-- dump date 20120504_161756 -- class Genbank::misc_feature -- table misc_feature_note -- id note 580332000001 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 580332000002 DnaA N-terminal domain; Region: DnaA_N; pfam11638 580332000003 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 580332000004 Walker A motif; other site 580332000005 ATP binding site [chemical binding]; other site 580332000006 Walker B motif; other site 580332000007 arginine finger; other site 580332000008 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 580332000009 DnaA box-binding interface [nucleotide binding]; other site 580332000010 DNA polymerase III subunit beta; Validated; Region: PRK05643 580332000011 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 580332000012 putative DNA binding surface [nucleotide binding]; other site 580332000013 dimer interface [polypeptide binding]; other site 580332000014 beta-clamp/clamp loader binding surface; other site 580332000015 beta-clamp/translesion DNA polymerase binding surface; other site 580332000016 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 580332000017 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 580332000018 ATP binding site [chemical binding]; other site 580332000019 Mg2+ binding site [ion binding]; other site 580332000020 G-X-G motif; other site 580332000021 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 580332000022 anchoring element; other site 580332000023 dimer interface [polypeptide binding]; other site 580332000024 ATP binding site [chemical binding]; other site 580332000025 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 580332000026 active site 580332000027 putative metal-binding site [ion binding]; other site 580332000028 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 580332000029 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 580332000030 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 580332000031 active site 580332000032 interdomain interaction site; other site 580332000033 putative metal-binding site [ion binding]; other site 580332000034 nucleotide binding site [chemical binding]; other site 580332000035 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 580332000036 domain I; other site 580332000037 DNA binding groove [nucleotide binding] 580332000038 phosphate binding site [ion binding]; other site 580332000039 domain II; other site 580332000040 domain III; other site 580332000041 nucleotide binding site [chemical binding]; other site 580332000042 catalytic site [active] 580332000043 domain IV; other site 580332000044 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 580332000045 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 580332000046 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 580332000047 Protein of unknown function (DUF494); Region: DUF494; cl01103 580332000048 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 580332000049 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 580332000050 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 580332000051 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 580332000052 active site 580332000053 catalytic residues [active] 580332000054 metal binding site [ion binding]; metal-binding site 580332000055 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 580332000056 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 580332000057 putative active site [active] 580332000058 substrate binding site [chemical binding]; other site 580332000059 putative cosubstrate binding site; other site 580332000060 catalytic site [active] 580332000061 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 580332000062 substrate binding site [chemical binding]; other site 580332000063 16S rRNA methyltransferase B; Provisional; Region: PRK10901 580332000064 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 580332000065 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 580332000066 S-adenosylmethionine binding site [chemical binding]; other site 580332000067 Domain of unknown function (DUF4390); Region: DUF4390; pfam14334 580332000068 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 580332000069 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 580332000070 dimerization interface [polypeptide binding]; other site 580332000071 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 580332000072 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 580332000073 dimer interface [polypeptide binding]; other site 580332000074 phosphorylation site [posttranslational modification] 580332000075 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 580332000076 ATP binding site [chemical binding]; other site 580332000077 Mg2+ binding site [ion binding]; other site 580332000078 G-X-G motif; other site 580332000079 Response regulator receiver domain; Region: Response_reg; pfam00072 580332000080 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 580332000081 active site 580332000082 phosphorylation site [posttranslational modification] 580332000083 intermolecular recognition site; other site 580332000084 dimerization interface [polypeptide binding]; other site 580332000085 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 580332000086 Helix-turn-helix domains; Region: HTH; cl00088 580332000087 transketolase; Reviewed; Region: PRK12753 580332000088 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 580332000089 TPP-binding site [chemical binding]; other site 580332000090 dimer interface [polypeptide binding]; other site 580332000091 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 580332000092 PYR/PP interface [polypeptide binding]; other site 580332000093 dimer interface [polypeptide binding]; other site 580332000094 TPP binding site [chemical binding]; other site 580332000095 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 580332000096 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332000097 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 580332000098 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 580332000099 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 580332000100 Phosphoglycerate kinase; Region: PGK; pfam00162 580332000101 substrate binding site [chemical binding]; other site 580332000102 hinge regions; other site 580332000103 ADP binding site [chemical binding]; other site 580332000104 catalytic site [active] 580332000105 pyruvate kinase; Provisional; Region: PRK05826 580332000106 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 580332000107 domain interfaces; other site 580332000108 active site 580332000109 hypothetical protein; Provisional; Region: PRK08185 580332000110 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 580332000111 intersubunit interface [polypeptide binding]; other site 580332000112 active site 580332000113 zinc binding site [ion binding]; other site 580332000114 Na+ binding site [ion binding]; other site 580332000115 Cytochrome c; Region: Cytochrom_C; cl11414 580332000116 EamA-like transporter family; Region: EamA; cl01037 580332000117 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 580332000118 EamA-like transporter family; Region: EamA; cl01037 580332000119 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 580332000120 Helix-turn-helix domains; Region: HTH; cl00088 580332000121 The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; Region: PBP2_CbbR_RubisCO_like; cd08419 580332000122 putative dimerization interface [polypeptide binding]; other site 580332000123 ribulose bisphosphate carboxylase; Provisional; Region: PRK13475 580332000124 Ribulose bisphosphate carboxylase large chain, Form II; Region: RuBisCO_large_II; cd08211 580332000125 dimer interface [polypeptide binding]; other site 580332000126 active site 580332000127 catalytic residue [active] 580332000128 metal binding site [ion binding]; metal-binding site 580332000129 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332000130 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 580332000131 norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial...; Region: vWA_norD_type; cd01454 580332000132 metal ion-dependent adhesion site (MIDAS); other site 580332000133 Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1; Region: FBPase; cd00354 580332000134 AMP binding site [chemical binding]; other site 580332000135 metal binding site [ion binding]; metal-binding site 580332000136 active site 580332000137 AIR carboxylase; Region: AIRC; cl00310 580332000138 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 580332000139 ATP binding site [chemical binding]; other site 580332000140 active site 580332000141 substrate binding site [chemical binding]; other site 580332000142 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeB; cd00884 580332000143 active site clefts [active] 580332000144 zinc binding site [ion binding]; other site 580332000145 dimer interface [polypeptide binding]; other site 580332000146 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 580332000147 AAA domain; Region: AAA_13; pfam13166 580332000148 orotate phosphoribosyltransferase; Validated; Region: pyrE; PRK00455 580332000149 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 580332000150 active site 580332000151 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 580332000152 putative active site [active] 580332000153 putative catalytic site [active] 580332000154 putative DNA binding site [nucleotide binding]; other site 580332000155 putative phosphate binding site [ion binding]; other site 580332000156 metal binding site A [ion binding]; metal-binding site 580332000157 putative AP binding site [nucleotide binding]; other site 580332000158 putative metal binding site B [ion binding]; other site 580332000159 Predicted membrane protein (DUF2238); Region: DUF2238; cl01464 580332000160 muropeptide transporter; Validated; Region: ampG; PRK11010 580332000161 AmpG-related permease; Region: 2A0125; TIGR00901 580332000162 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 580332000163 S-adenosylmethionine binding site [chemical binding]; other site 580332000164 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 580332000165 Homoserine acetyltransferase [Amino acid transport and metabolism]; Region: MET2; COG2021 580332000166 Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the...; Region: ALAD_PBGS_aspartate_rich; cd04823 580332000167 dimer interface [polypeptide binding]; other site 580332000168 active site 580332000169 aspartate-rich active site metal binding site; other site 580332000170 allosteric magnesium binding site [ion binding]; other site 580332000171 Schiff base residues; other site 580332000172 Predicted GTPase [General function prediction only]; Region: COG0218 580332000173 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 580332000174 G1 box; other site 580332000175 GTP/Mg2+ binding site [chemical binding]; other site 580332000176 Switch I region; other site 580332000177 G2 box; other site 580332000178 G3 box; other site 580332000179 Switch II region; other site 580332000180 G4 box; other site 580332000181 G5 box; other site 580332000182 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 580332000183 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 580332000184 inhibitor-cofactor binding pocket; inhibition site 580332000185 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332000186 catalytic residue [active] 580332000187 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 580332000188 thiamine phosphate binding site [chemical binding]; other site 580332000189 active site 580332000190 pyrophosphate binding site [ion binding]; other site 580332000191 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 580332000192 dimer interface [polypeptide binding]; other site 580332000193 substrate binding site [chemical binding]; other site 580332000194 ATP binding site [chemical binding]; other site 580332000195 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332000196 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 580332000197 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 580332000198 SurA N-terminal domain; Region: SurA_N_3; cl07813 580332000199 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 580332000200 PPIC-type PPIASE domain; Region: Rotamase; cl08278 580332000201 PPIC-type PPIASE domain; Region: Rotamase; cl08278 580332000202 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 580332000203 Organic solvent tolerance protein; Region: OstA_C; pfam04453 580332000204 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 580332000205 Phosphotransferase enzyme family; Region: APH; pfam01636 580332000206 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 580332000207 Substrate binding site; other site 580332000208 metal-binding site 580332000209 Aminopeptidase P, N-terminal domain; Region: AMP_N; cl08433 580332000210 proline aminopeptidase P II; Provisional; Region: PRK10879 580332000211 Prolidase. E.C. 3.4.13.9. Also known as Xaa-Pro dipeptidase, X-Pro dipeptidase, proline dipeptidase., imidodipeptidase, peptidase D, gamma-peptidase. Catalyses hydrolysis of Xaa-Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action on...; Region: Prolidase; cd01087 580332000212 active site 580332000213 2-polyprenyl-6-methoxyphenol 4-hydroxylase; Region: UbiH; TIGR01984 580332000214 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332000215 cyclase homology domain; Region: CHD; cd07302 580332000216 nucleotidyl binding site; other site 580332000217 metal binding site [ion binding]; metal-binding site 580332000218 dimer interface [polypeptide binding]; other site 580332000219 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; cl00062 580332000220 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 580332000221 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 580332000222 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 580332000223 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 580332000224 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 580332000225 Protein of unknown function, DUF486; Region: DUF486; cl01236 580332000226 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 580332000227 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this...; Region: Band_7; cl02525 580332000228 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 580332000229 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 580332000230 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 580332000231 excinuclease ABC, C subunit; Region: uvrC; TIGR00194 580332000232 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 580332000233 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 580332000234 MeTr subgroup of pterin binding enzymes. This family includes cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). Cobalamin-dependent...; Region: MeTr; cd00740 580332000235 substrate binding pocket [chemical binding]; other site 580332000236 B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy); Region: methionine_synthase_B12_BD; cd02069 580332000237 B12 binding site [chemical binding]; other site 580332000238 cobalt ligand [ion binding]; other site 580332000239 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 580332000240 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 580332000241 octamerization interface [polypeptide binding]; other site 580332000242 diferric-oxygen binding site [ion binding]; other site 580332000243 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 580332000244 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 580332000245 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332000246 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 580332000247 Membrane fusogenic activity; Region: BMFP; cl01115 580332000248 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 580332000249 Nitrogen regulatory protein P-II; Region: P-II; cl00412 580332000250 Nitrogen regulatory protein P-II; Region: P-II; smart00938 580332000251 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 580332000252 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 580332000253 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 580332000254 putative active site [active] 580332000255 heme pocket [chemical binding]; other site 580332000256 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 580332000257 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 580332000258 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332000259 metal binding site [ion binding]; metal-binding site 580332000260 active site 580332000261 I-site; other site 580332000262 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 580332000263 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332000264 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 580332000265 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332000266 dimer interface [polypeptide binding]; other site 580332000267 putative CheW interface [polypeptide binding]; other site 580332000268 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 580332000269 substrate binding site [chemical binding]; other site 580332000270 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 580332000271 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 580332000272 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 580332000273 putative active site [active] 580332000274 putative substrate binding site [chemical binding]; other site 580332000275 putative cosubstrate binding site; other site 580332000276 catalytic site [active] 580332000277 Putative catalytic NodB homology domain of uncharacterized BH0857 protein from Bacillus halodurans and its bacterial homologs; Region: CE4_BH0857_like; cd10955 580332000278 NodB motif; other site 580332000279 putative active site [active] 580332000280 putative catalytic site [active] 580332000281 MltA-interacting protein MipA; Region: MipA; cl01504 580332000282 Iron-binding zinc finger CDGSH type; Region: zf-CDGSH; cl02748 580332000283 Iron-binding zinc finger CDGSH type; Region: zf-CDGSH; cl02748 580332000284 urea carboxylase-associated protein 1; Region: urea_degr_1; TIGR03424 580332000285 Domain of unknown function (DUF1989); Region: DUF1989; cl01474 580332000286 urea carboxylase-associated protein 1; Region: urea_degr_1; TIGR03424 580332000287 Domain of unknown function (DUF1989); Region: DUF1989; cl01474 580332000288 urea carboxylase; Region: urea_carbox; TIGR02712 580332000289 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 580332000290 ATP-grasp domain; Region: ATP-grasp_4; cl03087 580332000291 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 580332000292 Allophanate hydrolase subunit 2; Region: AHS2; cl00865 580332000293 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; cl00896 580332000294 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 580332000295 carboxyltransferase (CT) interaction site; other site 580332000296 biotinylation site [posttranslational modification]; other site 580332000297 allophanate hydrolase; Provisional; Region: PRK08186 580332000298 Amidase; Region: Amidase; cl11426 580332000299 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 580332000300 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 580332000301 non-specific DNA binding site [nucleotide binding]; other site 580332000302 salt bridge; other site 580332000303 sequence-specific DNA binding site [nucleotide binding]; other site 580332000304 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 580332000305 putative active site [active] 580332000306 putative NTP binding site [chemical binding]; other site 580332000307 putative nucleic acid binding site [nucleotide binding]; other site 580332000308 PIN domain of ribonucleases (toxins), VapC, FitB, and PAE0151 of bacterial and archaeal toxin/antitoxin-like operons, and other similar homologs; Region: PIN_VapC-like; cd09861 580332000309 putative active site [active] 580332000310 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 580332000311 NMT1-like family; Region: NMT1_2; cl15260 580332000312 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 580332000313 dimer interface [polypeptide binding]; other site 580332000314 conserved gate region; other site 580332000315 putative PBP binding loops; other site 580332000316 ABC-ATPase subunit interface; other site 580332000317 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 580332000318 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 580332000319 Walker A/P-loop; other site 580332000320 ATP binding site [chemical binding]; other site 580332000321 Q-loop/lid; other site 580332000322 ABC transporter signature motif; other site 580332000323 Walker B; other site 580332000324 D-loop; other site 580332000325 H-loop/switch region; other site 580332000326 Creatinine amidohydrolase; Region: Creatininase; cl00618 580332000327 glutamine synthetase, type III; Region: gln_synth_III; TIGR03105 580332000328 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 580332000329 Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Transcription]; Region: NikR; COG0864 580332000330 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 580332000331 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 580332000332 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 580332000333 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332000334 Walker A/P-loop; other site 580332000335 ATP binding site [chemical binding]; other site 580332000336 ABC transporter signature motif; other site 580332000337 Walker B; other site 580332000338 D-loop; other site 580332000339 H-loop/switch region; other site 580332000340 ABC transporter; Region: ABC_tran_2; pfam12848 580332000341 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 580332000342 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 580332000343 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 580332000344 glutamate--cysteine ligase, T. ferrooxidans family; Region: gshA_ferroox; TIGR02049 580332000345 Glutamate-cysteine ligase; Region: GshA; pfam08886 580332000346 ApbE family; Region: ApbE; cl00643 580332000347 PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIA_man; cd00006 580332000348 active pocket/dimerization site; other site 580332000349 active site 580332000350 phosphorylation site [posttranslational modification] 580332000351 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 580332000352 dimerization domain swap beta strand [polypeptide binding]; other site 580332000353 regulatory protein interface [polypeptide binding]; other site 580332000354 active site 580332000355 regulatory phosphorylation site [posttranslational modification]; other site 580332000356 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 580332000357 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 580332000358 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 580332000359 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 580332000360 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 580332000361 metal binding triad [ion binding]; metal-binding site 580332000362 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 580332000363 Transglycosylase; Region: Transgly; cl07896 580332000364 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 580332000365 Cell division protein FtsA; Region: FtsA; cl11496 580332000366 Competence protein A; Region: Competence_A; pfam11104 580332000367 Cell division protein FtsA; Region: FtsA; cl11496 580332000368 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 580332000369 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 580332000370 Pilus assembly protein, PilO; Region: PilO; cl01234 580332000371 Pilus assembly protein, PilP; Region: PilP; cl01235 580332000372 AMIN domain; Region: AMIN; pfam11741 580332000373 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 580332000374 Secretin and TonB N terminus short domain; Region: STN; cl06624 580332000375 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 580332000376 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 580332000377 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 580332000378 bifunctional shikimate kinase/3-dehydroquinate synthase; Provisional; Region: PRK14021 580332000379 ADP binding site [chemical binding]; other site 580332000380 magnesium binding site [ion binding]; other site 580332000381 putative shikimate binding site; other site 580332000382 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 580332000383 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 580332000384 active site 580332000385 dimer interface [polypeptide binding]; other site 580332000386 metal binding site [ion binding]; metal-binding site 580332000387 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 580332000388 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332000389 Zn2+ binding site [ion binding]; other site 580332000390 Mg2+ binding site [ion binding]; other site 580332000391 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 580332000392 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 580332000393 Glutamine amidotransferases class-II (Gn-AT), glutamate synthase (GltS)-type. GltS is a homodimer that synthesizes L-glutamate from 2-oxoglutarate and L-glutamine, an important step in ammonia assimilation in bacteria, cyanobacteria and plants. The...; Region: GltS; cd00713 580332000394 active site 580332000395 dimer interface [polypeptide binding]; other site 580332000396 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 580332000397 Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast...; Region: GltS_FMN; cd02808 580332000398 active site 580332000399 FMN binding site [chemical binding]; other site 580332000400 substrate binding site [chemical binding]; other site 580332000401 3Fe-4S cluster binding site [ion binding]; other site 580332000402 gltb_C. This domain is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS). GltS encodes a complex iron-sulfur flavoprotein that catalyzes the synthesis of L-glutamate from L-glutamine and 2-oxoglutarate. It requires the...; Region: gltB_C; cd00982 580332000403 domain interface; other site 580332000404 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 580332000405 Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction...; Region: URO-D; cd00717 580332000406 methyltransferase, MtaA/CmuA family; Region: mtaA_cmuA; TIGR01463 580332000407 substrate binding site [chemical binding]; other site 580332000408 active site 580332000409 primosome assembly protein PriA; Validated; Region: PRK05580 580332000410 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 580332000411 ATP binding site [chemical binding]; other site 580332000412 putative Mg++ binding site [ion binding]; other site 580332000413 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332000414 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 580332000415 FAD binding domain; Region: FAD_binding_4; pfam01565 580332000416 LabA_like proteins; Region: LabA_like; cd06167 580332000417 putative metal binding site [ion binding]; other site 580332000418 C-terminal domain of LabA_like proteins; Region: LabA_like_C; cd10146 580332000419 ferredoxin--NADP+ reductase; Provisional; Region: PLN03116 580332000420 Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport...; Region: FNR_like; cl06868 580332000421 FAD binding pocket [chemical binding]; other site 580332000422 conserved FAD binding motif [chemical binding]; other site 580332000423 phosphate binding motif [ion binding]; other site 580332000424 beta-alpha-beta structure motif; other site 580332000425 NAD binding pocket [chemical binding]; other site 580332000426 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cd01610 580332000427 active site 580332000428 Domain of unknown function (DUF4337); Region: DUF4337; pfam14235 580332000429 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 580332000430 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 580332000431 active site 580332000432 catalytic tetrad [active] 580332000433 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 580332000434 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; cl04104 580332000435 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 580332000436 active site 580332000437 HIGH motif; other site 580332000438 KMSK motif region; other site 580332000439 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 580332000440 tRNA binding surface [nucleotide binding]; other site 580332000441 anticodon binding site; other site 580332000442 Sporulation related domain; Region: SPOR; cl10051 580332000443 DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol...; Region: DsbA_DsbA; cd03019 580332000444 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 580332000445 catalytic residues [active] 580332000446 hinge region; other site 580332000447 alpha helical domain; other site 580332000448 