00186 1231072008168 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 1231072008169 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 1231072008170 FAD-dependent thymidylate synthase; Reviewed; Region: thyX; PRK00847 1231072008171 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 1231072008172 active site 1231072008173 metal binding site [ion binding]; metal-binding site 1231072008174 dimerization interface [polypeptide binding]; other site 1231072008175 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 1231072008176 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1231072008177 active site 1231072008178 HIGH motif; other site 1231072008179 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1231072008180 KMSKS motif; other site 1231072008181 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 1231072008182 tRNA binding surface [nucleotide binding]; other site 1231072008183 anticodon binding site; other site 1231072008184 threonine dehydratase; Provisional; Region: PRK08198 1231072008185 Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly...; Region: Thr-dehyd; cd01562 1231072008186 tetramer interface [polypeptide binding]; other site 1231072008187 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1231072008188 catalytic residue [active] 1231072008189 C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains; Region: ACT_ThrD-II-like; cd04886 1231072008190 prolyl-tRNA synthetase; Provisional; Region: PRK09194 1231072008191 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 1231072008192 dimer interface [polypeptide binding]; other site 1231072008193 motif 1; other site 1231072008194 active site 1231072008195 motif 2; other site 1231072008196 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 1231072008197 putative deacylase active site [active] 1231072008198 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 1231072008199 active site 1231072008200 motif 3; other site 1231072008201 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 1231072008202 anticodon binding site; other site 1231072008203 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 1231072008204 substrate binding site; other site 1231072008205 dimer interface; other site 1231072008206 Integral membrane protein (PIN domain superfamily) [General function prediction only]; Region: COG4956 1231072008207 PIN domain of Thermus Thermophilus Hb8, uncharacterized Bacillus subtilis YacL, and other bacterial homologs; Region: PIN_YacL; cd09877 1231072008208 putative active site [active] 1231072008209 DNA integrity scanning protein DisA; Provisional; Region: PRK13482 1231072008210 DisA bacterial checkpoint controller nucleotide-binding; Region: DisA_N; pfam02457 1231072008211 DisA bacterial checkpoint controller linker region; Region: DisA-linker; pfam10635 1231072008212 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 1231072008213 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 1231072008214 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 1231072008215 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 1231072008216 AAA domain; Region: AAA_25; pfam13481 1231072008217 Walker A motif; other site 1231072008218 ATP binding site [chemical binding]; other site 1231072008219 Walker B motif; other site 1231072008220 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 1231072008221 GlcN6P_deaminase: Glucosamine-6-phosphate (GlcN6P) deaminase subfamily; GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium. The reaction is an aldo-keto isomerization coupled with an amination or...; Region: GlcN6P_deaminase; cd01399 1231072008222 active site 1231072008223 trimer interface [polypeptide binding]; other site 1231072008224 allosteric site; other site 1231072008225 active site lid [active] 1231072008226 hexamer (dimer of trimers) interface [polypeptide binding]; other site 1231072008227 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 1231072008228 Clp amino terminal domain; Region: Clp_N; pfam02861 1231072008229 Clp amino terminal domain; Region: Clp_N; pfam02861 1231072008230 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 1231072008231 Walker A motif; other site 1231072008232 ATP binding site [chemical binding]; other site 1231072008233 Walker B motif; other site 1231072008234 arginine finger; other site 1231072008235 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 1231072008236 Walker A motif; other site 1231072008237 ATP binding site [chemical binding]; other site 1231072008238 Walker B motif; other site 1231072008239 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1231072008240 ATP:guanido phosphotransferase; Provisional; Region: PRK01059 1231072008241 Phosphagen (guanidino) kinases found in bacteria; Region: bacterial_phosphagen_kinase; cd07930 1231072008242 ADP binding site [chemical binding]; other site 1231072008243 phosphagen binding site; other site 1231072008244 substrate specificity loop; other site 1231072008245 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]; Region: COG3880 1231072008246 Firmicute transcriptional repressor of class III stress genes (CtsR); Region: CtsR; pfam05848 1231072008247 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 1231072008248 catalytic core [active] 1231072008249 Rubrerythrin [Energy production and conversion]; Region: COG1592 1231072008250 Rubrerythrin, ferritin-like diiron-binding domain; Region: Rubrerythrin; cd01041 1231072008251 binuclear metal center [ion binding]; other site 1231072008252 Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and...; Region: rubredoxin_SM; cd00729 1231072008253 iron binding site [ion binding]; other site 1231072008254 Elongation factor G (EF-G) family; Region: EF-G_bact; cd04170 1231072008255 elongation factor G; Reviewed; Region: PRK12740 1231072008256 G1 box; other site 1231072008257 putative GEF interaction site [polypeptide binding]; other site 1231072008258 