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 580332000449 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332000450 NAD(P) binding site [chemical binding]; other site 580332000451 active site 580332000452 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 580332000453 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including...; Region: Rieske_cytochrome_bc1; cd03470 580332000454 [2Fe-2S] cluster binding site [ion binding]; other site 580332000455 cytochrome b; Provisional; Region: CYTB; MTH00119 580332000456 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cd00284 580332000457 Qi binding site; other site 580332000458 intrachain domain interface; other site 580332000459 interchain domain interface [polypeptide binding]; other site 580332000460 heme bH binding site [chemical binding]; other site 580332000461 heme bL binding site [chemical binding]; other site 580332000462 Qo binding site; other site 580332000463 Cytochrome b(C-terminus)/b6/petD: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: cytochrome_b_C; cd00290 580332000464 interchain domain interface [polypeptide binding]; other site 580332000465 intrachain domain interface; other site 580332000466 Qi binding site; other site 580332000467 Qo binding site; other site 580332000468 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 580332000469 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 580332000470 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 580332000471 GatB domain; Region: GatB_Yqey; cl11497 580332000472 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 580332000473 Amidase; Region: Amidase; cl11426 580332000474 Glu-tRNAGln amidotransferase C subunit; Region: Glu-tRNAGln; cl00495 580332000475 rod shape-determining protein MreB; Provisional; Region: PRK13927 580332000476 Cell division protein FtsA; Region: FtsA; cl11496 580332000477 rod shape-determining protein MreC; Region: mreC; TIGR00219 580332000478 rod shape-determining protein MreC; Region: MreC; pfam04085 580332000479 rod shape-determining protein MreD; Region: MreD; cl01087 580332000480 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 580332000481 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 580332000482 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 580332000483 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 580332000484 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 580332000485 Sporulation related domain; Region: SPOR; cl10051 580332000486 Protein of unknown function (DUF1304); Region: DUF1304; cl01533 580332000487 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 580332000488 active site residue [active] 580332000489 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 580332000490 active site residue [active] 580332000491 PUA domain; Region: PUA; cl00607 580332000492 23S rRNA m(5)C1962 methyltransferase; Provisional; Region: PRK15128 580332000493 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 580332000494 S-adenosylmethionine binding site [chemical binding]; other site 580332000495 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 580332000496 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 580332000497 active site 580332000498 Int/Topo IB signature motif; other site 580332000499 GAF domain; Region: GAF; cl15785 580332000500 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 580332000501 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 580332000502 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 580332000503 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332000504 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 580332000505 Predicted membrane protein (DUF2339); Region: DUF2339; pfam10101 580332000506 Bacterial ABC transporter protein EcsB; Region: EcsB; cl11542 580332000507 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 580332000508 Histidine kinase; Region: HisKA_3; pfam07730 580332000509 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 580332000510 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 580332000511 active site 580332000512 phosphorylation site [posttranslational modification] 580332000513 intermolecular recognition site; other site 580332000514 dimerization interface [polypeptide binding]; other site 580332000515 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 580332000516 DNA binding residues [nucleotide binding] 580332000517 dimerization interface [polypeptide binding]; other site 580332000518 Nitrate and nitrite sensing; Region: NIT; pfam08376 580332000519 ANTAR domain; Region: ANTAR; cl04297 580332000520 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 580332000521 NMT1-like family; Region: NMT1_2; cl15260 580332000522 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 580332000523 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 580332000524 dimer interface [polypeptide binding]; other site 580332000525 conserved gate region; other site 580332000526 putative PBP binding loops; other site 580332000527 ABC-ATPase subunit interface; other site 580332000528 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 580332000529 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 580332000530 Walker A/P-loop; other site 580332000531 ATP binding site [chemical binding]; other site 580332000532 Q-loop/lid; other site 580332000533 ABC transporter signature motif; other site 580332000534 Walker B; other site 580332000535 D-loop; other site 580332000536 H-loop/switch region; other site 580332000537 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 580332000538 nitrate transport ATP-binding subunits C and D; Region: ntrCD; TIGR01184 580332000539 Walker A/P-loop; other site 580332000540 ATP binding site [chemical binding]; other site 580332000541 Q-loop/lid; other site 580332000542 ABC transporter signature motif; other site 580332000543 Walker B; other site 580332000544 D-loop; other site 580332000545 H-loop/switch region; other site 580332000546 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 580332000547 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 580332000548 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 580332000549 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 580332000550 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 580332000551 Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain...; Region: Rieske_NirD_small_Bacillus; cd03530 580332000552 [2Fe-2S] cluster binding site [ion binding]; other site 580332000553 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_Nitrate-R-NapA-like; cd02754 580332000554 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 580332000555 [4Fe-4S] binding site [ion binding]; other site 580332000556 molybdopterin cofactor binding site; other site 580332000557 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 580332000558 molybdopterin cofactor binding site; other site 580332000559 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 580332000560 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 580332000561 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; cl02930 580332000562 plasma-membrane proton-efflux P-type ATPase; Region: ATPase-IIIA_H; TIGR01647 580332000563 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 580332000564 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 580332000565 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 580332000566 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 580332000567 lytic murein transglycosylase; Provisional; Region: PRK11619 580332000568 lytic murein transglycosylase; Provisional; Region: PRK11619 580332000569 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 580332000570 N-acetyl-D-glucosamine binding site [chemical binding]; other site 580332000571 catalytic residue [active] 580332000572 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 580332000573 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 580332000574 active site 580332000575 NTP binding site [chemical binding]; other site 580332000576 metal binding triad [ion binding]; metal-binding site 580332000577 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 580332000578 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 580332000579 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 580332000580 putative active site [active] 580332000581 Uncharacterized conserved protein [Function unknown]; Region: COG1565 580332000582 Putative S-adenosyl-L-methionine-dependent methyltransferase; Region: Methyltransf_28; pfam02636 580332000583 pteridine reductase; Provisional; Region: PRK09135 580332000584 pteridine reductase (PR), classical (c) SDRs; Region: PR_SDR_c; cd05357 580332000585 NADP binding site [chemical binding]; other site 580332000586 substrate binding pocket [chemical binding]; other site 580332000587 active site 580332000588 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 580332000589 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 580332000590 Ligand Binding Site [chemical binding]; other site 580332000591 Domain of unknown function (DUF386); Region: DUF386; cl01047 580332000592 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 580332000593 putative protease; Provisional; Region: PRK15452 580332000594 Peptidase family U32; Region: Peptidase_U32; cl03113 580332000595 Methylenetetrahydrofolate reductase; Region: MTHFR; pfam02219 580332000596 Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase...; Region: MTHFR; cd00537 580332000597 FAD binding site [chemical binding]; other site 580332000598 Membrane protein of unknown function; Region: DUF360; cl00850 580332000599 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 580332000600 S-adenosyl-L-homocysteine hydrolase (AdoHycase) catalyzes the hydrolysis of S-adenosyl-L-homocysteine (AdoHyc) to form adenosine (Ado) and homocysteine (Hcy). The equilibrium lies far on the side of AdoHyc synthesis, but in nature the removal of Ado and...; Region: AdoHcyase; cd00401 580332000601 oligomerization interface [polypeptide binding]; other site 580332000602 active site 580332000603 NAD+ binding site [chemical binding]; other site 580332000604 S-adenosylmethionine synthetase; Validated; Region: PRK05250 580332000605 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 580332000606 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 580332000607 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 580332000608 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 580332000609 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 580332000610 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 580332000611 putative acyl-acceptor binding pocket; other site 580332000612 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 580332000613 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 580332000614 putative acyl-acceptor binding pocket; other site 580332000615 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 580332000616 putative active site [active] 580332000617 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 580332000618 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 580332000619 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 4) [Cell envelope biogenesis, outer membrane]; Region: DacB; COG2027 580332000620 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 580332000621 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK06943 580332000622 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 580332000623 inhibitor-cofactor binding pocket; inhibition site 580332000624 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332000625 catalytic residue [active] 580332000626 atypical (a) SDRs, subgroup 8; Region: SDR_a8; cd05242 580332000627 TIGR01777 family protein; Region: yfcH 580332000628 putative NAD(P) binding site [chemical binding]; other site 580332000629 putative active site [active] 580332000630 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 580332000631 oligomerisation interface [polypeptide binding]; other site 580332000632 mobile loop; other site 580332000633 roof hairpin; other site 580332000634 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 580332000635 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 580332000636 ring oligomerisation interface [polypeptide binding]; other site 580332000637 ATP/Mg binding site [chemical binding]; other site 580332000638 stacking interactions; other site 580332000639 hinge regions; other site 580332000640 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 580332000641 non-specific DNA binding site [nucleotide binding]; other site 580332000642 Predicted transcriptional regulator [Transcription]; Region: COG2932 580332000643 salt bridge; other site 580332000644 sequence-specific DNA binding site [nucleotide binding]; other site 580332000645 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 580332000646 Catalytic site [active] 580332000647 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 580332000648 putative transposase OrfB; Reviewed; Region: PHA02517 580332000649 Integrase core domain; Region: rve; cl01316 580332000650 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 580332000651 AAA domain; Region: AAA_22; pfam13401 580332000652 RT_Bac_retron_I: 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_I; cd01646 580332000653 putative active site [active] 580332000654 putative NTP binding site [chemical binding]; other site 580332000655 putative nucleic acid binding site [nucleotide binding]; other site 580332000656 Replication protein A C terminal; Region: RPA_C; pfam08784 580332000657 ASC-1 homology domain, ASC-1-like subfamily. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain...; Region: ASCH_ASC-1_like; cd06554 580332000658 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 580332000659 IHF - DNA interface [nucleotide binding]; other site 580332000660 IHF dimer interface [polypeptide binding]; other site 580332000661 Protein of unknown function (DUF1018); Region: DUF1018; cl01815 580332000662 Mor transcription activator family; Region: Mor; cl02360 580332000663 Protein of unknown function (DUF4063); Region: DUF4063; pfam13272 580332000664 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 580332000665 N-acetyl-D-glucosamine binding site [chemical binding]; other site 580332000666 catalytic residue [active] 580332000667 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 580332000668 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1223 580332000669 Protein of unknown function (DUF1804); Region: DUF1804; pfam08822 580332000670 Phage-related terminase [General function prediction only]; Region: COG5362; cl02216 580332000671 Mu-like prophage protein gp29 [Function unknown]; Region: COG4383 580332000672 Protein of unknown function (DUF935); Region: DUF935; pfam06074 580332000673 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 580332000674 Phage virion morphogenesis family; Region: Phage_tail_S; cl02089 580332000675 Mu-like prophage I protein [General function prediction only]; Region: COG4388 580332000676 Mu-like prophage I protein; Region: Mu-like_Pro; pfam10123 580332000677 Mu-like prophage major head subunit gpT; Region: Mu-like_gpT; cl01826 580332000678 Mu-like prophage major head subunit gpT; Region: Mu-like_gpT; cl01826 580332000679 Phage protein (N4 Gp49/phage Sf6 gene 66) family; Region: Phage_gp49_66; cl10351 580332000680 Protein of unknown function (DUF1320); Region: DUF1320; cl01818 580332000681 Domain of unknown function (DUF1834); Region: DUF1834; cl02087 580332000682 Protein of unknown function (DUF2635); Region: DUF2635; pfam10948 580332000683 Mu-like prophage tail sheath protein gpL [General function prediction only]; Region: COG4386 580332000684 Phage tail sheath protein; Region: Phage_sheath_1; cl01389 580332000685 Phage tail sheath protein; Region: Phage_sheath_1; cl01389 580332000686 Phage-related minor tail protein; Region: PhageMin_Tail; pfam10145 580332000687 Mu-like prophage DNA circulation protein [General function prediction only]; Region: COG4228 580332000688 DNA circulation protein N-terminus; Region: DNA_circ_N; pfam07157 580332000689 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 580332000690 Bacteriophage Mu Gp45 protein; Region: Phage_Mu_Gp45; cl15410 580332000691 Phage protein GP46; Region: GP46; cl01814 580332000692 Baseplate J-like protein; Region: Baseplate_J; cl01294 580332000693 Uncharacterized protein conserved in bacteria (DUF2313); Region: DUF2313; cl01542 580332000694 Domain of unknown function (DUF4376); Region: DUF4376; pfam14301 580332000695 Mu-like prophage protein Com; Region: Mu-like_Com; cl11540 580332000696 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332000697 CHASE2 domain; Region: CHASE2; cl01732 580332000698 Predicted transmembrane sensor domain [Signal transduction mechanisms]; Region: COG4252 580332000699 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 580332000700 cyclase homology domain; Region: CHD; cd07302 580332000701 nucleotidyl binding site; other site 580332000702 metal binding site [ion binding]; metal-binding site 580332000703 dimer interface [polypeptide binding]; other site 580332000704 haloacid dehalogenase-like hydrolase family protein; Region: PLN02919 580332000705 NHL repeat; Region: NHL; pfam01436 580332000706 Fibronectin type 3 domain-containing protein [General function prediction only]; Region: COG3401 580332000707 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cl00065 580332000708 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 580332000709 TPR motif; other site 580332000710 TPR repeat; Region: TPR_11; pfam13414 580332000711 binding surface 580332000712 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 580332000713 binding surface 580332000714 TPR motif; other site 580332000715 Tetratricopeptide repeat; Region: TPR_6; pfam13174 580332000716 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 580332000717 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 580332000718 tRNA; other site 580332000719 putative tRNA binding site [nucleotide binding]; other site 580332000720 putative NADP binding site [chemical binding]; other site 580332000721 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 580332000722 peptide chain release factor 1; Validated; Region: prfA; PRK00591 580332000723 RF-1 domain; Region: RF-1; cl02875 580332000724 RF-1 domain; Region: RF-1; cl02875 580332000725 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 580332000726 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 580332000727 S-adenosylmethionine binding site [chemical binding]; other site 580332000728 argininosuccinate lyase; Provisional; Region: PRK00855 580332000729 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 580332000730 active sites [active] 580332000731 tetramer interface [polypeptide binding]; other site 580332000732 Histidine kinase; Region: His_kinase; pfam06580 580332000733 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 580332000734 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 580332000735 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 580332000736 active site 580332000737 phosphorylation site [posttranslational modification] 580332000738 intermolecular recognition site; other site 580332000739 dimerization interface [polypeptide binding]; other site 580332000740 LytTr DNA-binding domain; Region: LytTR; cl04498 580332000741 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 580332000742 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 580332000743 active site 580332000744 phosphorylation site [posttranslational modification] 580332000745 intermolecular recognition site; other site 580332000746 dimerization interface [polypeptide binding]; other site 580332000747 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 580332000748 DNA binding site [nucleotide binding] 580332000749 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 580332000750 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 580332000751 dimer interface [polypeptide binding]; other site 580332000752 phosphorylation site [posttranslational modification] 580332000753 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 580332000754 ATP binding site [chemical binding]; other site 580332000755 Mg2+ binding site [ion binding]; other site 580332000756 G-X-G motif; other site 580332000757 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 580332000758 Phosphoenolpyruvate carboxylase; Region: PEPcase; cl14656 580332000759 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 580332000760 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 580332000761 domain interfaces; other site 580332000762 active site 580332000763 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 580332000764 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 580332000765 active site 580332000766 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 580332000767 Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]; Region: HemY; COG3071 580332000768 HemY protein N-terminus; Region: HemY_N; pfam07219 580332000769 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 580332000770 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 580332000771 catalytic motif [active] 580332000772 Catalytic residue [active] 580332000773 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 580332000774 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 580332000775 catalytic loop [active] 580332000776 iron binding site [ion binding]; other site 580332000777 NAD(P)H dependent flavin oxidoreductases use flavin as a substrate in mediating electron transfer from iron complexes or iron proteins. Structurally similar to ferredoxin reductases, but with only 15% sequence identity, flavin reductases reduce FAD, FMN; Region: flavin_oxioreductase; cd06189 580332000778 FAD binding pocket [chemical binding]; other site 580332000779 FAD binding motif [chemical binding]; other site 580332000780 phosphate binding motif [ion binding]; other site 580332000781 beta-alpha-beta structure motif; other site 580332000782 NAD binding pocket [chemical binding]; other site 580332000783 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 580332000784 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 580332000785 putative NAD(P) binding site [chemical binding]; other site 580332000786 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 580332000787 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 580332000788 synthetase active site [active] 580332000789 NTP binding site [chemical binding]; other site 580332000790 metal binding site [ion binding]; metal-binding site 580332000791 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 580332000792 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 580332000793 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 580332000794 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 580332000795 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 580332000796 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 580332000797 glutamine binding [chemical binding]; other site 580332000798 catalytic triad [active] 580332000799 anthranilate synthase component I; Provisional; Region: PRK13565 580332000800 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 580332000801 chorismate binding enzyme; Region: Chorismate_bind; cl10555 580332000802 phosphoglycolate phosphatase; Provisional; Region: PRK13222 580332000803 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 580332000804 motif II; other site 580332000805 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 580332000806 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 580332000807 substrate binding site [chemical binding]; other site 580332000808 hexamer interface [polypeptide binding]; other site 580332000809 metal binding site [ion binding]; metal-binding site 580332000810 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 580332000811 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 580332000812 dimer interface [polypeptide binding]; other site 580332000813 phosphorylation site [posttranslational modification] 580332000814 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 580332000815 ATP binding site [chemical binding]; other site 580332000816 Mg2+ binding site [ion binding]; other site 580332000817 G-X-G motif; other site 580332000818 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 580332000819 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 580332000820 active site 580332000821 ATP binding site [chemical binding]; other site 580332000822 substrate binding site [chemical binding]; other site 580332000823 activation loop (A-loop); other site 580332000824 Response regulator receiver domain; Region: Response_reg; pfam00072 580332000825 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 580332000826 active site 580332000827 phosphorylation site [posttranslational modification] 580332000828 intermolecular recognition site; other site 580332000829 dimerization interface [polypeptide binding]; other site 580332000830 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 580332000831 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 580332000832 active site 580332000833 phosphorylation site [posttranslational modification] 580332000834 intermolecular recognition site; other site 580332000835 dimerization interface [polypeptide binding]; other site 580332000836 Protein of unknown function (DUF525); Region: DUF525; cl01119 580332000837 Membrane-bound lytic murein transglycosylase [Cell envelope biogenesis, outer membrane]; Region: MltA; COG2821 580332000838 MltA specific insert domain; Region: MltA; cl08398 580332000839 3D domain; Region: 3D; cl01439 580332000840 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 580332000841 active site residue [active] 580332000842 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 580332000843 ligand binding site [chemical binding]; other site 580332000844 flexible hinge region; other site 580332000845 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 580332000846 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 580332000847 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 580332000848 dimerization domain [polypeptide binding]; other site 580332000849 dimer interface [polypeptide binding]; other site 580332000850 catalytic residues [active] 580332000851 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332000852 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 580332000853 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 580332000854 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 580332000855 FMN binding site [chemical binding]; other site 580332000856 active site 580332000857 catalytic residues [active] 580332000858 substrate binding site [chemical binding]; other site 580332000859 Helix-turn-helix domains; Region: HTH; cl00088 580332000860 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 580332000861 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 580332000862 purine monophosphate binding site [chemical binding]; other site 580332000863 dimer interface [polypeptide binding]; other site 580332000864 putative catalytic residues [active] 580332000865 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 580332000866 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 580332000867 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 580332000868 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 580332000869 ATP-grasp domain; Region: ATP-grasp_4; cl03087 580332000870 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 580332000871 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 580332000872 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl00433 580332000873 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 580332000874 S-adenosylmethionine binding site [chemical binding]; other site 580332000875 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332000876 Zn2+ binding site [ion binding]; other site 580332000877 Mg2+ binding site [ion binding]; other site 580332000878 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 580332000879 S-adenosylmethionine binding site [chemical binding]; other site 580332000880 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 580332000881 Helix-turn-helix domains; Region: HTH; cl00088 580332000882 The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_OxyR; cd08411 580332000883 dimerization interface [polypeptide binding]; other site 580332000884 Rubrerythrin, ferritin-like diiron-binding domain; Region: Rubrerythrin; cd01041 580332000885 Ferritin-like domain; Region: Ferritin; pfam00210 580332000886 binuclear metal center [ion binding]; other site 580332000887 CitB domain protein; Region: CitB; TIGR02484 580332000888 sn-glycerol-3-phosphate dehydrogenase subunit C; Provisional; Region: glpC; PRK11168 580332000889 Cysteine-rich domain; Region: CCG; pfam02754 580332000890 Protein of unknown function (DUF3501); Region: DUF3501; pfam12007 580332000891 Ferritin-like domain; Region: Ferritin; pfam00210 580332000892 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 580332000893 dimerization interface [polypeptide binding]; other site 580332000894 DPS ferroxidase diiron center [ion binding]; other site 580332000895 ion pore; other site 580332000896 NnrS protein; Region: NnrS; cl01258 580332000897 UbiA prenyltransferase family; Region: UbiA; cl00337 580332000898 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 580332000899 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 580332000900 generic binding surface II; other site 580332000901 ssDNA binding site; other site 580332000902 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 580332000903 ATP binding site [chemical binding]; other site 580332000904 putative Mg++ binding site [ion binding]; other site 580332000905 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 580332000906 nucleotide binding region [chemical binding]; other site 580332000907 ATP-binding site [chemical binding]; other site 580332000908 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 580332000909 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 580332000910 active site 580332000911 ATP binding site [chemical binding]; other site 580332000912 substrate binding site [chemical binding]; other site 580332000913 activation loop (A-loop); other site 580332000914 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 580332000915 ligand binding site [chemical binding]; other site 580332000916 flexible hinge region; other site 580332000917 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 580332000918 homotrimer interaction site [polypeptide binding]; other site 580332000919 putative active site [active] 580332000920 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 580332000921 Catalytic domain of Protein Kinases; Region: PKc; cd00180 580332000922 active site 580332000923 ATP binding site [chemical binding]; other site 580332000924 substrate binding site [chemical binding]; other site 580332000925 activation loop (A-loop); other site 580332000926 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 580332000927 ligand binding site [chemical binding]; other site 580332000928 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 580332000929 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 580332000930 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 580332000931 putative active site [active] 580332000932 GtrA-like protein; Region: GtrA; cl00971 580332000933 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 580332000934 Sialidases or neuraminidases function to bind and hydrolyze terminal sialic acid residues from various glycoconjugates as well as playing roles in pathogenesis, bacterial nutrition and cellular interactions. They have a six-bladed, beta-propeller fold...; Region: Sialidase; cl01922 580332000935 BNR repeat-like domain; Region: BNR_2; pfam13088 580332000936 metabolite-proton symporter; Region: 2A0106; TIGR00883 580332000937 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 580332000938 putative substrate translocation pore; other site 580332000939 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 580332000940 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 580332000941 substrate binding pocket [chemical binding]; other site 580332000942 chain length determination region; other site 580332000943 substrate-Mg2+ binding site; other site 580332000944 catalytic residues [active] 580332000945 aspartate-rich region 1; other site 580332000946 active site lid residues [active] 580332000947 aspartate-rich region 2; other site 580332000948 sensory histidine kinase AtoS; Provisional; Region: PRK11360 580332000949 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 580332000950 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 580332000951 PAS domain; Region: PAS_9; pfam13426 580332000952 putative active site [active] 580332000953 heme pocket [chemical binding]; other site 580332000954 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332000955 metal binding site [ion binding]; metal-binding site 580332000956 active site 580332000957 I-site; other site 580332000958 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 580332000959 Survival protein SurE; Region: SurE; cl00448 580332000960 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 580332000961 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 580332000962 S-adenosylmethionine binding site [chemical binding]; other site 580332000963 lipoprotein NlpD; Provisional; Region: nlpD; PRK10871 580332000964 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 580332000965 putative peptidoglycan binding site; other site 580332000966 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 580332000967 FeS/SAM binding site; other site 580332000968 Sodium:solute symporter family; Region: SSF; cl00456 580332000969 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 580332000970 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 580332000971 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 580332000972 active site 580332000973 phosphorylation site [posttranslational modification] 580332000974 intermolecular recognition site; other site 580332000975 dimerization interface [polypeptide binding]; other site 580332000976 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 580332000977 DNA binding site [nucleotide binding] 580332000978 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 580332000979 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 580332000980 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 580332000981 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 580332000982 dimer interface [polypeptide binding]; other site 580332000983 phosphorylation site [posttranslational modification] 580332000984 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 580332000985 ATP binding site [chemical binding]; other site 580332000986 Mg2+ binding site [ion binding]; other site 580332000987 G-X-G motif; other site 580332000988 Protein of unknown function (DUF3683); Region: DUF3683; pfam12447 580332000989 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 580332000990 FAD binding domain; Region: FAD_binding_4; pfam01565 580332000991 FAD linked oxidases, C-terminal domain; Region: FAD-oxidase_C; pfam02913 580332000992 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 580332000993 Cysteine-rich domain; Region: CCG; pfam02754 580332000994 Domain of unknown function (DUF3400); Region: DUF3400; pfam11880 580332000995 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 580332000996 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 580332000997 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 580332000998 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 580332000999 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 580332001000 putative ATP binding site [chemical binding]; other site 580332001001 putative substrate interface [chemical binding]; other site 580332001002 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 580332001003 active site 580332001004 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR6; cd08272 580332001005 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 580332001006 putative NAD(P) binding site [chemical binding]; other site 580332001007 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 580332001008 Tetramer interface [polypeptide binding]; other site 580332001009 active site 580332001010 FMN-binding site [chemical binding]; other site 580332001011 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 580332001012 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl15769 580332001013 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl15769 580332001014 Putative Zn-dependent protease [General function prediction only]; Region: COG4784 580332001015 Peptidase family M48; Region: Peptidase_M48; cl12018 580332001016 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 580332001017 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and...; Region: DHNA_DHNTPE; cd00534 580332001018 homooctamer interface [polypeptide binding]; other site 580332001019 active site 580332001020 Glycerol-3-phosphate acyltransferase; Region: G3P_acyltransf; cl00410 580332001021 UGMP family protein; Validated; Region: PRK09604 580332001022 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 580332001023 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 580332001024 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 580332001025 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 580332001026 FeS/SAM binding site; other site 580332001027 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK09185 580332001028 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 580332001029 dimer interface [polypeptide binding]; other site 580332001030 active site 580332001031 Beta-ketoacyl synthase, N-terminal domain; Region: Ketoacyl-synt_2; pfam13723 580332001032 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 580332001033 active site 2 [active] 580332001034 active site 1 [active] 580332001035 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 580332001036 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332001037 NAD(P) binding site [chemical binding]; other site 580332001038 active site 580332001039 Phosphopantetheine attachment site; Region: PP-binding; cl09936 580332001040 Phosphopantetheine attachment site; Region: PP-binding; cl09936 580332001041 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK09185 580332001042 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 580332001043 active site 580332001044 benzoate 1,2-dioxygenase, large subunit; Region: benzo_1_2_benA; TIGR03229 580332001045 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK06816 580332001046 'initiating' condensing enzymes are a subclass of decarboxylating condensing enzymes, including beta-ketoacyl [ACP] synthase, type III and polyketide synthases, type III, which include chalcone synthase and related enzymes. They are characterized by the...; Region: init_cond_enzymes; cd00827 580332001047 dimer interface [polypeptide binding]; other site 580332001048 active site 580332001049 A predicted NlpC/p60-like peptidase; Region: BtrH; pfam14399 580332001050 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 580332001051 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 580332001052 S-adenosylmethionine binding site [chemical binding]; other site 580332001053 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332001054 Predicted membrane protein [Function unknown]; Region: COG4648 580332001055 O-succinylbenzoic acid--CoA ligase; Provisional; Region: PRK07824 580332001056 AMP-binding enzyme; Region: AMP-binding; cl15778 580332001057 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 580332001058 active site 2 [active] 580332001059 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 580332001060 putative acyl-acceptor binding pocket; other site 580332001061 Predicted exporter [General function prediction only]; Region: COG4258 580332001062 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 580332001063 Phospholipid methyltransferase; Region: PEMT; cl00763 580332001064 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_5; cd06153 580332001065 homotrimer interaction site [polypeptide binding]; other site 580332001066 putative active site [active] 580332001067 MltA-interacting protein MipA; Region: MipA; cl01504 580332001068 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 580332001069 putative acyl-acceptor binding pocket; other site 580332001070 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 580332001071 Ligand binding site; other site 580332001072 Putative Catalytic site; other site 580332001073 DXD motif; other site 580332001074 Fe-S oxidoreductase [Energy production and conversion]; Region: COG1032 580332001075 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 580332001076 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 580332001077 FeS/SAM binding site; other site 580332001078 integron integrase; Region: integrase_gron; TIGR02249 580332001079 IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains. This CD includes integrases which are components of multiresistant integrons and mediate recombination between a proximal attI site and...; Region: INT_IntI; cd01193 580332001080 Int/Topo IB signature motif; other site 580332001081 Protein of unknown function (DUF497); Region: DUF497; cl01108 580332001082 Domain of unknown function (DUF4415); Region: DUF4415; cl01401 580332001083 Putative addiction module component; Region: Unstab_antitox; cl09921 580332001084 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 580332001085 active site 580332001086 aminodeoxychorismate synthase subunit I; Provisional; Region: pabB; PRK15465 580332001087 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 580332001088 chorismate binding enzyme; Region: Chorismate_bind; cl10555 580332001089 Uncharacterized conserved protein [Function unknown]; Region: COG1656; cl09136 580332001090 Protein of unknown function DUF82; Region: DUF82; pfam01927 580332001091 Protein of unknown function (DUF2905); Region: DUF2905; pfam11146 580332001092 carbonyl reductase sniffer-like, classical (c) SDRs; Region: carb_red_sniffer_like_SDR_c; cd05325 580332001093 NADP binding site [chemical binding]; other site 580332001094 homodimer interface [polypeptide binding]; other site 580332001095 active site 580332001096 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 580332001097 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 580332001098 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 580332001099 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 580332001100 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard...; Region: 6PGL; cd01400 580332001101 putative active site [active] 580332001102 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332001103 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK12490 580332001104 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 580332001105 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 580332001106 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 580332001107 Glycoside hydrolase family 15, N-terminal domain; Region: GH15_N; cd07430 580332001108 Domain interface; other site 580332001109 glucan 1,4-alpha-glucosidase; Region: glucan_glucosid; TIGR01535 580332001110 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 580332001111 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 580332001112 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional; Region: PRK11092 580332001113 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 580332001114 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 580332001115 synthetase active site [active] 580332001116 NTP binding site [chemical binding]; other site 580332001117 metal binding site [ion binding]; metal-binding site 580332001118 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 580332001119 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 580332001120 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 580332001121 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 580332001122 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 580332001123 catalytic site [active] 580332001124 G-X2-G-X-G-K; other site 580332001125 hypothetical protein; Provisional; Region: PRK11820 580332001126 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 580332001127 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 580332001128 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 580332001129 active site 580332001130 ribonuclease PH; Reviewed; Region: rph; PRK00173 580332001131 Ribonuclease PH; Region: RNase_PH_bact; cd11362 580332001132 hexamer interface [polypeptide binding]; other site 580332001133 active site 580332001134 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 580332001135 active site 580332001136 dimerization interface [polypeptide binding]; other site 580332001137 coproporphyrinogen III oxidase; Provisional; Region: PRK08898 580332001138 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 580332001139 FeS/SAM binding site; other site 580332001140 HemN C-terminal domain; Region: HemN_C; pfam06969 580332001141 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 580332001142 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 580332001143 ThiS interaction site; other site 580332001144 putative active site [active] 580332001145 tetramer interface [polypeptide binding]; other site 580332001146 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 580332001147 thiS-thiF/thiG interaction site; other site 580332001148 Cytochrome cbb3 oxidase subunit I. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction...; Region: cbb3_Oxidase_I; cd01661 580332001149 Low-spin heme binding site [chemical binding]; other site 580332001150 Putative water exit pathway; other site 580332001151 Binuclear center (active site) [active] 580332001152 Putative proton exit pathway; other site 580332001153 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 580332001154 Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2...; Region: cbb3_Oxidase_CcoQ; cl00282 580332001155 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 580332001156 Cytochrome c; Region: Cytochrom_C; cl11414 580332001157 Cytochrome c; Region: Cytochrom_C; cl11414 580332001158 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 580332001159 4Fe-4S binding domain; Region: Fer4_5; pfam12801 580332001160 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 580332001161 FixH; Region: FixH; cl01254 580332001162 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor...; Region: Ribosomal_L24e_L24; cl00909 580332001163 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 580332001164 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 580332001165 metal-binding site [ion binding] 580332001166 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 580332001167 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 580332001168 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; cl01253 580332001169 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 580332001170 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 580332001171 ligand binding site [chemical binding]; other site 580332001172 flexible hinge region; other site 580332001173 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 580332001174 putative switch regulator; other site 580332001175 non-specific DNA interactions [nucleotide binding]; other site 580332001176 DNA binding site [nucleotide binding] 580332001177 sequence specific DNA binding site [nucleotide binding]; other site 580332001178 putative cAMP binding site [chemical binding]; other site 580332001179 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 580332001180 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 580332001181 FeS/SAM binding site; other site 580332001182 HemN C-terminal domain; Region: HemN_C; pfam06969 580332001183 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 580332001184 FMN binding site [chemical binding]; other site 580332001185 substrate binding site [chemical binding]; other site 580332001186 putative catalytic residue [active] 580332001187 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 580332001188 AsmA-like C-terminal region; Region: AsmA_2; cl15864 580332001189 A/G-specific adenine glycosylase; Region: mutY; TIGR01084 580332001190 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 580332001191 minor groove reading motif; other site 580332001192 helix-hairpin-helix signature motif; other site 580332001193 substrate binding pocket [chemical binding]; other site 580332001194 active site 580332001195 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 580332001196 DNA glycosylase (MutY in bacteria and hMYH in humans) is responsible for repairing misread A*oxoG residues to C*G by removing the inappropriately paired adenine base from the DNA backbone. It belongs to the Nudix hydrolase superfamily and is important...; Region: DNA_Glycosylase_C; cd03431 580332001197 DNA binding and oxoG recognition site [nucleotide binding] 580332001198 aromatic acid decarboxylase; Validated; Region: PRK05920 580332001199 Flavoprotein; Region: Flavoprotein; cl08021 580332001200 Heptaprenyl diphosphate synthase component I; Region: Hpre_diP_synt_I; cl01973 580332001201 NGN-insert domain found between N-terminal domain (D1) and C-terminal KOW domain (DIII) repeats of some N-Utilization Substance G (NusG) N-terminal (NGN); Region: NGN-insert_like; cd09910 580332001202 P-loop ATPase protein family; Region: ATP_bind_2; cl15794 580332001203 Predicted P-loop-containing kinase [General function prediction only]; Region: COG1660 580332001204 HPr kinase/phosphorylase; Provisional; Region: PRK05428 580332001205 DRTGG domain; Region: DRTGG; cl12147 580332001206 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 580332001207 Hpr binding site; other site 580332001208 active site 580332001209 homohexamer subunit interaction site [polypeptide binding]; other site 580332001210 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 580332001211 active site 580332001212 phosphorylation site [posttranslational modification] 580332001213 RaiA ('ribosome-associated inhibitor A', also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site; Region: RaiA; cd00552 580332001214 30S subunit binding site; other site 580332001215 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 580332001216 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 580332001217 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 580332001218 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 580332001219 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 580332001220 The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids. The genes yhbG and yhbN are located in a single operon and may function together in...; Region: ABC_YhbG; cd03218 580332001221 Walker A/P-loop; other site 580332001222 ATP binding site [chemical binding]; other site 580332001223 Q-loop/lid; other site 580332001224 ABC transporter signature motif; other site 580332001225 Walker B; other site 580332001226 D-loop; other site 580332001227 H-loop/switch region; other site 580332001228 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1934 580332001229 OstA-like protein; Region: OstA; cl00844 580332001230 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 580332001231 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 580332001232 Low specificity phosphatase (HAD superfamily) [General function prediction only]; Region: COG1778 580332001233 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 580332001234 active site 580332001235 motif I; other site 580332001236 motif II; other site 580332001237 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 580332001238 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 580332001239 putative active site [active] 580332001240 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with KpsF/GutQ domains in the API [A5P (D-arabinose 5-phosphate) isomerase] protein. These APIs catalyze the conversion of the pentose pathway...; Region: CBS_pair_KpsF_GutQ_assoc; cd04604 580332001241 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 580332001242 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 580332001243 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 580332001244 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332001245 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 580332001246 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 580332001247 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 580332001248 ATP binding site [chemical binding]; other site 580332001249 Mg2+ binding site [ion binding]; other site 580332001250 G-X-G motif; other site 580332001251 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 580332001252 ATP binding site [chemical binding]; other site 580332001253 putative Mg++ binding site [ion binding]; other site 580332001254 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 580332001255 putative active site [active] 580332001256 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 580332001257 nucleotide binding region [chemical binding]; other site 580332001258 ATP-binding site [chemical binding]; other site 580332001259 Helicase associated domain (HA2); Region: HA2; cl04503 580332001260 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 580332001261 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 580332001262 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332001263 Predicted dehydrogenase [General function prediction only]; Region: COG0579 580332001264 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 580332001265 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 580332001266 dimer interface [polypeptide binding]; other site 580332001267 active site 580332001268 Phosphopantetheine attachment site; Region: PP-binding; cl09936 580332001269 Esterase/lipase [General function prediction only]; Region: COG1647 580332001270 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 580332001271 Malic enzyme, N-terminal domain; Region: malic; pfam00390 580332001272 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 580332001273 putative NAD(P) binding site [chemical binding]; other site 580332001274 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 580332001275 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 580332001276 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 580332001277 active site 580332001278 nucleophile elbow; other site 580332001279 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 580332001280 Helix-turn-helix domains; Region: HTH; cl00088 580332001281 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 580332001282 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 580332001283 Type III pantothenate kinase; Region: Pan_kinase; cl09130 580332001284 Sporulation related domain; Region: SPOR; cl10051 580332001285 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 580332001286 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 580332001287 TRAM domain; Region: TRAM; cl01282 580332001288 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 580332001289 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332001290 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 580332001291 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 580332001292 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in...; Region: CBS_pair_CorC_HlyC_assoc; cd04590 580332001293 Transporter associated domain; Region: CorC_HlyC; cl08393 580332001294 lysophospholipid transporter LplT; Provisional; Region: PRK11195 580332001295 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 580332001296 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 580332001297 RNA binding surface [nucleotide binding]; other site 580332001298 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 580332001299 active site 580332001300 MarC family integral membrane protein; Region: MarC; cl00919 580332001301 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 580332001302 ligand binding site [chemical binding]; other site 580332001303 flexible hinge region; other site 580332001304 apolipoprotein N-acyltransferase; Region: lnt; TIGR00546 580332001305 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 580332001306 putative active site [active] 580332001307 catalytic triad [active] 580332001308 putative dimer interface [polypeptide binding]; other site 580332001309 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 580332001310 GIY-YIG motif/motif A; other site 580332001311 putative active site [active] 580332001312 putative metal binding site [ion binding]; other site 580332001313 Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes and in arabidopsis. It is responsible for the...; Region: GlyRS_alpha_core; cd00733 580332001314 dimer interface [polypeptide binding]; other site 580332001315 motif 1; other site 580332001316 active site 580332001317 motif 2; other site 580332001318 motif 3; other site 580332001319 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 580332001320 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 580332001321 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 580332001322 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 580332001323 active site 580332001324 motif I; other site 580332001325 motif II; other site 580332001326 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 580332001327 putative acyl-acceptor binding pocket; other site 580332001328 Protein of unknown