GTP/Mg2+ binding site [chemical binding]; other site 1231072008259 Switch I region; other site 1231072008260 G2 box; other site 1231072008261 G3 box; other site 1231072008262 Switch II region; other site 1231072008263 G4 box; other site 1231072008264 G5 box; other site 1231072008265 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 1231072008266 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 1231072008267 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 1231072008268 YcxB-like protein; Region: YcxB; pfam14317 1231072008269 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 1231072008270 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1231072008271 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 1231072008272 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1231072008273 Plasmid segregation protein ParM and similar proteins; Region: ParM_like; cd10227 1231072008274 Mg binding site [ion binding]; other site 1231072008275 nucleotide binding site [chemical binding]; other site 1231072008276 putative protofilament interface [polypeptide binding]; other site 1231072008277 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1231072008278 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1231072008279 Walker A/P-loop; other site 1231072008280 ATP binding site [chemical binding]; other site 1231072008281 Q-loop/lid; other site 1231072008282 ABC transporter signature motif; other site 1231072008283 Walker B; other site 1231072008284 D-loop; other site 1231072008285 H-loop/switch region; other site 1231072008286 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 1231072008287 FtsX-like permease family; Region: FtsX; pfam02687 1231072008288 FtsX-like permease family; Region: FtsX; pfam02687 1231072008289 M28 Zn-Peptidases containing a PA domain insert; Region: M28_like_PA; cd03877 1231072008290 Peptidase family M28; Region: Peptidase_M28; pfam04389 1231072008291 metal binding site [ion binding]; metal-binding site 1231072008292 Domain of unknown function (DUF4250); Region: DUF4250; pfam14056 1231072008293 Domain of unknown function (DUF4351); Region: DUF4351; pfam14261 1231072008294 ABC-2 family transporter protein; Region: ABC2_membrane_4; pfam12730 1231072008295 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 1231072008296 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1231072008297 ABC transporter signature motif; other site 1231072008298 Walker B; other site 1231072008299 D-loop; other site 1231072008300 H-loop/switch region; other site 1231072008301 Domain of unknown function (DUF4160); Region: DUF4160; pfam13711 1231072008302 Protein of unknown function (DUF2442); Region: DUF2442; pfam10387 1231072008303 Protein of unknown function (DUF3791); Region: DUF3791; pfam12668 1231072008304 Peptidase family M9 N-terminal; Region: Peptidase_M9_N; pfam08453 1231072008305 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 1231072008306 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 1231072008307 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 1231072008308 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1231072008309 Walker B; other site 1231072008310 D-loop; other site 1231072008311 H-loop/switch region; other site 1231072008312 Domain of unknown function (DUF4351); Region: DUF4351; pfam14261 1231072008313 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 1231072008314 active site 1231072008315 NTP binding site [chemical binding]; other site 1231072008316 metal binding triad [ion binding]; metal-binding site 1231072008317 INT_SG3, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 3, catalytic domain. The CD contains various predicted bacterial and phage integrase/recombinase sequences for which not much experimental characterization is available; Region: INT_SG3_C; cd01186 1231072008318 Int/Topo IB signature motif; other site 1231072008319 YcxB-like protein; Region: YcxB; pfam14317 1231072008320 YcxB-like protein; Region: YcxB; pfam14317 1231072008321 Predicted transcriptional regulators [Transcription]; Region: COG1695 1231072008322 Transcriptional regulator PadR-like family; Region: PadR; cl17335 1231072008323 Acyltransferase family; Region: Acyl_transf_3; pfam01757 1231072008324 Predicted O-acyltransferase [General function prediction only]; Region: COG3274 1231072008325 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 1231072008326 amidase catalytic site [active] 1231072008327 Zn binding residues [ion binding]; other site 1231072008328 substrate binding site [chemical binding]; other site 1231072008329 Putative peptidoglycan-binding domain-containing protein [Cell envelope biogenesis, outer membrane]; Region: COG3409 1231072008330 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 1231072008331 M28 Zn-peptidases include aminopeptidases and carboxypeptidases; Region: M28; cd02690 1231072008332 Predicted aminopeptidases [General function prediction only]; Region: Iap; COG2234 1231072008333 metal binding site [ion binding]; metal-binding site 1231072008334 Protein of unknown function (DUF2922); Region: DUF2922; pfam11148 1231072008335 Protein of unknown function (DUF1659); Region: DUF1659; pfam07872 1231072008336 YvrJ protein family; Region: YvrJ; pfam12841 1231072008337 Clostridial neurotoxin zinc protease; Region: Peptidase_M27; pfam01742 1231072008338 Clostridium neurotoxin, Translocation domain; Region: Toxin_trans; pfam07952 1231072008339 Clostridium neurotoxin, N-terminal receptor binding; Region: Toxin_R_bind_N; pfam07953 1231072008340 Clostridium neurotoxin, C-terminal receptor binding; Region: Toxin_R_bind_C; pfam07951 1231072008341 clostridium toxin-associated regulator BotR; Region: P21_Cbot; TIGR03209 1231072008342 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 1231072008343 DNA binding residues [nucleotide binding] 1231072008344 MjaII restriction endonuclease; Region: RE_MjaII; pfam09520