function DUF45; Region: DUF45; cl00636 580332001329 Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate in...; Region: Frataxin; cd00503 580332001330 putative iron binding site [ion binding]; other site 580332001331 Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate in...; Region: Frataxin; cl00238 580332001332 putative iron binding site [ion binding]; other site 580332001333 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 580332001334 catalytic motif [active] 580332001335 Catalytic residue [active] 580332001336 diaminopimelate decarboxylase; Region: lysA; TIGR01048 580332001337 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 580332001338 active site 580332001339 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 580332001340 substrate binding site [chemical binding]; other site 580332001341 catalytic residues [active] 580332001342 dimer interface [polypeptide binding]; other site 580332001343 HDOD domain; Region: HDOD; pfam08668 580332001344 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 580332001345 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 580332001346 PAS fold; Region: PAS_3; pfam08447 580332001347 putative active site [active] 580332001348 heme pocket [chemical binding]; other site 580332001349 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332001350 metal binding site [ion binding]; metal-binding site 580332001351 active site 580332001352 I-site; other site 580332001353 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 580332001354 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 580332001355 MgtE intracellular N domain; Region: MgtE_N; cl15244 580332001356 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 580332001357 Divalent cation transporter; Region: MgtE; cl00786 580332001358 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 580332001359 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 580332001360 Transglycosylase; Region: Transgly; cl07896 580332001361 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 580332001362 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 580332001363 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 580332001364 shikimate binding site; other site 580332001365 NAD(P) binding site [chemical binding]; other site 580332001366 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 580332001367 dimerization interface [polypeptide binding]; other site 580332001368 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 580332001369 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 580332001370 ATP binding site [chemical binding]; other site 580332001371 Mg2+ binding site [ion binding]; other site 580332001372 G-X-G motif; other site 580332001373 osmolarity response regulator; Provisional; Region: ompR; PRK09468 580332001374 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 580332001375 active site 580332001376 phosphorylation site [posttranslational modification] 580332001377 intermolecular recognition site; other site 580332001378 dimerization interface [polypeptide binding]; other site 580332001379 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 580332001380 DNA binding site [nucleotide binding] 580332001381 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cl01482 580332001382 Type II secretion system (T2SS), protein N; Region: T2SN; pfam01203 580332001383 Type II secretion system (T2SS), protein M; Region: T2SM; cl01222 580332001384 Type II secretion system (T2SS), protein L; Region: T2SL; pfam05134 580332001385 GspL periplasmic domain; Region: GspL_C; cl14909 580332001386 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 580332001387 general secretion pathway protein J; Region: gspJ; TIGR01711 580332001388 Type II secretion system (T2SS), protein J; Region: T2SJ; pfam11612 580332001389 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 580332001390 general secretion pathway protein H; Region: typeII_sec_gspH; TIGR01708 580332001391 general secretion pathway protein G; Region: typeII_sec_gspG; TIGR01710 580332001392 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 580332001393 general secretion pathway protein F; Region: GspF; TIGR02120 580332001394 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 580332001395 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 580332001396 general secretory pathway protein E; Region: type_II_gspE; TIGR02533 580332001397 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 580332001398 Walker A motif; other site 580332001399 ATP binding site [chemical binding]; other site 580332001400 Walker B motif; other site 580332001401 general secretion pathway protein D; Region: type_II_gspD; TIGR02517 580332001402 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 580332001403 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 580332001404 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 580332001405 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 580332001406 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; cl00462 580332001407 Periplasmic binding protein TroA_c. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a...; Region: TroA_c; cd01145 580332001408 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 580332001409 putative ligand binding site [chemical binding]; other site 580332001410 haloacid dehalogenase-like hydrolase family protein; Region: PLN02919 580332001411 Gram-negative bacterial tonB protein; Region: TonB; cl10048 580332001412 This domain is the catalytic domain of ribonuclease II; Region: RNB; smart00955 580332001413 RNB domain; Region: RNB; pfam00773 580332001414 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl08302 580332001415 EF-hand domain pair; Region: EF_hand_5; pfam13499 580332001416 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl08302 580332001417 transaldolase/EF-hand domain-containing protein; Provisional; Region: PRK12309 580332001418 Secreted protein acidic and rich in cysteine Ca binding region; Region: SPARC_Ca_bdg; pfam10591 580332001419 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl08302 580332001420 Cytochrome c; Region: Cytochrom_C; cl11414 580332001421 Transcriptional regulator; Region: Transcrip_reg; cl00361 580332001422 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cd00529 580332001423 active site 580332001424 putative DNA-binding cleft [nucleotide binding]; other site 580332001425 dimer interface [polypeptide binding]; other site 580332001426 UbiA prenyltransferase family; Region: UbiA; cl00337 580332001427 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 580332001428 RuvA N terminal domain; Region: RuvA_N; pfam01330 580332001429 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 580332001430 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 580332001431 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 580332001432 Walker A motif; other site 580332001433 ATP binding site [chemical binding]; other site 580332001434 Walker B motif; other site 580332001435 arginine finger; other site 580332001436 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 580332001437 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 580332001438 active site 580332001439 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 580332001440 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 580332001441 Gram-negative bacterial tonB protein; Region: TonB; cl10048 580332001442 translocation protein TolB; Provisional; Region: tolB; PRK02889 580332001443 TolB amino-terminal domain; Region: TolB_N; cl00639 580332001444 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 580332001445 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 580332001446 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 580332001447 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 580332001448 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 580332001449 ligand binding site [chemical binding]; other site 580332001450 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 580332001451 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 580332001452 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, clostridial; Region: rSAM_QueE_Clost; TIGR03963 580332001453 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 580332001454 FeS/SAM binding site; other site 580332001455 ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In...; Region: ExsB; cd01995 580332001456 Ligand Binding Site [chemical binding]; other site 580332001457 Ferredoxin [Energy production and conversion]; Region: COG1146 580332001458 4Fe-4S binding domain; Region: Fer4; cl02805 580332001459 4Fe-4S binding domain; Region: Fer4; cl02805 580332001460 putative bacillithiol system oxidoreductase, YpdA family; Region: Bthiol_YpdA; TIGR04018 580332001461 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 580332001462 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 580332001463 ATP-grasp domain; Region: ATP-grasp_4; cl03087 580332001464 CoA-ligase; Region: Ligase_CoA; cl02894 580332001465 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 580332001466 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332001467 CoA-ligase; Region: Ligase_CoA; cl02894 580332001468 Integral membrane protein TerC family; Region: TerC; cl10468 580332001469 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 580332001470 Ligand Binding Site [chemical binding]; other site 580332001471 Predicted transmembrane sensor domain [Signal transduction mechanisms]; Region: COG4252 580332001472 CHASE2 domain; Region: CHASE2; cl01732 580332001473 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 580332001474 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 580332001475 active site 580332001476 ATP binding site [chemical binding]; other site 580332001477 substrate binding site [chemical binding]; other site 580332001478 activation loop (A-loop); other site 580332001479 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 580332001480 active site 580332001481 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 580332001482 phosphopeptide binding site; other site 580332001483 CHASE2 domain; Region: CHASE2; cl01732 580332001484 Adenylyl- / guanylyl cyclase, catalytic domain; Region: CYCc; smart00044 580332001485 cyclase homology domain; Region: CHD; cd07302 580332001486 nucleotidyl binding site; other site 580332001487 metal binding site [ion binding]; metal-binding site 580332001488 dimer interface [polypeptide binding]; other site 580332001489 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 580332001490 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 580332001491 ligand binding site [chemical binding]; other site 580332001492 flexible hinge region; other site 580332001493 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 580332001494 active site residue [active] 580332001495 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 580332001496 GAF domain; Region: GAF; cl15785 580332001497 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 580332001498 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 580332001499 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332001500 Walker A motif; other site 580332001501 ATP binding site [chemical binding]; other site 580332001502 Walker B motif; other site 580332001503 GAF domain; Region: GAF_2; pfam13185 580332001504 GAF domain; Region: GAF; cl15785 580332001505 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 580332001506 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332001507 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 580332001508 Pilin (bacterial filament); Region: Pilin; pfam00114 580332001509 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 580332001510 binding surface 580332001511 TPR repeat; Region: TPR_11; pfam13414 580332001512 TPR motif; other site 580332001513 Flagellar transcriptional activator (FlhD); Region: FlhD; cl05012 580332001514 Flagellar transcriptional activator (FlhC); Region: FlhC; cl05036 580332001515 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 580332001516 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 580332001517 flagellar motor protein MotB; Validated; Region: motB; PRK09041 580332001518 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 580332001519 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 580332001520 ligand binding site [chemical binding]; other site 580332001521 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: VicK; COG5002 580332001522 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 580332001523 dimerization interface [polypeptide binding]; other site 580332001524 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 580332001525 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332001526 dimer interface [polypeptide binding]; other site 580332001527 putative CheW interface [polypeptide binding]; other site 580332001528 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 580332001529 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 580332001530 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332001531 dimer interface [polypeptide binding]; other site 580332001532 putative CheW interface [polypeptide binding]; other site 580332001533 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 580332001534 PAS domain; Region: PAS_9; pfam13426 580332001535 putative active site [active] 580332001536 heme pocket [chemical binding]; other site 580332001537 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 580332001538 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332001539 dimer interface [polypeptide binding]; other site 580332001540 putative CheW interface [polypeptide binding]; other site 580332001541 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 580332001542 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 580332001543 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 580332001544 active site 580332001545 phosphorylation site [posttranslational modification] 580332001546 intermolecular recognition site; other site 580332001547 dimerization interface [polypeptide binding]; other site 580332001548 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 580332001549 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 580332001550 active site 580332001551 phosphorylation site [posttranslational modification] 580332001552 intermolecular recognition site; other site 580332001553 dimerization interface [polypeptide binding]; other site 580332001554 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 580332001555 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 580332001556 active site 580332001557 phosphorylation site [posttranslational modification] 580332001558 intermolecular recognition site; other site 580332001559 dimerization interface [polypeptide binding]; other site 580332001560 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 580332001561 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 580332001562 putative binding surface; other site 580332001563 active site 580332001564 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 580332001565 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 580332001566 ATP binding site [chemical binding]; other site 580332001567 Mg2+ binding site [ion binding]; other site 580332001568 G-X-G motif; other site 580332001569 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 580332001570 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332001571 dimer interface [polypeptide binding]; other site 580332001572 putative CheW interface [polypeptide binding]; other site 580332001573 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 580332001574 chemotaxis methyltransferase CheR; Provisional; Region: PRK10611 580332001575 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 580332001576 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332001577 CheB methylesterase; Region: CheB_methylest; pfam01339 580332001578 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 580332001579 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 580332001580 flagellar biosynthesis protein FlhA; Validated; Region: flhA; cl07980 580332001581 FHIPEP family; Region: FHIPEP; pfam00771 580332001582 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK06995 580332001583 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332001584 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 580332001585 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332001586 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332001587 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 580332001588 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 580332001589 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 580332001590 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 580332001591 DNA binding residues [nucleotide binding] 580332001592 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 580332001593 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 580332001594 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 580332001595 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 580332001596 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 580332001597 ligand binding site [chemical binding]; other site 580332001598 FlgN protein; Region: FlgN; cl09176 580332001599 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 580332001600 SAF domain; Region: SAF; cl00555 580332001601 SAF-like; Region: SAF_2; pfam13144 580332001602 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 580332001603 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 580332001604 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 580332001605 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 580332001606 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 580332001607 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 580332001608 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 580332001609 FlgD Ig-like domain; Region: FlgD_ig; cl15790 580332001610 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 580332001611 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 580332001612 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 580332001613 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 580332001614 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 580332001615 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 580332001616 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 580332001617 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 580332001618 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 580332001619 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 580332001620 Flagellar L-ring protein; Region: FlgH; cl00905 580332001621 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 580332001622 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 580332001623 flagellar rod assembly protein/muramidase FlgJ; Validated; Region: flgJ; PRK05684 580332001624 Rod binding protein; Region: Rod-binding; cl01626 580332001625 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 580332001626 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 580332001627 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 580332001628 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 580332001629 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 580332001630 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 580332001631 TPR repeat; Region: TPR_11; pfam13414 580332001632 binding surface 580332001633 TPR motif; other site 580332001634 TPR repeat; Region: TPR_11; pfam13414 580332001635 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 580332001636 binding surface 580332001637 TPR motif; other site 580332001638 TPR repeat; Region: TPR_11; pfam13414 580332001639 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 580332001640 ADP-heptose:LPS heptosyltransferase II; Provisional; Region: PRK10916; cl15782 580332001641 ABC-2 type transporter; Region: ABC2_membrane; cl11417 580332001642 ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system; Region: PQQ_ABC_ATP; TIGR03864 580332001643 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332001644 Walker A/P-loop; other site 580332001645 ATP binding site [chemical binding]; other site 580332001646 Q-loop/lid; other site 580332001647 ABC transporter signature motif; other site 580332001648 Walker B; other site 580332001649 D-loop; other site 580332001650 H-loop/switch region; other site 580332001651 Uncharacterized protein conserved in bacteria (DUF2252); Region: DUF2252; cl12088 580332001652 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 580332001653 TPR motif; other site 580332001654 binding surface 580332001655 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 580332001656 binding surface 580332001657 TPR motif; other site 580332001658 Predicted methyltransferase (contains TPR repeat) [General function prediction only]; Region: COG4976 580332001659 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 580332001660 S-adenosylmethionine binding site [chemical binding]; other site 580332001661 SCP-2 sterol transfer family; Region: SCP2; cl01225 580332001662 Peptidase family U32; Region: Peptidase_U32; cl03113 580332001663 Peptidase family U32; Region: Peptidase_U32; cl03113 580332001664 Response regulator receiver domain; Region: Response_reg; pfam00072 580332001665 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 580332001666 active site 580332001667 phosphorylation site [posttranslational modification] 580332001668 intermolecular recognition site; other site 580332001669 dimerization interface [polypeptide binding]; other site 580332001670 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 580332001671 Response regulator receiver domain; Region: Response_reg; pfam00072 580332001672 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 580332001673 active site 580332001674 phosphorylation site [posttranslational modification] 580332001675 intermolecular recognition site; other site 580332001676 dimerization interface [polypeptide binding]; other site 580332001677 PAS fold; Region: PAS_4; pfam08448 580332001678 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 580332001679 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 580332001680 dimer interface [polypeptide binding]; other site 580332001681 phosphorylation site [posttranslational modification] 580332001682 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 580332001683 ATP binding site [chemical binding]; other site 580332001684 Mg2+ binding site [ion binding]; other site 580332001685 G-X-G motif; other site 580332001686 Response regulator receiver domain; Region: Response_reg; pfam00072 580332001687 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 580332001688 active site 580332001689 phosphorylation site [posttranslational modification] 580332001690 intermolecular recognition site; other site 580332001691 dimerization interface [polypeptide binding]; other site 580332001692 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 580332001693 putative binding surface; other site 580332001694 active site 580332001695 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 580332001696 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 580332001697 FliP family; Region: FliP; cl00593 580332001698 Flagellar biosynthesis protein, FliO; Region: FliO; cl01247 580332001699 flagellar motor switch protein; Validated; Region: fliN; PRK05698 580332001700 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 580332001701 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 580332001702 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 580332001703 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 580332001704 Flagellar hook-length control protein FliK; Region: Flg_hook; cl15269 580332001705 flagellar export protein FliJ; Region: flagell_FliJ; TIGR02473 580332001706 flagellar biosynthesis chaperone; Validated; Region: fliJ; cl09161 580332001707 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 580332001708 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 580332001709 Walker A motif/ATP binding site; other site 580332001710 Walker B motif; other site 580332001711 Flagellar assembly protein FliH; Region: FliH; pfam02108 580332001712 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 580332001713 FliG C-terminal domain; Region: FliG_C; pfam01706 580332001714 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 580332001715 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 580332001716 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 580332001717 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 580332001718 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 580332001719 binding surface 580332001720 TPR motif; other site 580332001721 TPR repeat; Region: TPR_11; pfam13414 580332001722 TPR repeat; Region: TPR_11; pfam13414 580332001723 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 580332001724 binding surface 580332001725 TPR motif; other site 580332001726 TPR repeat; Region: TPR_11; pfam13414 580332001727 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 580332001728 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 580332001729 binding surface 580332001730 TPR motif; other site 580332001731 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 580332001732 binding surface 580332001733 TPR motif; other site 580332001734 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 580332001735 binding surface 580332001736 TPR motif; other site 580332001737 TPR repeat; Region: TPR_11; pfam13414 580332001738 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 580332001739 binding surface 580332001740 TPR motif; other site 580332001741 Predicted methyltransferase (contains TPR repeat) [General function prediction only]; Region: COG4976 580332001742 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 580332001743 S-adenosylmethionine binding site [chemical binding]; other site 580332001744 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332001745 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 580332001746 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 580332001747 inhibitor-cofactor binding pocket; inhibition site 580332001748 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332001749 catalytic residue [active] 580332001750 WbqC-like protein family; Region: WbqC; pfam08889 580332001751 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332001752 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 580332001753 Putative Acyltransferase (AT), Left-handed parallel beta-Helix (LbH) domain; This group is composed of mostly uncharacterized proteins containing an N-terminal helical subdomain followed by a LbH domain. The alignment contains 6 turns, each containing...; Region: LbH_AT_putative; cd03360 580332001754 putative trimer interface [polypeptide binding]; other site 580332001755 putative CoA binding site [chemical binding]; other site 580332001756 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332001757 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 580332001758 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 580332001759 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 580332001760 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 580332001761 active site 580332001762 Glycosyltransferase like family; Region: Glyco_tranf_2_5; pfam13712 580332001763 TPR repeat; Region: TPR_11; pfam13414 580332001764 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 580332001765 binding surface 580332001766 TPR motif; other site 580332001767 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 580332001768 binding surface 580332001769 TPR motif; other site 580332001770 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 580332001771 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 580332001772 binding surface 580332001773 TPR motif; other site 580332001774 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 580332001775 binding surface 580332001776 TPR motif; other site 580332001777 Flagellar regulator YcgR; Region: YcgR; pfam07317 580332001778 PilZ domain; Region: PilZ; cl01260 580332001779 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 580332001780 Flagellar hook-length control protein FliK; Region: Flg_hook; cl15269 580332001781 Flagellar protein FliT; Region: FliT; cl05125 580332001782 Flagellar protein FliS; Region: FliS; cl00654 580332001783 flagellar capping protein; Reviewed; Region: fliD; PRK08032 580332001784 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 580332001785 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 580332001786 FlaG protein; Region: FlaG; cl00591 580332001787 flagellin; Provisional; Region: PRK12802 580332001788 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 580332001789 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 580332001790 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 580332001791 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332001792 metal binding site [ion binding]; metal-binding site 580332001793 active site 580332001794 I-site; other site 580332001795 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 580332001796 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 580332001797 active site 580332001798 phosphorylation site [posttranslational modification] 580332001799 intermolecular recognition site; other site 580332001800 dimerization interface [polypeptide binding]; other site 580332001801 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 580332001802 DNA binding residues [nucleotide binding] 580332001803 dimerization interface [polypeptide binding]; other site 580332001804 hypothetical protein; Provisional; Region: PRK13560 580332001805 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 580332001806 heme pocket [chemical binding]; other site 580332001807 putative active site [active] 580332001808 Histidine kinase; Region: HisKA_3; pfam07730 580332001809 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 580332001810 ATP binding site [chemical binding]; other site 580332001811 Mg2+ binding site [ion binding]; other site 580332001812 G-X-G motif; other site 580332001813 histidinol-phosphate aminotransferase; Region: hisC; TIGR01141 580332001814 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 580332001815 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332001816 homodimer interface [polypeptide binding]; other site 580332001817 catalytic residue [active] 580332001818 imidazoleglycerol-phosphate dehydratase; Validated; Region: hisB; PRK00951 580332001819 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 580332001820 putative active site pocket [active] 580332001821 4-fold oligomerization interface [polypeptide binding]; other site 580332001822 metal binding residues [ion binding]; metal-binding site 580332001823 3-fold/trimer interface [polypeptide binding]; other site 580332001824 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 580332001825 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 580332001826 putative active site [active] 580332001827 oxyanion strand; other site 580332001828 catalytic triad [active] 580332001829 HisA. Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1...; Region: HisA; cd04732 580332001830 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 580332001831 catalytic residues [active] 580332001832 The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)...; Region: HisF; cd04731 580332001833 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 580332001834 substrate binding site [chemical binding]; other site 580332001835 glutamase interaction surface [polypeptide binding]; other site 580332001836 Phosphoribosyl-AMP cyclohydrolase; Region: PRA-CH; cl00344 580332001837 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 580332001838 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 580332001839 nucleotide binding site/active site [active] 580332001840 HIT family signature motif; other site 580332001841 catalytic residue [active] 580332001842 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 580332001843 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 580332001844 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 580332001845 periplasmic serine pepetdase DegS; Region: protease_degS; TIGR02038 580332001846 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 580332001847 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 580332001848 protein binding site [polypeptide binding]; other site 580332001849 Uncharacterized conserved protein [Function unknown]; Region: COG0327 580332001850 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 580332001851 MgtC family; Region: MgtC; pfam02308 580332001852 Predicted transcriptional regulators [Transcription]; Region: COG1510 580332001853 Helix-turn-helix domains; Region: HTH; cl00088 580332001854 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cd08168 580332001855 heme-binding residues [chemical binding]; other site 580332001856 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 580332001857 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 580332001858 molybdopterin cofactor binding site; other site 580332001859 The MopB_CT_PHLH CD includes a group of related uncharacterized putative hydrogenase-like homologs (PHLH) of molybdopterin binding proteins. This CD is of the PHLH region homologous to the conserved molybdopterin-binding C-terminal (MopB_CT) region...; Region: MopB_CT_PHLH; cd02784 580332001860 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 580332001861 Polysulphide reductase, NrfD; Region: NrfD; cl01295 580332001862 Protein of unknown function (DUF3341); Region: DUF3341; pfam11821 580332001863 Cytochrome c; Region: Cytochrom_C; cl11414 580332001864 Polysulphide reductase, NrfD; Region: NrfD; cl01295 580332001865 stringent starvation protein A; Provisional; Region: sspA; PRK09481 580332001866 GST_N family, Stringent starvation protein A (SspA) subfamily; SspA is a RNA polymerase (RNAP)-associated protein required for the lytic development of phage P1 and for stationary phase-induced acid tolerance of E. coli. It is implicated in survival...; Region: GST_N_SspA; cd03059 580332001867 C-terminal domain interface [polypeptide binding]; other site 580332001868 putative GSH binding site (G-site) [chemical binding]; other site 580332001869 dimer interface [polypeptide binding]; other site 580332001870 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 580332001871 dimer interface [polypeptide binding]; other site 580332001872 N-terminal domain interface [polypeptide binding]; other site 580332001873 Stringent starvation protein B; Region: SspB; cl01120 580332001874 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 580332001875 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 580332001876 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 580332001877 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 580332001878 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 580332001879 Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl...; Region: SHMT; cd00378 580332001880 dimer interface [polypeptide binding]; other site 580332001881 active site 580332001882 glycine-pyridoxal phosphate binding site [chemical binding]; other site 580332001883 folate binding site [chemical binding]; other site 580332001884 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 580332001885 ATP cone domain; Region: ATP-cone; pfam03477 580332001886 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 580332001887 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 580332001888 catalytic motif [active] 580332001889 Zn binding site [ion binding]; other site 580332001890 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cl00161 580332001891 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 580332001892 Lumazine binding domain; Region: Lum_binding; pfam00677 580332001893 Lumazine binding domain; Region: Lum_binding; pfam00677 580332001894 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 580332001895 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 580332001896 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cl00522 580332001897 dimerization interface [polypeptide binding]; other site 580332001898 active site 580332001899 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 580332001900 homopentamer interface [polypeptide binding]; other site 580332001901 active site 580332001902 Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus...; Region: Terminator_NusB; cd00619 580332001903 putative RNA binding site [nucleotide binding]; other site 580332001904 thiamine monophosphate kinase; Provisional; Region: PRK05731 580332001905 ThiL (Thiamine-monophosphate kinase) plays a dual role in de novo biosynthesis and in salvage of exogenous thiamine. Thiamine salvage occurs in two steps, with thiamine kinase catalyzing the formation of thiamine phosphate, and ThiL catalyzing the...; Region: ThiL; cd02194 580332001906 ATP binding site [chemical binding]; other site 580332001907 dimerization interface [polypeptide binding]; other site 580332001908 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 580332001909 tetramer interfaces [polypeptide binding]; other site 580332001910 binuclear metal-binding site [ion binding]; other site 580332001911 Staphylococcal nuclease homologues; Region: SNc; smart00318 580332001912 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cd00175 580332001913 Catalytic site; other site 580332001914 Excalibur calcium-binding domain; Region: Excalibur; cl05460 580332001915 Helix-turn-helix domains; Region: HTH; cl00088 580332001916 Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing...; Region: OYE_YqiM_FMN; cd02932 580332001917 active site 580332001918 FMN binding site [chemical binding]; other site 580332001919 substrate binding site [chemical binding]; other site 580332001920 homotetramer interface [polypeptide binding]; other site 580332001921 catalytic residue [active] 580332001922 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 580332001923 PAS domain S-box; Region: sensory_box; TIGR00229 580332001924 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 580332001925 putative active site [active] 580332001926 heme pocket [chemical binding]; other site 580332001927 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 580332001928 PAS domain; Region: PAS_9; pfam13426 580332001929 putative active site [active] 580332001930 heme pocket [chemical binding]; other site 580332001931 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332001932 metal binding site [ion binding]; metal-binding site 580332001933 active site 580332001934 I-site; other site 580332001935 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 580332001936 Protein of unknown function (DUF3820); Region: DUF3820; cl01411 580332001937 Protein of unknown function DUF45; Region: DUF45; cl00636 580332001938 Domain of unknown function (DUF4156); Region: DUF4156; pfam13698 580332001939 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 580332001940 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 580332001941 ATP binding site [chemical binding]; other site 580332001942 Mg++ binding site [ion binding]; other site 580332001943 motif III; other site 580332001944 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 580332001945 nucleotide binding region [chemical binding]; other site 580332001946 ATP-binding site [chemical binding]; other site 580332001947 DbpA RNA binding domain; Region: DbpA; pfam03880 580332001948 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 580332001949 putative active site [active] 580332001950 putative metal binding site [ion binding]; other site 580332001951 peptidyl-prolyl cis-trans isomerase B (rotamase B); Provisional; Region: PRK10791 580332001952 cyclophilin_EcCYP_like: cyclophilin-type A-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to the cytosolic E. coli cyclophilin A and Streptomyces antibioticus SanCyp18. Compared to the archetypal cyclophilin Human cyclophilin A, these...; Region: cyclophilin_EcCYP_like; cd01920 580332001953 substrate binding site [chemical binding]; other site 580332001954 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 580332001955 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 580332001956 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 580332001957 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 580332001958 TPR motif; other site 580332001959 binding surface 580332001960 TPR repeat; Region: TPR_11; pfam13414 580332001961 TPR repeat; Region: TPR_11; pfam13414 580332001962 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 580332001963 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 580332001964 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 580332001965 active site 580332001966 HIGH motif; other site 580332001967 nucleotide binding site [chemical binding]; other site 580332001968 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 580332001969 KMSKS motif; other site 580332001970 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 580332001971 Predicted membrane protein [Function unknown]; Region: COG3671 580332001972 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 580332001973 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 580332001974 active site 580332001975 HIGH motif; other site 580332001976 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 580332001977 KMSKS motif; other site 580332001978 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 580332001979 tRNA binding surface [nucleotide binding]; other site 580332001980 anticodon binding site; other site 580332001981 Uncharacterized conserved protein [Function unknown]; Region: COG1656; cl09136 580332001982 Protein of unknown function (DUF433); Region: DUF433; cl01030 580332001983 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 580332001984 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 580332001985 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 580332001986 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 580332001987 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 580332001988 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 580332001989 Walker A motif; other site 580332001990 ATP binding site [chemical binding]; other site 580332001991 Walker B motif; other site 580332001992 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 580332001993 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 580332001994 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 580332001995 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 580332001996 Walker A motif; other site 580332001997 ATP binding site [chemical binding]; other site 580332001998 Walker B motif; other site 580332001999 arginine finger; other site 580332002000 Uncharacterized protein conserved in bacteria [Function unknown]; Region: DamX; COG3266 580332002001 Sporulation related domain; Region: SPOR; cl10051 580332002002 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 580332002003 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 580332002004 active site 580332002005 phosphorylation site [posttranslational modification] 580332002006 intermolecular recognition site; other site 580332002007 dimerization interface [polypeptide binding]; other site 580332002008 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 580332002009 Walker A motif; other site 580332002010 ATP binding site [chemical binding]; other site 580332002011 Walker B motif; other site 580332002012 arginine finger; other site 580332002013 Helix-turn-helix domains; Region: HTH; cl00088 580332002014 putative ABC transporter ATP-binding protein YrbF; Provisional; Region: PRK11831 580332002015 ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex...; Region: ABC_Org_Solvent_Resistant; cd03261 580332002016 Walker A/P-loop; other site 580332002017 ATP binding site [chemical binding]; other site 580332002018 Q-loop/lid; other site 580332002019 ABC transporter signature motif; other site 580332002020 Walker B; other site 580332002021 D-loop; other site 580332002022 H-loop/switch region; other site 580332002023 Permease; Region: Permease; cl00510 580332002024 mce related protein; Region: MCE; pfam02470 580332002025 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; cl01074 580332002026 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 580332002027 anti sigma factor interaction site; other site 580332002028 regulatory phosphorylation site [posttranslational modification]; other site 580332002029 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 580332002030 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 580332002031 hinge; other site 580332002032 active site 580332002033 ATP phosphoribosyltransferase; Region: HisG; cl15266 580332002034 Histidinol dehydrogenase, HisD, E.C 1.1.1.23. Histidinol dehydrogenase catalyzes the last two steps in the L-histidine biosynthesis pathway, which is conserved in bacteria, archaea, fungi, and plants. These last two steps are (i) the NAD-dependent...; Region: Histidinol_dh; cd06572 580332002035 histidinol dehydrogenase; Region: hisD; TIGR00069 580332002036 NAD binding site [chemical binding]; other site 580332002037 dimerization interface [polypeptide binding]; other site 580332002038 product binding site; other site 580332002039 substrate binding site [chemical binding]; other site 580332002040 zinc binding site [ion binding]; other site 580332002041 catalytic residues [active] 580332002042 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 580332002043 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 580332002044 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 580332002045 EamA-like transporter family; Region: EamA; cl01037 580332002046 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 580332002047 Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable...; Region: Rieske_RO_Alpha_N; cd03469 580332002048 [2Fe-2S] cluster binding site [ion binding]; other site 580332002049 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 580332002050 alpha subunit interface [polypeptide binding]; other site 580332002051 active site 580332002052 substrate binding site [chemical binding]; other site 580332002053 Fe binding site [ion binding]; other site 580332002054 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 580332002055 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 580332002056 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 580332002057 substrate binding pocket [chemical binding]; other site 580332002058 chain length determination region; other site 580332002059 substrate-Mg2+ binding site; other site 580332002060 catalytic residues [active] 580332002061 aspartate-rich region 1; other site 580332002062 active site lid residues [active] 580332002063 aspartate-rich region 2; other site 580332002064 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 580332002065 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 580332002066 TPP-binding site; other site 580332002067 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 580332002068 PYR/PP interface [polypeptide binding]; other site 580332002069 dimer interface [polypeptide binding]; other site 580332002070 TPP binding site [chemical binding]; other site 580332002071 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 580332002072 Type I GTP cyclohydrolase folE2; Region: GCHY-1; cl00642 580332002073 heat shock protein 90; Provisional; Region: PRK05218 580332002074 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 580332002075 ATP binding site [chemical binding]; other site 580332002076 Mg2+ binding site [ion binding]; other site 580332002077 G-X-G motif; other site 580332002078 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 580332002079 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 580332002080 catalytic triad [active] 580332002081 Ferredoxin [Energy production and conversion]; Region: COG1146 580332002082 4Fe-4S binding domain; Region: Fer4; cl02805 580332002083 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 580332002084 Inactivated superfamily I helicase [DNA replication, recombination, and repair]; Region: COG3893 580332002085 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 580332002086 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 580332002087 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332002088 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 580332002089 putative heme binding pocket [chemical binding]; other site 580332002090 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 580332002091 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 580332002092 Coenzyme A binding pocket [chemical binding]; other site 580332002093 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 580332002094 CoenzymeA binding site [chemical binding]; other site 580332002095 subunit interaction site [polypeptide binding]; other site 580332002096 PHB binding site; other site 580332002097 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 580332002098 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 580332002099 IHF dimer interface [polypeptide binding]; other site 580332002100 IHF - DNA interface [nucleotide binding]; other site 580332002101 ABC-2 type transporter; Region: ABC2_membrane; cl11417 580332002102 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 580332002103 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332002104 Walker A/P-loop; other site 580332002105 ATP binding site [chemical binding]; other site 580332002106 Q-loop/lid; other site 580332002107 ABC transporter signature motif; other site 580332002108 Walker B; other site 580332002109 D-loop; other site 580332002110 H-loop/switch region; other site 580332002111 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 580332002112 Protein of unknown function (DUF493); Region: DUF493; cl01102 580332002113 D-Alanine aminotransferase (D-AAT_like): D-amino acid aminotransferase catalyzes transamination between D-amino acids and their respective alpha-keto acids. It plays a major role in the synthesis of bacterial cell wall components like D-alanine and...; Region: D-AAT_like; cd01558 580332002114 homodimer interface [polypeptide binding]; other site 580332002115 substrate-cofactor binding pocket; other site 580332002116 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332002117 catalytic residue [active] 580332002118 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 580332002119 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 580332002120 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; cl06814 580332002121 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 580332002122 5-bromo-4-chloroindolyl phosphate hydrolysis protein; Region: Halogen_Hydrol; cl02059 580332002123 HDOD domain; Region: HDOD; pfam08668 580332002124 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 580332002125 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 580332002126 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 580332002127 active site 580332002128 phosphorylation site [posttranslational modification] 580332002129 intermolecular recognition site; other site 580332002130 dimerization interface [polypeptide binding]; other site 580332002131 Helix-turn-helix domains; Region: HTH; cl00088 580332002132 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 580332002133 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 580332002134 dimer interface [polypeptide binding]; other site 580332002135 phosphorylation site [posttranslational modification] 580332002136 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 580332002137 ATP binding site [chemical binding]; other site 580332002138 G-X-G motif; other site 580332002139 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 580332002140 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 580332002141 N-terminal plug; other site 580332002142 ligand-binding site [chemical binding]; other site 580332002143 Protein of unknown function (DUF461); Region: DUF461; cl01071 580332002144 Protein of unknown function (DUF461); Region: DUF461; cl01071 580332002145 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 580332002146 alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins; Region: alpha-crystallin-Hsps_p23-like; cl00175 580332002147 AAK_NAGK-C: N-Acetyl-L-glutamate kinase - cyclic (NAGK-C) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in some bacteria and photosynthetic organisms using the...; Region: AAK_NAGK-C; cd04250 580332002148 feedback inhibition sensing region; other site 580332002149 homohexameric interface [polypeptide binding]; other site 580332002150 carbamate kinase; Reviewed; Region: PRK12686 580332002151 nucleotide binding site [chemical binding]; other site 580332002152 N-acetyl-L-glutamate binding site [chemical binding]; other site 580332002153 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 580332002154 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 580332002155 motif II; other site 580332002156 division inhibitor protein; Provisional; Region: slmA; PRK09480 580332002157 Helix-turn-helix domains; Region: HTH; cl00088 580332002158 3-deoxy-7-phosphoheptulonate synthase; Reviewed; Region: PRK08673 580332002159 NeuB family; Region: NeuB; cl00496 580332002160 2-isopropylmalate synthase; Validated; Region: PRK00915 580332002161 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 580332002162 active site 580332002163 catalytic residues [active] 580332002164 metal binding site [ion binding]; metal-binding site 580332002165 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 580332002166 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 580332002167 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 580332002168 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 580332002169 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 580332002170 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 580332002171 catalytic residues [active] 580332002172 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 580332002173 N-acetyl-D-glucosamine binding site [chemical binding]; other site 580332002174 catalytic residue [active] 580332002175 prolyl-tRNA synthetase; Provisional; Region: PRK09194 580332002176 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of...; Region: ProRS_core_prok; cd00779 580332002177 dimer interface [polypeptide binding]; other site 580332002178 motif 1; other site 580332002179 active site 580332002180 motif 2; other site 580332002181 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 580332002182 putative deacylase active site [active] 580332002183 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it attaches...; Region: class_II_aaRS-like_core; cl00268 580332002184 active site 580332002185 motif 3; other site 580332002186 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 580332002187 anticodon binding site; other site 580332002188 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant...; Region: Ap4A_hydrolase_plant_like; cd03671 580332002189 putative active site [active] 580332002190 Ap4A binding site [chemical binding]; other site 580332002191 nudix motif; other site 580332002192 putative metal binding site [ion binding]; other site 580332002193 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 580332002194 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 580332002195 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 580332002196 trimer interface [polypeptide binding]; other site 580332002197 active site 580332002198 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 580332002199 Flavoprotein; Region: Flavoprotein; cl08021 580332002200 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 580332002201 hypothetical protein; Reviewed; Region: PRK00024 580332002202 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 580332002203 MPN+ (JAMM) motif; other site 580332002204 Zinc-binding site [ion binding]; other site 580332002205 elongation factor Tu; Reviewed; Region: PRK00049 580332002206 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 580332002207 G1 box; other site 580332002208 GEF interaction site [polypeptide binding]; other site 580332002209 GTP/Mg2+ binding site [chemical binding]; other site 580332002210 Switch I region; other site 580332002211 G2 box; other site 580332002212 G3 box; other site 580332002213 Switch II region; other site 580332002214 G4 box; other site 580332002215 G5 box; other site 580332002216 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 580332002217 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 580332002218 Antibiotic Binding Site [chemical binding]; other site 580332002219 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 580332002220 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 580332002221 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 580332002222 putative homodimer interface [polypeptide binding]; other site 580332002223 KOW motif; Region: KOW; cl00354 580332002224 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 580332002225 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 580332002226 23S rRNA interface [nucleotide binding]; other site 580332002227 L7/L12 interface [polypeptide binding]; other site 580332002228 putative thiostrepton binding site; other site 580332002229 L25 interface [polypeptide binding]; other site 580332002230 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 580332002231 mRNA/rRNA interface [nucleotide binding]; other site 580332002232 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 580332002233 23S rRNA interface [nucleotide binding]; other site 580332002234 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 580332002235 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 580332002236 core dimer interface [polypeptide binding]; other site 580332002237 L10 interface [polypeptide binding]; other site 580332002238 L11 interface [polypeptide binding]; other site 580332002239 putative EF-Tu interaction site [polypeptide binding]; other site 580332002240 putative EF-G interaction site [polypeptide binding]; other site 580332002241 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl04593 580332002242 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 580332002243 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 580332002244 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 580332002245 RPB12 interaction site [polypeptide binding]; other site 580332002246 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl04593 580332002247 RPB11 interaction site [polypeptide binding]; other site 580332002248 RPB12 interaction site [polypeptide binding]; other site 580332002249 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 580332002250 RPB3 interaction site [polypeptide binding]; other site 580332002251 RPB1 interaction site [polypeptide binding]; other site 580332002252 RPB11 interaction site [polypeptide binding]; other site 580332002253 RPB10 interaction site [polypeptide binding]; other site 580332002254 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 580332002255 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 580332002256 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 580332002257 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 580332002258 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 580332002259 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 580332002260 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 580332002261 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 580332002262 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 580332002263 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 580332002264 DNA binding site [nucleotide binding] 580332002265 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 580332002266 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 580332002267 S17 interaction site [polypeptide binding]; other site 580332002268 S8 interaction site; other site 580332002269 16S rRNA interaction site [nucleotide binding]; other site 580332002270 streptomycin interaction site [chemical binding]; other site 580332002271 23S rRNA interaction site [nucleotide binding]; other site 580332002272 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 580332002273 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 580332002274 elongation factor G; Reviewed; Region: PRK00007 580332002275 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 580332002276 G1 box; other site 580332002277 putative GEF interaction site [polypeptide binding]; other site 580332002278 GTP/Mg2+ binding site [chemical binding]; other site 580332002279 Switch I region; other site 580332002280 G2 box; other site 580332002281 G3 box; other site 580332002282 Switch II region; other site 580332002283 G4 box; other site 580332002284 G5 box; other site 580332002285 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 580332002286 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 580332002287 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 580332002288 elongation factor Tu; Reviewed; Region: PRK00049 580332002289 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 580332002290 G1 box; other site 580332002291 GEF interaction site [polypeptide binding]; other site 580332002292 GTP/Mg2+ binding site [chemical binding]; other site 580332002293 Switch I region; other site 580332002294 G2 box; other site 580332002295 G3 box; other site 580332002296 Switch II region; other site 580332002297 G4 box; other site 580332002298 G5 box; other site 580332002299 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 580332002300 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 580332002301 Antibiotic Binding Site [chemical binding]; other site 580332002302 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 580332002303 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 580332002304 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 580332002305 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 580332002306 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 580332002307 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 580332002308 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 580332002309 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 580332002310 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 580332002311 putative translocon binding site; other site 580332002312 protein-rRNA interface [nucleotide binding]; other site 580332002313 ribosomal protein S3, bacterial type; Region: rpsC_bact; TIGR01009 580332002314 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 580332002315 G-X-X-G motif; other site 580332002316 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 580332002317 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 580332002318 23S rRNA interface [nucleotide binding]; other site 580332002319 5S rRNA interface [nucleotide binding]; other site 580332002320 putative antibiotic binding site [chemical binding]; other site 580332002321 L25 interface [polypeptide binding]; other site 580332002322 L27 interface [polypeptide binding]; other site 580332002323 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 580332002324 23S rRNA interface [nucleotide binding]; other site 580332002325 putative translocon interaction site; other site 580332002326 signal recognition particle (SRP54) interaction site; other site 580332002327 L23 interface [polypeptide binding]; other site 580332002328 trigger factor interaction site; other site 580332002329 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 580332002330 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 580332002331 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 580332002332 KOW motif; Region: KOW; cl00354 580332002333 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 580332002334 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 580332002335 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 580332002336 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 580332002337 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 580332002338 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 580332002339 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 580332002340 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 580332002341 5S rRNA interface [nucleotide binding]; other site 580332002342 23S rRNA interface [nucleotide binding]; other site 580332002343 L5 interface [polypeptide binding]; other site 580332002344 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 580332002345 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 580332002346 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 580332002347 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 580332002348 23S rRNA binding site [nucleotide binding]; other site 580332002349 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 580332002350 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 580332002351 SecY translocase; Region: SecY; pfam00344 580332002352 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 580332002353 rRNA binding site [nucleotide binding]; other site 580332002354 predicted 30S ribosome binding site; other site 580332002355 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 580332002356 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 580332002357 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 580332002358 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 580332002359 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 580332002360 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 580332002361 RNA binding surface [nucleotide binding]; other site 580332002362 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 580332002363 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 580332002364 alphaNTD homodimer interface [polypeptide binding]; other site 580332002365 alphaNTD - beta interaction site [polypeptide binding]; other site 580332002366 alphaNTD - beta' interaction site [polypeptide binding]; other site 580332002367 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 580332002368 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 580332002369 SCP_PR-1_like: SCP-like extracellular protein domain, PR-1 like subfamily. The wider family of SCP containing proteins includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal...; Region: SCP_PR-1_like; cd05381 580332002370 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 580332002371 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 580332002372 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 580332002373 The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_II; cd03271 580332002374 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 580332002375 Major Facilitator Superfamily; Region: MFS_1; pfam07690 580332002376 putative substrate translocation pore; other site 580332002377 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 580332002378 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 580332002379 dimer interface [polypeptide binding]; other site 580332002380 ssDNA binding site [nucleotide binding]; other site 580332002381 tetramer (dimer of dimers) interface [polypeptide binding]; other site 580332002382 PAS fold; Region: PAS_4; pfam08448 580332002383 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 580332002384 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 580332002385 Walker A motif; other site 580332002386 ATP binding site [chemical binding]; other site 580332002387 Walker B motif; other site 580332002388 arginine finger; other site 580332002389 Helix-turn-helix domains; Region: HTH; cl00088 580332002390 hypothetical protein; Provisional; Region: PRK13795 580332002391 This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This...; Region: NifX_NifB; cd00562 580332002392 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 580332002393 Fe-S cluster assembly protein NifU; Region: NifU_proper; TIGR02000 580332002394 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 580332002395 trimerization site [polypeptide binding]; other site 580332002396 active site 580332002397 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 580332002398 NifU-like domain; Region: NifU; cl00484 580332002399 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 580332002400 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 580332002401 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 580332002402 catalytic residue [active] 580332002403 homocitrate synthase NifV; Region: nifV_homocitr; TIGR02660 580332002404 Streptomyces rubellomurinus FrbC and related proteins, catalytic TIM barrel domain; Region: DRE_TIM_NifV; cd07939 580332002405 active site 580332002406 catalytic residues [active] 580332002407 metal binding site [ion binding]; metal-binding site 580332002408 serine O-acetyltransferase; Region: cysE; TIGR01172 580332002409 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 580332002410 trimer interface [polypeptide binding]; other site 580332002411 active site 580332002412 substrate binding site [chemical binding]; other site 580332002413 CoA binding site [chemical binding]; other site 580332002414 Nitrogen fixation protein NifW; Region: NifW; cl03935 580332002415 NifZ domain; Region: NifZ; pfam04319 580332002416 nitrogen fixation protein NifM; Region: nifM_nitrog; TIGR02933 580332002417 PPIC-type PPIASE domain; Region: Rotamase; cl08278 580332002418 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 580332002419 HicB family; Region: HicB; pfam05534 580332002420 DctM-like transporters; Region: DctM; pfam06808 580332002421 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 580332002422 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 580332002423 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 580332002424 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 580332002425 Cysteine-rich domain; Region: CCG; pfam02754 580332002426 Cysteine-rich domain; Region: CCG; pfam02754 580332002427 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; cl00674 580332002428 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; cl00674 580332002429 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 580332002430 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 580332002431 Domain of unknown function (DUF3390); Region: DUF3390; pfam11870 580332002432 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 580332002433 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 580332002434 homodimer interface [polypeptide binding]; other site 580332002435 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332002436 catalytic residue [active] 580332002437 glycolate oxidase iron-sulfur subunit; Provisional; Region: glcF; PRK11274 580332002438 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 580332002439 Cysteine-rich domain; Region: CCG; pfam02754 580332002440 Cysteine-rich domain; Region: CCG; pfam02754 580332002441 glycolate oxidase FAD binding subunit; Provisional; Region: glcE; PRK11282 580332002442 FAD binding domain; Region: FAD_binding_4; pfam01565 580332002443 glycolate oxidase subunit GlcD; Provisional; Region: PRK11230 580332002444 FAD binding domain; Region: FAD_binding_4; pfam01565 580332002445 Pirin-related protein [General function prediction only]; Region: COG1741 580332002446 Cupin domain; Region: Cupin_2; cl09118 580332002447 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 580332002448 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 580332002449 active site 580332002450 DNA binding site [nucleotide binding] 580332002451 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 580332002452 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 580332002453 Catalytic site [active] 580332002454 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; cl00614 580332002455 NifQ; Region: NifQ; pfam04891 580332002456 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 580332002457 catalytic loop [active] 580332002458 iron binding site [ion binding]; other site 580332002459 Arsenate Reductase (ArsC) family, 15kD protein subfamily; composed of proteins of unknown function with similarity to thioredoxin-fold arsenic reductases, ArsC. It is encoded by an ORF present in a gene cluster associated with nitrogen fixation that also...; Region: ArsC_15kD; cd03033 580332002460 ArsC family; Region: ArsC; pfam03960 580332002461 putative catalytic residues [active] 580332002462 hypothetical protein; Provisional; Region: PRK13795 580332002463 nitrogenase cofactor biosynthesis protein NifB; Region: nifB; TIGR01290 580332002464 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 580332002465 FeS/SAM binding site; other site 580332002466 NifB belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme as part of...; Region: NifB; cd00852 580332002467 NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. The protein...; Region: NifX; cd00853 580332002468 sn-glycerol-3-phosphate dehydrogenase subunit C; Provisional; Region: glpC; PRK11168 580332002469 Oxygen tolerance; Region: BatD; pfam13584 580332002470 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 580332002471 metal ion-dependent adhesion site (MIDAS); other site 580332002472 Domain of unknown function (DUF4381); Region: DUF4381; pfam14316 580332002473 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 580332002474 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 580332002475 MoxR-like ATPases [General function prediction only]; Region: COG0714 580332002476 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332002477 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332002478 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332002479 Walker A/P-loop; other site 580332002480 ATP binding site [chemical binding]; other site 580332002481 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332002482 Q-loop/lid; other site 580332002483 ABC transporter signature motif; other site 580332002484 Walker B; other site 580332002485 D-loop; other site 580332002486 H-loop/switch region; other site 580332002487 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 580332002488 Protein of unknown function (DUF3620); Region: DUF3620; cl02233 580332002489 Nitrogen fixation protein of unknown function; Region: Nif11; cl06756 580332002490 Nif-specific regulatory protein; Region: nifA; TIGR01817 580332002491 GAF domain; Region: GAF; cl15785 580332002492 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 580332002493 Walker A motif; other site 580332002494 ATP binding site [chemical binding]; other site 580332002495 Walker B motif; other site 580332002496 arginine finger; other site 580332002497 Helix-turn-helix domains; Region: HTH; cl00088 580332002498 nitrogen fixation negative regulator NifL; Region: nifL_nitrog; TIGR02938 580332002499 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 580332002500 putative active site [active] 580332002501 heme pocket [chemical binding]; other site 580332002502 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 580332002503 ATP binding site [chemical binding]; other site 580332002504 Mg2+ binding site [ion binding]; other site 580332002505 G-X-G motif; other site 580332002506 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 580332002507 electron transport complex protein RnfB; Provisional; Region: PRK05113 580332002508 Putative Fe-S cluster; Region: FeS; pfam04060 580332002509 4Fe-4S binding domain; Region: Fer4; cl02805 580332002510 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 580332002511 RnfC Barrel sandwich hybrid domain; Region: RnfC_N; pfam13375 580332002512 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 580332002513 SLBB domain; Region: SLBB; pfam10531 580332002514 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 580332002515 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 580332002516 FMN-binding domain; Region: FMN_bind; cl01081 580332002517 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 580332002518 The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information...; Region: TGS; cl15768 580332002519 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 580332002520 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 580332002521 Ferredoxin [Energy production and conversion]; Region: COG1146 580332002522 4Fe-4S binding domain; Region: Fer4; cl02805 580332002523 4Fe-4S binding domain; Region: Fer4; cl02805 580332002524 dihydrolipoamide dehydrogenase; Validated; Region: PRK06292 580332002525 putative bacillithiol system oxidoreductase, YpdA family; Region: Bthiol_YpdA; TIGR04018 580332002526 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 580332002527 chaperone protein DnaJ; Provisional; Region: PRK14280 580332002528 Cation efflux family; Region: Cation_efflux; cl00316 580332002529 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 580332002530 octamerization interface [polypeptide binding]; other site 580332002531 diferric-oxygen binding site [ion binding]; other site 580332002532 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; cl02542 580332002533 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 580332002534 Malonate/sodium symporter MadM subunit; Region: MadM; cl04274 580332002535 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 580332002536 PAS fold; Region: PAS_4; pfam08448 580332002537 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 580332002538 putative active site [active] 580332002539 heme pocket [chemical binding]; other site 580332002540 PAS domain S-box; Region: sensory_box; TIGR00229 580332002541 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 580332002542 putative active site [active] 580332002543 heme pocket [chemical binding]; other site 580332002544 PAS domain S-box; Region: sensory_box; TIGR00229 580332002545 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 580332002546 putative active site [active] 580332002547 heme pocket [chemical binding]; other site 580332002548 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 580332002549 PAS domain; Region: PAS_9; pfam13426 580332002550 putative active site [active] 580332002551 heme pocket [chemical binding]; other site 580332002552 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332002553 metal binding site [ion binding]; metal-binding site 580332002554 active site 580332002555 I-site; other site 580332002556 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 580332002557 Dinitrogenase reductase ADP-ribosyltransferase (DRAT); Region: DRAT; pfam07357 580332002558 NifH gene encodes component II (iron protein) of nitrogenase. Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the...; Region: NifH; cd02040 580332002559 nitrogenase iron protein; Region: nifH; TIGR01287 580332002560 Nucleotide-binding sites [chemical binding]; other site 580332002561 Walker A motif; other site 580332002562 Switch I region of nucleotide binding site; other site 580332002563 Fe4S4 binding sites [ion binding]; other site 580332002564 Switch II region of nucleotide binding site; other site 580332002565 nitrogenase molybdenum-iron cofactor biosynthesis protein NifE; Region: nifE; TIGR01283 580332002566 Nitrogenase_MoFe_alpha_II: Nitrogenase MoFe protein, beta subunit. A group of proteins similar to the alpha subunit of the MoFe protein of the molybdenum (Mo-) nitrogenase. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen to...; Region: Nitrogenase_MoFe_alpha; cd01976 580332002567 MoFe protein alpha/beta subunit interactions; other site 580332002568 Alpha subunit P cluster binding residues; other site 580332002569 FeMoco binding residues [chemical binding]; other site 580332002570 MoFe protein alpha subunit/Fe protein contacts; other site 580332002571 MoFe protein dimer/ dimer interactions; other site 580332002572 nitrogenase molybdenum-iron protein beta chain; Region: nifK; TIGR01286 580332002573 Domain of unknown function (DUF3364); Region: DUF3364; pfam11844 580332002574 Nitrogenase_MoFe_beta: Nitrogenase MoFe protein, beta subunit. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen to ammonia. The Molybdenum (Mo-) nitrogenase is the most widespread and best characterized of these systems; Region: Nitrogenase_MoFe_beta; cd01974 580332002575 MoFe protein beta/alpha subunit interactions; other site 580332002576 Beta subunit P cluster binding residues; other site 580332002577 MoFe protein beta subunit/Fe protein contacts; other site 580332002578 MoFe protein dimer/ dimer interactions; other site 580332002579 NifT/FixU protein; Region: NifT; cl02351 580332002580 glycine radical enzyme activase, YjjW family; Region: activase_YjjW; TIGR04041 580332002581 NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. The protein...; Region: NifX; cd00853 580332002582 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332002583 Zn2+ binding site [ion binding]; other site 580332002584 Mg2+ binding site [ion binding]; other site 580332002585 O-methyltransferase; Region: Methyltransf_3; pfam01596 580332002586 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 580332002587 S-adenosylmethionine binding site [chemical binding]; other site 580332002588 Protein of unknown function (DUF1311); Region: DUF1311; cl01530 580332002589 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 580332002590 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 580332002591 Helix-turn-helix domains; Region: HTH; cl00088 580332002592 DNA-binding transcriptional regulator ModE; Provisional; Region: PRK10676 580332002593 TOBE domain; Region: TOBE_2; cl01440 580332002594 TOBE domain; Region: TOBE_2; cl01440 580332002595 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 580332002596 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 580332002597 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 580332002598 putative PBP binding loops; other site 580332002599 dimer interface [polypeptide binding]; other site 580332002600 ABC-ATPase subunit interface; other site 580332002601 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332002602 molybdenum ABC transporter, ATP-binding protein; Region: modC_ABC; TIGR02142 580332002603 Walker A/P-loop; other site 580332002604 ATP binding site [chemical binding]; other site 580332002605 Q-loop/lid; other site 580332002606 ABC transporter signature motif; other site 580332002607 Walker B; other site 580332002608 D-loop; other site 580332002609 H-loop/switch region; other site 580332002610 TOBE domain; Region: TOBE_2; cl01440 580332002611 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 580332002612 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 580332002613 Coenzyme A binding pocket [chemical binding]; other site 580332002614 LRV protein FeS4 cluster; Region: LRV_FeS; pfam05484 580332002615 putative oxidoreductase/HEAT repeat-containing protein; Provisional; Region: PRK13800 580332002616 nitrogenase molybdenum-iron cofactor biosynthesis protein NifE; Region: nifE; TIGR01283 580332002617 The nitrogenase enzyme system catalyzes the ATP-dependent reduction of dinitrogen to ammonia. This group contains both alpha and beta subunits of component 1 of the three known genetically distinct types of nitrogenase systems: a molybdenum-dependent; Region: Oxidoreductase_nitrogenase; cl02775 580332002618 Nitrogenase_nifN1: A subgroup of the NifN subunit of the NifEN complex: NifN forms an alpha2beta2 tetramer with NifE. NifN and nifE are structurally homologous to nitrogenase MoFe protein beta and alpha subunits respectively. NifEN participates in the...; Region: Nitrogenase_NifN_1; cd01966 580332002619 Nitrogenase component 1 type Oxidoreductase; Region: Oxidored_nitro; pfam00148 580332002620 NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. The protein...; Region: NifX; cd00853 580332002621 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; cl01178 580332002622 Protein of unknown function, DUF269; Region: DUF269; cl03973 580332002623 Rop-like; Region: Rop-like; cl02247 580332002624 ferredoxin III, nif-specific; Region: fdxN_nitrog; TIGR02936 580332002625 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 580332002626 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:...; Region: TRX_Fd_family; cd02980 580332002627 dimer interface [polypeptide binding]; other site 580332002628 [2Fe-2S] cluster binding site [ion binding]; other site 580332002629 NifZ domain; Region: NifZ; pfam04319 580332002630 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin...; Region: mcbC-like_oxidoreductase; cd02142 580332002631 putative FMN binding site [chemical binding]; other site 580332002632 NADPH bind site [chemical binding]; other site 580332002633 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin...; Region: mcbC-like_oxidoreductase; cd02142 580332002634 putative FMN binding site [chemical binding]; other site 580332002635 NADPH bind site [chemical binding]; other site 580332002636 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 580332002637 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 580332002638 Domain of unknown function (DUF389); Region: DUF389; cl00781 580332002639 Na+/H+ antiporter, bacterial form; Region: a_cpa1; TIGR00831 580332002640 peptidoglycan-associated outer membrane lipoprotein; Provisional; Region: PRK10802 580332002641 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 580332002642 ligand binding site [chemical binding]; other site 580332002643 ClC chloride channel family. These protein sequences, closely related to the ClC Eric family, are putative halogen ion (Cl-, Br- and I-) transport proteins found in eubacteria. They belong to the ClC superfamily of chloride ion channels, which share a...; Region: EriC_like; cd01034 580332002644 Voltage gated chloride channel; Region: Voltage_CLC; pfam00654 580332002645 putative ion selectivity filter; other site 580332002646 putative pore gating glutamate residue; other site 580332002647 putative H+/Cl- coupling transport residue; other site 580332002648 pyruvate phosphate dikinase; Provisional; Region: PRK09279 580332002649 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 580332002650 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 580332002651 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 580332002652 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 580332002653 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 580332002654 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 580332002655 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 580332002656 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 580332002657 RNA polymerase sigma factor; Provisional; Region: PRK12513 580332002658 biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Region: BVR-B_like_SDR_a; cd05244 580332002659 NAD binding site [chemical binding]; other site 580332002660 substrate binding site [chemical binding]; other site 580332002661 putative active site [active] 580332002662 Helix-turn-helix domains; Region: HTH; cl00088 580332002663 Domain of unknown function (DUF1956); Region: DUF1956; pfam09209 580332002664 Membrane-fusion protein [Cell envelope biogenesis, outer membrane]; Region: AcrA; COG0845 580332002665 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 580332002666 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 580332002667 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 580332002668 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 580332002669 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 580332002670 putative inner membrane diguanylate cyclase; Provisional; Region: PRK09966 580332002671 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: VicK; COG5002 580332002672 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 580332002673 dimerization interface [polypeptide binding]; other site 580332002674 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 580332002675 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332002676 metal binding site [ion binding]; metal-binding site 580332002677 active site 580332002678 I-site; other site 580332002679 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 580332002680 Domain of unknown function (DUF4154); Region: DUF4154; pfam13689 580332002681 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 580332002682 N-terminal plug; other site 580332002683 ligand-binding site [chemical binding]; other site 580332002684 16S rRNA methyltransferase B; Provisional; Region: PRK14901 580332002685 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 580332002686 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 580332002687 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 580332002688 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 580332002689 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 580332002690 active site 580332002691 substrate binding site [chemical binding]; other site 580332002692 cosubstrate binding site; other site 580332002693 catalytic site [active] 580332002694 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 580332002695 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 580332002696 dimerization interface [polypeptide binding]; other site 580332002697 putative ATP binding site [chemical binding]; other site 580332002698 DnaA regulatory inactivator Hda; Region: DnaA_homol_Hda; TIGR03420 580332002699 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332002700 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 580332002701 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 580332002702 poly(A) polymerase; Region: pcnB; TIGR01942 580332002703 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 580332002704 active site 580332002705 NTP binding site [chemical binding]; other site 580332002706 metal binding triad [ion binding]; metal-binding site 580332002707 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 580332002708 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 580332002709 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after...; Region: HPPK; cd00483 580332002710 catalytic center binding site [active] 580332002711 ATP binding site [chemical binding]; other site 580332002712 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 580332002713 Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1; Region: dNK; cd01673 580332002714 Substrate-binding site [chemical binding]; other site 580332002715 Substrate specificity [chemical binding]; other site 580332002716 Ketopantoate hydroxymethyltransferase (KPHMT) is the first enzyme in the pantothenate biosynthesis pathway. Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate (vitamin B5), which is a...; Region: KPHMT-like; cd06557 580332002717 oligomerization interface [polypeptide binding]; other site 580332002718 active site 580332002719 metal binding site [ion binding]; metal-binding site 580332002720 pantoate--beta-alanine ligase; Region: panC; TIGR00018 580332002721 Pantoate-beta-alanine ligase; Region: PanC; cd00560 580332002722 active site 580332002723 ATP-binding site [chemical binding]; other site 580332002724 pantoate-binding site; other site 580332002725 HXXH motif; other site 580332002726 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 580332002727 tetramerization interface [polypeptide binding]; other site 580332002728 active site 580332002729 adenylosuccinate lyase; Provisional; Region: PRK09285 580332002730 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 580332002731 tetramer interface [polypeptide binding]; other site 580332002732 active site 580332002733 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 580332002734 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 580332002735 Contains a crystal structure of the Nudix hydrolase from Nitrosomonas europaea, which has an unknown function. In general, members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes...; Region: Nudix_Hydrolase_2; cd03675 580332002736 nudix motif; other site 580332002737 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 580332002738 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 580332002739 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; cl00409 580332002740 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 580332002741 Preprotein translocase subunit; Region: YajC; cl00806 580332002742 SecD export protein N-terminal TM region; Region: SecD-TM1; cl08136 580332002743 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 580332002744 Protein export membrane protein; Region: SecD_SecF; cl14618 580332002745 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 580332002746 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 580332002747 Protein export membrane protein; Region: SecD_SecF; cl14618 580332002748 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 580332002749 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 580332002750 active site 580332002751 HIGH motif; other site 580332002752 nucleotide binding site [chemical binding]; other site 580332002753 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 580332002754 active site 580332002755 KMSKS motif; other site 580332002756 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 580332002757 Clp amino terminal domain; Region: Clp_N; pfam02861 580332002758 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 580332002759 Walker A motif; other site 580332002760 ATP binding site [chemical binding]; other site 580332002761 Walker B motif; other site 580332002762 arginine finger; other site 580332002763 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 580332002764 Walker A motif; other site 580332002765 ATP binding site [chemical binding]; other site 580332002766 Walker B motif; other site 580332002767 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 580332002768 ATP-dependent Clp protease adaptor protein ClpS; Region: ClpS; cl00933 580332002769 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein; Region: CSP_CDS; cd04458 580332002770 DNA-binding site [nucleotide binding]; DNA binding site 580332002771 RNA-binding motif; other site 580332002772 Monomeric isocitrate dehydrogenase; Region: IDH; cl15383 580332002773 PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE. This group is comprised of bacterial proteins similar to E. coli RluE. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines; Region: PseudoU_synth_RluE; cd02566 580332002774 pseudouridine synthase; Region: TIGR00093 580332002775 probable active site [active] 580332002776 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 580332002777 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 580332002778 active site 580332002779 homodimer interface [polypeptide binding]; other site 580332002780 Zinc ribbon domain; Region: CxxC_CxxC_SSSS; cl00993 580332002781 putative regulatory protein, FmdB family; Region: CxxC_CxxC_SSSS; TIGR02605 580332002782 Protein of unknown function (DUF502); Region: DUF502; cl01107 580332002783 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 580332002784 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 580332002785 dimer interface [polypeptide binding]; other site 580332002786 anticodon binding site; other site 580332002787 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the...; Region: AspRS_core; cd00777 580332002788 homodimer interface [polypeptide binding]; other site 580332002789 motif 1; other site 580332002790 active site 580332002791 motif 2; other site 580332002792 GAD domain; Region: GAD; pfam02938 580332002793 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the...; Region: AspRS_core; cd00777 580332002794 motif 3; other site 580332002795 RNase_Sa. Ribonucleases first isolated from Streptomyces aureofaciens. In general, ribonucleases cleave phosphodiester bonds in RNA and are essential for both non-specific RNA degradation and for numerous forms of RNA processing. RNAse Sa is a guanylate...; Region: RNase_Sa; cd00607 580332002796 active site 580332002797 barstar interaction site; other site 580332002798 Barstar_evA4336-like contains uncharacterized sequences similar to the uncharacterized, predicted RNAase inhibitor evA4336 found in Azoarcus sp. EvN1. This is a subfamily of the Barstar family of RNAase inhibitors. Barstar is an intracellular inhibitor...; Region: Barstar_evA4336-like; cd05141 580332002799 putative RNAase interaction site [polypeptide binding]; other site 580332002800 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_7; cd04664 580332002801 nudix motif; other site 580332002802 Quinolinate synthetase A protein; Region: NadA; cl00420 580332002803 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 580332002804 putative catalytic site [active] 580332002805 putative metal binding site [ion binding]; other site 580332002806 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 580332002807 PLD-like domain; Region: PLDc_2; pfam13091 580332002808 putative active site [active] 580332002809 catalytic site [active] 580332002810 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 580332002811 PLD-like domain; Region: PLDc_2; pfam13091 580332002812 putative active site [active] 580332002813 catalytic site [active] 580332002814 This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of...; Region: GT1_Glycogen_Phosphorylase; cd04300 580332002815 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 580332002816 homodimer interface [polypeptide binding]; other site 580332002817 active site pocket [active] 580332002818 glucokinase, proteobacterial type; Region: glk; TIGR00749 580332002819 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 580332002820 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 580332002821 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 580332002822 ATM1 is an ABC transporter that is expressed in the mitochondria. Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to...; Region: ABCC_ATM1_transporter; cd03253 580332002823 Walker A/P-loop; other site 580332002824 ATP binding site [chemical binding]; other site 580332002825 Q-loop/lid; other site 580332002826 ABC transporter signature motif; other site 580332002827 Walker B; other site 580332002828 D-loop; other site 580332002829 H-loop/switch region; other site 580332002830 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 580332002831 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 580332002832 Helix-turn-helix domains; Region: HTH; cl00088 580332002833 aminoethylphosphonate catabolism associated LysR family transcriptional regulator; Region: phn_lysR; TIGR03339 580332002834 The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; Region: PBP2_CbbR_RubisCO_like; cd08419 580332002835 putative dimerization interface [polypeptide binding]; other site 580332002836 ribulose bisophosphate carboxylase; Reviewed; Region: rbcL; PRK04208 580332002837 Ribulose bisphosphate carboxylase large chain; Region: RuBisCO_large; cl08232 580332002838 dimer interface [polypeptide binding]; other site 580332002839 catalytic residue [active] 580332002840 metal binding site [ion binding]; metal-binding site 580332002841 Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco...; Region: RuBisCO_small; cd03527 580332002842 multimerization interface [polypeptide binding]; other site 580332002843 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332002844 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 580332002845 norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial...; Region: vWA_norD_type; cd01454 580332002846 metal ion-dependent adhesion site (MIDAS); other site 580332002847 AIR carboxylase; Region: AIRC; cl00310 580332002848 hypothetical protein; Provisional; Region: PRK08185 580332002849 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 580332002850 intersubunit interface [polypeptide binding]; other site 580332002851 active site 580332002852 zinc binding site [ion binding]; other site 580332002853 Na+ binding site [ion binding]; other site 580332002854 Stress responsive A/B Barrel Domain; Region: Dabb; cl15807 580332002855 EamA-like transporter family; Region: EamA; cl01037 580332002856 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 580332002857 putative DNA binding site [nucleotide binding]; other site 580332002858 putative Zn2+ binding site [ion binding]; other site 580332002859 Low molecular weight phosphatase family; Region: LMWPc; cd00115 580332002860 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 580332002861 active site 580332002862 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 580332002863 Membrane transport protein; Region: Mem_trans; cl09117 580332002864 RNA polymerase sigma factor, SigZ family; Region: SigZ; TIGR02959 580332002865 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 580332002866 Predicted permeases [General function prediction only]; Region: COG0701 580332002867 Predicted permease; Region: DUF318; pfam03773 580332002868 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 580332002869 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 580332002870 OsmC-like protein; Region: OsmC; cl00767 580332002871 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 580332002872 gamma-glutamyl kinase; Provisional; Region: PRK05429 580332002873 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 580332002874 nucleotide binding site [chemical binding]; other site 580332002875 homotetrameric interface [polypeptide binding]; other site 580332002876 putative phosphate binding site [ion binding]; other site 580332002877 putative allosteric binding site; other site 580332002878 PUA domain; Region: PUA; cl00607 580332002879 GTPase CgtA; Reviewed; Region: obgE; PRK12299 580332002880 GTP1/OBG; Region: GTP1_OBG; pfam01018 580332002881 Obg GTPase; Region: Obg; cd01898 580332002882 G1 box; other site 580332002883 GTP/Mg2+ binding site [chemical binding]; other site 580332002884 Switch I region; other site 580332002885 G2 box; other site 580332002886 G3 box; other site 580332002887 Switch II region; other site 580332002888 G4 box; other site 580332002889 G5 box; other site 580332002890 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 580332002891 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 580332002892 transcription termination factor Rho; Provisional; Region: rho; PRK09376 580332002893 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 580332002894 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 580332002895 RNA binding site [nucleotide binding]; other site 580332002896 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 580332002897 multimer interface [polypeptide binding]; other site 580332002898 Walker A motif; other site 580332002899 ATP binding site [chemical binding]; other site 580332002900 Walker B motif; other site 580332002901 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 580332002902 catalytic residues [active] 580332002903 sensor protein QseC; Provisional; Region: PRK10337 580332002904 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 580332002905 dimer interface [polypeptide binding]; other site 580332002906 phosphorylation site [posttranslational modification] 580332002907 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 580332002908 ATP binding site [chemical binding]; other site 580332002909 G-X-G motif; other site 580332002910 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 580332002911 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 580332002912 active site 580332002913 phosphorylation site [posttranslational modification] 580332002914 intermolecular recognition site; other site 580332002915 dimerization interface [polypeptide binding]; other site 580332002916 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 580332002917 DNA binding site [nucleotide binding] 580332002918 Dihaem cytochrome c; Region: DHC; pfam09626 580332002919 acyl-CoA synthetase; Validated; Region: PRK08316 580332002920 Domain of unknown function (DUF1924); Region: DUF1924; pfam09086 580332002921 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332002922 DJ-1 family protein; Region: not_thiJ; TIGR01383 580332002923 Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1; Region: GATase1_DJ-1; cd03135 580332002924 conserved cys residue [active] 580332002925 PAP2_like_5 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_5; cd03394 580332002926 active site 580332002927 Protein of unknown function (DUF520); Region: DUF520; cl00723 580332002928 Protein of unknown function (DUF1255); Region: DUF1255; cl01202 580332002929 Macro domain, Poa1p_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose...; Region: Macro_Poa1p_like; cd02901 580332002930 ADP-ribose binding site [chemical binding]; other site 580332002931 Argininosuccinate synthase [Amino acid transport and metabolism]; Region: ArgG; COG0137 580332002932 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 580332002933 ANP binding site [chemical binding]; other site 580332002934 Substrate Binding Site II [chemical binding]; other site 580332002935 Substrate Binding Site I [chemical binding]; other site 580332002936 ornithine carbamoyltransferase; Provisional; Region: PRK00779 580332002937 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 580332002938 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332002939 acetylornithine aminotransferase; Provisional; Region: PRK02627 580332002940 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 580332002941 inhibitor-cofactor binding pocket; inhibition site 580332002942 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332002943 catalytic residue [active] 580332002944 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 580332002945 Protein of unknown function (DUF3579); Region: DUF3579; pfam12112 580332002946 Protein of unknown function (DUF3579); Region: DUF3579; pfam12112 580332002947 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 580332002948 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332002949 PAS domain S-box; Region: sensory_box; TIGR00229 580332002950 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 580332002951 putative active site [active] 580332002952 heme pocket [chemical binding]; other site 580332002953 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332002954 metal binding site [ion binding]; metal-binding site 580332002955 active site 580332002956 I-site; other site 580332002957 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12684 580332002958 Helix-turn-helix domains; Region: HTH; cl00088 580332002959 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 580332002960 substrate binding site [chemical binding]; other site 580332002961 dimerization interface [polypeptide binding]; other site 580332002962 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 580332002963 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 580332002964 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 580332002965 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 580332002966 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 580332002967 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 580332002968 Active Sites [active] 580332002969 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 580332002970 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 580332002971 Active Sites [active] 580332002972 sulfate adenylyltransferase, large subunit; Region: CysN; TIGR02034 580332002973 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 580332002974 CysD dimerization site [polypeptide binding]; other site 580332002975 G1 box; other site 580332002976 putative GEF interaction site [polypeptide binding]; other site 580332002977 GTP/Mg2+ binding site [chemical binding]; other site 580332002978 Switch I region; other site 580332002979 G2 box; other site 580332002980 G3 box; other site 580332002981 Switch II region; other site 580332002982 G4 box; other site 580332002983 G5 box; other site 580332002984 CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NodQ_II; cd03695 580332002985 TCysN_NoDQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NoDQ_III; cd04095 580332002986 CobD/Cbib protein; Region: CobD_Cbib; cl00561 580332002987 4-alpha-glucanotransferase; Region: Glyco_hydro_77; cl00711 580332002988 alpha-L-glutamate ligases, RimK family; Region: rimK_fam; TIGR00768 580332002989 GTPase RsgA; Reviewed; Region: PRK00098 580332002990 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 580332002991 RNA binding site [nucleotide binding]; other site 580332002992 homodimer interface [polypeptide binding]; other site 580332002993 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 580332002994 GTPase/Zn-binding domain interface [polypeptide binding]; other site 580332002995 GTP/Mg2+ binding site [chemical binding]; other site 580332002996 G4 box; other site 580332002997 G5 box; other site 580332002998 G1 box; other site 580332002999 Switch I region; other site 580332003000 G2 box; other site 580332003001 G3 box; other site 580332003002 Switch II region; other site 580332003003 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH_subfamily_a; cd00913 580332003004 aromatic arch; other site 580332003005 DCoH dimer interaction site [polypeptide binding]; other site 580332003006 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 580332003007 DCoH tetramer interaction site [polypeptide binding]; other site 580332003008 substrate binding site [chemical binding]; other site 580332003009 Cytochrome c; Region: Cytochrom_C; cl11414 580332003010 Peptidase family M48; Region: Peptidase_M48; cl12018 580332003011 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 580332003012 catalytic site [active] 580332003013 putative active site [active] 580332003014 putative substrate binding site [chemical binding]; other site 580332003015 dimer interface [polypeptide binding]; other site 580332003016 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 580332003017 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 580332003018 PAS domain; Region: PAS_9; pfam13426 580332003019 putative active site [active] 580332003020 heme pocket [chemical binding]; other site 580332003021 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332003022 metal binding site [ion binding]; metal-binding site 580332003023 active site 580332003024 I-site; other site 580332003025 Flagellar regulator YcgR; Region: YcgR; pfam07317 580332003026 PilZ domain; Region: PilZ; cl01260 580332003027 ferrochelatase; Reviewed; Region: hemH; PRK00035 580332003028 Ferrochelatase, N-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_N; cd03411 580332003029 C-terminal domain interface [polypeptide binding]; other site 580332003030 active site 580332003031 Ferrochelatase, C-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_C; cd00419 580332003032 active site 580332003033 N-terminal domain interface [polypeptide binding]; other site 580332003034 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 580332003035 Helix-turn-helix domains; Region: HTH; cl00088 580332003036 HrcA protein C terminal domain; Region: HrcA; pfam01628 580332003037 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 580332003038 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK03708 580332003039 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 580332003040 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 580332003041 Walker A/P-loop; other site 580332003042 ATP binding site [chemical binding]; other site 580332003043 Q-loop/lid; other site 580332003044 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 580332003045 ABC transporter signature motif; other site 580332003046 Walker B; other site 580332003047 D-loop; other site 580332003048 H-loop/switch region; other site 580332003049 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 580332003050 dihydrodipicolinate reductase; Provisional; Region: PRK00048 580332003051 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332003052 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 580332003053 zinc-ribbon domain; Region: zf-ribbon_3; cl11198 580332003054 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 580332003055 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 580332003056 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332003057 metal binding site [ion binding]; metal-binding site 580332003058 active site 580332003059 I-site; other site 580332003060 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 580332003061 Predicted membrane protein [Function unknown]; Region: COG1971 580332003062 Domain of unknown function DUF; Region: DUF204; pfam02659 580332003063 Domain of unknown function DUF; Region: DUF204; pfam02659 580332003064 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 580332003065 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; cl03056 580332003066 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 580332003067 catalytic site [active] 580332003068 subunit interface [polypeptide binding]; other site 580332003069 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 580332003070 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 580332003071 ATP-grasp domain; Region: ATP-grasp_4; cl03087 580332003072 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 580332003073 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 580332003074 ATP-grasp domain; Region: ATP-grasp_4; cl03087 580332003075 Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways...; Region: MGS_CPS_II; cd01424 580332003076 IMP binding site; other site 580332003077 dimer interface [polypeptide binding]; other site 580332003078 interdomain contacts; other site 580332003079 partial ornithine binding site; other site 580332003080 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 580332003081 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 580332003082 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 580332003083 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; cl00663 580332003084 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 580332003085 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 580332003086 FtsH Extracellular; Region: FtsH_ext; pfam06480 580332003087 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 580332003088 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 580332003089 Walker A motif; other site 580332003090 ATP binding site [chemical binding]; other site 580332003091 Walker B motif; other site 580332003092 arginine finger; other site 580332003093 Peptidase family M41; Region: Peptidase_M41; pfam01434 580332003094 DHPS subgroup of Pterin binding enzymes. DHPS (dihydropteroate synthase), a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and...; Region: DHPS; cd00739 580332003095 dihydropteroate synthase; Region: DHPS; TIGR01496 580332003096 substrate binding pocket [chemical binding]; other site 580332003097 dimer interface [polypeptide binding]; other site 580332003098 inhibitor binding site; inhibition site 580332003099 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 580332003100 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 580332003101 active site 580332003102 substrate binding site [chemical binding]; other site 580332003103 metal binding site [ion binding]; metal-binding site 580332003104 phosphate transporter ATP-binding protein; Provisional; Region: pstB; PRK10744 580332003105 Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient. The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein...; Region: ABC_PstB_phosphate_transporter; cd03260 580332003106 Walker A/P-loop; other site 580332003107 ATP binding site [chemical binding]; other site 580332003108 Q-loop/lid; other site 580332003109 ABC transporter signature motif; other site 580332003110 Walker B; other site 580332003111 D-loop; other site 580332003112 H-loop/switch region; other site 580332003113 phosphate transporter permease subunit PtsA; Provisional; Region: pstA; PRK11268 580332003114 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 580332003115 dimer interface [polypeptide binding]; other site 580332003116 conserved gate region; other site 580332003117 putative PBP binding loops; other site 580332003118 ABC-ATPase subunit interface; other site 580332003119 phosphate ABC transporter, permease protein PstC; Region: phosphate_pstC; TIGR02138 580332003120 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 580332003121 dimer interface [polypeptide binding]; other site 580332003122 conserved gate region; other site 580332003123 putative PBP binding loops; other site 580332003124 ABC-ATPase subunit interface; other site 580332003125 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 580332003126 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 580332003127 substrate binding site [chemical binding]; other site 580332003128 dimer interface [polypeptide binding]; other site 580332003129 catalytic triad [active] 580332003130 Preprotein translocase SecG subunit; Region: SecG; cl09123 580332003131 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 580332003132 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl15792 580332003133 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl15771 580332003134 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 580332003135 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; pfam00346 580332003136 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 580332003137 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 580332003138 putative dimer interface [polypeptide binding]; other site 580332003139 [2Fe-2S] cluster binding site [ion binding]; other site 580332003140 NADH-quinone oxidoreductase, F subunit; Region: nuoF_fam; TIGR01959 580332003141 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 580332003142 SLBB domain; Region: SLBB; pfam10531 580332003143 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; cl11211 580332003144 NADH dehydrogenase subunit G; Validated; Region: PRK09129 580332003145 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 580332003146 catalytic loop [active] 580332003147 iron binding site [ion binding]; other site 580332003148 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; cl11210 580332003149 MopB_NDH-1_NuoG2: The second domain of the NuoG subunit of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1), found in beta- and gammaproteobacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as...; Region: MopB_NDH-1_NuoG2; cd02772 580332003150 NADH dehydrogenase; Region: NADHdh; cl00469 580332003151 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 580332003152 4Fe-4S binding domain; Region: Fer4; cl02805 580332003153 4Fe-4S binding domain; Region: Fer4; cl02805 580332003154 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 580332003155 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 580332003156 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 580332003157 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 580332003158 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 580332003159 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 580332003160 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 580332003161 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 580332003162 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 580332003163 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 580332003164 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 580332003165 dimer interface [polypeptide binding]; other site 580332003166 ADP-ribose binding site [chemical binding]; other site 580332003167 active site 580332003168 nudix motif; other site 580332003169 metal binding site [ion binding]; metal-binding site 580332003170 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 580332003171 TniQ; Region: TniQ; pfam06527 580332003172 Protein of unknown function (DUF429); Region: DUF429; cl12046 580332003173 GIY-YIG nuclease domain superfamily; Region: GIY-YIG_SF; cd00719 580332003174 GIY-YIG motif/motif A; other site 580332003175 active site 580332003176 catalytic site [active] 580332003177 metal binding site [ion binding]; metal-binding site 580332003178 Domain of unknown function (DUF4357); Region: DUF4357; pfam14267 580332003179 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 580332003180 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 580332003181 S-adenosylmethionine binding site [chemical binding]; other site 580332003182 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 580332003183 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 580332003184 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: HsdR; COG4096 580332003185 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 580332003186 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 580332003187 putative Mg++ binding site [ion binding]; other site 580332003188 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 580332003189 DNA-binding interface [nucleotide binding]; DNA binding site 580332003190 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 580332003191 AAA domain; Region: AAA_22; pfam13401 580332003192 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 580332003193 Superfamily II helicase [General function prediction only]; Region: COG1204 580332003194 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 580332003195 ATP binding site [chemical binding]; other site 580332003196 putative Mg++ binding site [ion binding]; other site 580332003197 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 580332003198 nucleotide binding region [chemical binding]; other site 580332003199 ATP-binding site [chemical binding]; other site 580332003200 FRG domain; Region: FRG; cl07460 580332003201 Mannitol repressor; Region: MtlR; cl11450 580332003202 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cl00161 580332003203 Protein of unknown function (DUF1444); Region: DUF1444; cl02011 580332003204 TPR repeat; Region: TPR_11; pfam13414 580332003205 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 580332003206 binding surface 580332003207 TPR motif; other site 580332003208 Protein of unknown function (DUF1260); Region: DUF1260; pfam06877 580332003209 Domain of unknown function (DUF4272); Region: DUF4272; pfam14094 580332003210 Low molecular weight phosphatase family; Region: LMWPc; cl00105 580332003211 active site 580332003212 Family of unknown function (DUF695); Region: DUF695; pfam05117 580332003213 Protein of unknown function (DUF1260); Region: DUF1260; pfam06877 580332003214 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 580332003215 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 580332003216 ligand binding site [chemical binding]; other site 580332003217 flexible hinge region; other site 580332003218 Helix-turn-helix domains; Region: HTH; cl00088 580332003219 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 580332003220 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 580332003221 CPxP motif; other site 580332003222 Cytochrome c; Region: Cytochrom_C; cl11414 580332003223 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 580332003224 Low-spin heme binding site [chemical binding]; other site 580332003225 D-pathway; other site 580332003226 Putative water exit pathway; other site 580332003227 Binuclear center (active site) [active] 580332003228 K-pathway; other site 580332003229 Putative proton exit pathway; other site 580332003230 NorE_like subfamily of heme-copper oxidase subunit III. Heme-copper oxidases include cytochrome c and ubiquinol oxidases. Alcaligenes faecalis norE is found in a gene cluster containing norCB. norCB encodes the cytochrome c and cytochrome b subunits of...; Region: NorE_like; cd02862 580332003231 Subunit I/III interface [polypeptide binding]; other site 580332003232 Prokaryotic Cytochrome C oxidase subunit IV; Region: COX4_pro; cl01204 580332003233 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332003234 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 580332003235 4Fe-4S binding domain; Region: Fer4_5; pfam12801 580332003236 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 580332003237 Nitric oxide reductase activation protein [Inorganic ion transport and metabolism]; Region: NorD; COG4548 580332003238 norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial...; Region: vWA_norD_type; cd01454 580332003239 Cytochrome c; Region: Cytochrom_C; cl11414 580332003240 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 580332003241 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 580332003242 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 580332003243 N-terminal plug; other site 580332003244 ligand-binding site [chemical binding]; other site 580332003245 DsrC like protein; Region: DsrC; cl01101 580332003246 NnrS protein; Region: NnrS; cl01258 580332003247 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 580332003248 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 580332003249 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 580332003250 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 580332003251 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 580332003252 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 580332003253 Walker A/P-loop; other site 580332003254 ATP binding site [chemical binding]; other site 580332003255 Q-loop/lid; other site 580332003256 ABC transporter signature motif; other site 580332003257 Walker B; other site 580332003258 D-loop; other site 580332003259 H-loop/switch region; other site 580332003260 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 580332003261 Helix-turn-helix domains; Region: HTH; cl00088 580332003262 Domain of unknown function (DUF1840); Region: DUF1840; pfam08895 580332003263 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 580332003264 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 580332003265 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332003266 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 580332003267 Cyd operon protein YbgE (Cyd_oper_YbgE); Region: Cyd_oper_YbgE; cl11451 580332003268 Membrane bound YbgT-like protein; Region: YbgT_YccB; cl02039 580332003269 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 580332003270 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 580332003271 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 580332003272 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 580332003273 PAS fold; Region: PAS_4; pfam08448 580332003274 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 580332003275 putative active site [active] 580332003276 heme pocket [chemical binding]; other site 580332003277 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 580332003278 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 580332003279 Walker A motif; other site 580332003280 ATP binding site [chemical binding]; other site 580332003281 Walker B motif; other site 580332003282 arginine finger; other site 580332003283 Helix-turn-helix domains; Region: HTH; cl00088 580332003284 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 580332003285 S-adenosylmethionine binding site [chemical binding]; other site 580332003286 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; cl01267 580332003287 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 580332003288 IHF - DNA interface [nucleotide binding]; other site 580332003289 IHF dimer interface [polypeptide binding]; other site 580332003290 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 580332003291 dimer interface [polypeptide binding]; other site 580332003292 phosphorylation site [posttranslational modification] 580332003293 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 580332003294 ATP binding site [chemical binding]; other site 580332003295 Mg2+ binding site [ion binding]; other site 580332003296 G-X-G motif; other site 580332003297 Response regulator receiver domain; Region: Response_reg; pfam00072 580332003298 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 580332003299 active site 580332003300 phosphorylation site [posttranslational modification] 580332003301 intermolecular recognition site; other site 580332003302 dimerization interface [polypeptide binding]; other site 580332003303 Response regulator receiver domain; Region: Response_reg; pfam00072 580332003304 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 580332003305 active site 580332003306 phosphorylation site [posttranslational modification] 580332003307 intermolecular recognition site; other site 580332003308 dimerization interface [polypeptide binding]; other site 580332003309 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 580332003310 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 580332003311 Response regulator receiver domain; Region: Response_reg; pfam00072 580332003312 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 580332003313 active site 580332003314 phosphorylation site [posttranslational modification] 580332003315 intermolecular recognition site; other site 580332003316 dimerization interface [polypeptide binding]; other site 580332003317 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 580332003318 Ankyrin repeats (many copies); Region: Ank_5; pfam13857 580332003319 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 580332003320 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_7; cd03862 580332003321 putative active site [active] 580332003322 Zn binding site [ion binding]; other site 580332003323 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 580332003324 Helix-turn-helix domains; Region: HTH; cl00088 580332003325 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 580332003326 dimerization interface [polypeptide binding]; other site 580332003327 substrate binding pocket [chemical binding]; other site 580332003328 EamA-like transporter family; Region: EamA; cl01037 580332003329 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 580332003330 EamA-like transporter family; Region: EamA; cl01037 580332003331 Biofilm formation and stress response factor; Region: BsmA; cl01794 580332003332 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 580332003333 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 580332003334 dimer interface [polypeptide binding]; other site 580332003335 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332003336 catalytic residue [active] 580332003337 cysteine synthase B; Region: cysM; TIGR01138 580332003338 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 580332003339 dimer interface [polypeptide binding]; other site 580332003340 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332003341 catalytic residue [active] 580332003342 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 580332003343 catalytic residues [active] 580332003344 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 580332003345 MG2 domain; Region: A2M_N; pfam01835 580332003346 Alpha-2-macroglobulin family N-terminal region; Region: A2M_N_2; pfam07703 580332003347 Alpha-2-macroglobulin family; Region: A2M; pfam00207 580332003348 Proteins similar to alpha2-macroglobulin (alpha (2)-M). Alpha (2)-M is a major carrier protein in serum. It is a broadly specific proteinase inhibitor. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of...; Region: A2M_like; cd02891 580332003349 surface patch; other site 580332003350 thioester region; other site 580332003351 specificity defining residues; other site 580332003352 penicillin-binding protein 1C; Region: PBP_1c; TIGR02073 580332003353 Transglycosylase; Region: Transgly; cl07896 580332003354 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 580332003355 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 580332003356 AMIN domain; Region: AMIN; pfam11741 580332003357 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 580332003358 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 580332003359 active site 580332003360 metal binding site [ion binding]; metal-binding site 580332003361 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 580332003362 Uncharacterized Fe-S protein [Energy production and conversion]; Region: COG1600 580332003363 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 580332003364 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 580332003365 PAS domain; Region: PAS_9; pfam13426 580332003366 putative active site [active] 580332003367 heme pocket [chemical binding]; other site 580332003368 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332003369 metal binding site [ion binding]; metal-binding site 580332003370 active site 580332003371 I-site; other site 580332003372 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 580332003373 GAF domain; Region: GAF_2; pfam13185 580332003374 GAF domain; Region: GAF; cl15785 580332003375 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 580332003376 PAS domain; Region: PAS_9; pfam13426 580332003377 putative active site [active] 580332003378 heme pocket [chemical binding]; other site 580332003379 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332003380 metal binding site [ion binding]; metal-binding site 580332003381 active site 580332003382 I-site; other site 580332003383 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 580332003384 NMT1-like family; Region: NMT1_2; cl15260 580332003385 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 580332003386 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 580332003387 PAS domain; Region: PAS_9; pfam13426 580332003388 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 580332003389 Cupin domain; Region: Cupin_2; cl09118 580332003390 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 580332003391 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 580332003392 AMP-binding enzyme; Region: AMP-binding; cl15778 580332003393 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 580332003394 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 580332003395 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 580332003396 Citrate synthase (CS), citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CS catalyzes the condensation of acetyl coenzyme A; Region: CS_ACL-C_CCL; cl00416 580332003397 oxalacetate binding site [chemical binding]; other site 580332003398 citrylCoA binding site [chemical binding]; other site 580332003399 coenzyme A binding site [chemical binding]; other site 580332003400 catalytic triad [active] 580332003401 PEP phosphonomutase and related enzymes [Carbohydrate transport and metabolism]; Region: PrpB; COG2513 580332003402 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 580332003403 tetramer interface [polypeptide binding]; other site 580332003404 active site 580332003405 Mg2+/Mn2+ binding site [ion binding]; other site 580332003406 Transcriptional regulators [Transcription]; Region: GntR; COG1802 580332003407 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 580332003408 DNA-binding site [nucleotide binding]; DNA binding site 580332003409 FCD domain; Region: FCD; cl11656 580332003410 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 580332003411 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332003412 Walker A/P-loop; other site 580332003413 ATP binding site [chemical binding]; other site 580332003414 Q-loop/lid; other site 580332003415 ABC transporter signature motif; other site 580332003416 Walker B; other site 580332003417 D-loop; other site 580332003418 H-loop/switch region; other site 580332003419 TOBE domain; Region: TOBE_2; cl01440 580332003420 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 580332003421 dimer interface [polypeptide binding]; other site 580332003422 conserved gate region; other site 580332003423 putative PBP binding loops; other site 580332003424 ABC-ATPase subunit interface; other site 580332003425 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 580332003426 dimer interface [polypeptide binding]; other site 580332003427 conserved gate region; other site 580332003428 ABC-ATPase subunit interface; other site 580332003429 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 580332003430 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 580332003431 AAA domain; Region: AAA_32; pfam13654 580332003432 ATP-dependent protease, Lon family; Region: spore_lon_C; TIGR02903 580332003433 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 580332003434 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 580332003435 S-adenosylmethionine binding site [chemical binding]; other site 580332003436 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; cl02930 580332003437 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 580332003438 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 580332003439 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 580332003440 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 580332003441 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 580332003442 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 580332003443 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 580332003444 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 580332003445 ATP binding site [chemical binding]; other site 580332003446 Mg2+ binding site [ion binding]; other site 580332003447 G-X-G motif; other site 580332003448 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 580332003449 Response regulator receiver domain; Region: Response_reg; pfam00072 580332003450 active site 580332003451 phosphorylation site [posttranslational modification] 580332003452 intermolecular recognition site; other site 580332003453 dimerization interface [polypeptide binding]; other site 580332003454 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 580332003455 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 580332003456 binding surface 580332003457 TPR motif; other site 580332003458 transaldolase-like protein; Provisional; Region: PTZ00411 580332003459 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 580332003460 active site 580332003461 dimer interface [polypeptide binding]; other site 580332003462 catalytic residue [active] 580332003463 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 580332003464 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 580332003465 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 580332003466 ABC transporter; Region: ABC_tran_2; pfam12848 580332003467 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 580332003468 Protein of unknown function (DUF1566); Region: DUF1566; pfam07603 580332003469 Sel1 repeat; Region: Sel1; cl02723 580332003470 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 580332003471 Sel1 repeat; Region: Sel1; cl02723 580332003472 Sel1 repeat; Region: Sel1; cl02723 580332003473 Sel1 repeat; Region: Sel1; cl02723 580332003474 Sel1 repeat; Region: Sel1; cl02723 580332003475 Sel1 repeat; Region: Sel1; cl02723 580332003476 Sel1 repeat; Region: Sel1; cl02723 580332003477 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 580332003478 active site residue [active] 580332003479 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 580332003480 active site residue [active] 580332003481 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 580332003482 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 580332003483 Phospholipid methyltransferase; Region: PEMT; cl00763 580332003484 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct...; Region: Trunc_globin; cd00454 580332003485 apolar tunnel; other site 580332003486 heme binding site [chemical binding]; other site 580332003487 dimerization interface [polypeptide binding]; other site 580332003488 GTPase RsgA; Reviewed; Region: PRK01889 580332003489 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 580332003490 RNA binding site [nucleotide binding]; other site 580332003491 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 580332003492 GTPase/Zn-binding domain interface [polypeptide binding]; other site 580332003493 GTP/Mg2+ binding site [chemical binding]; other site 580332003494 G4 box; other site 580332003495 G5 box; other site 580332003496 G1 box; other site 580332003497 Switch I region; other site 580332003498 G2 box; other site 580332003499 G3 box; other site 580332003500 Switch II region; other site 580332003501 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 580332003502 ligand binding site [chemical binding]; other site 580332003503 flexible hinge region; other site 580332003504 NMT1-like family; Region: NMT1_2; cl15260 580332003505 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 580332003506 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cl00290 580332003507 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 580332003508 ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex...; Region: ABC_Org_Solvent_Resistant; cd03261 580332003509 Walker A/P-loop; other site 580332003510 ATP binding site [chemical binding]; other site 580332003511 Q-loop/lid; other site 580332003512 ABC transporter signature motif; other site 580332003513 Walker B; other site 580332003514 D-loop; other site 580332003515 H-loop/switch region; other site 580332003516 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 580332003517 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 580332003518 Coenzyme A binding pocket [chemical binding]; other site 580332003519 penicillin-binding protein 1B; Region: PBP_1b; TIGR02071 580332003520 Transglycosylase; Region: Transgly; cl07896 580332003521 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 580332003522 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 580332003523 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 580332003524 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 580332003525 Pilin (bacterial filament); Region: Pilin; pfam00114 580332003526 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily; Region: Alpha_ANH_like_IV; cd01994 580332003527 Ligand Binding Site [chemical binding]; other site 580332003528 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332003529 Zn2+ binding site [ion binding]; other site 580332003530 Mg2+ binding site [ion binding]; other site 580332003531 Etoposide-induced protein 2.4 (EI24); Region: EI24; cl01126 580332003532 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 580332003533 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 580332003534 metal binding site [ion binding]; metal-binding site 580332003535 dimer interface [polypeptide binding]; other site 580332003536 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332003537 metal binding site [ion binding]; metal-binding site 580332003538 active site 580332003539 I-site; other site 580332003540 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 580332003541 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332003542 metal binding site [ion binding]; metal-binding site 580332003543 active site 580332003544 I-site; other site 580332003545 RecX family; Region: RecX; cl00936 580332003546 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332003547 metal binding site [ion binding]; metal-binding site 580332003548 active site 580332003549 I-site; other site 580332003550 Mechanosensitive ion channel; Region: MS_channel; pfam00924 580332003551 TraB family; Region: TraB; cl12050 580332003552 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 580332003553 ligand binding site [chemical binding]; other site 580332003554 flexible hinge region; other site 580332003555 BolA-like protein; Region: BolA; cl00386 580332003556 Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain...; Region: GRX_PICOT_like; cd03028 580332003557 putative GSH binding site [chemical binding]; other site 580332003558 catalytic residues [active] 580332003559 YaeQ protein; Region: YaeQ; cl01913 580332003560 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 580332003561 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 580332003562 putative substrate translocation pore; other site 580332003563 DsrC like protein; Region: DsrC; cl01101 580332003564 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 580332003565 PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA...; Region: PseudoU_synth_RsuA; cd02553 580332003566 active site 580332003567 uracil binding [chemical binding]; other site 580332003568 Nitroreductase-like family 5. 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_5; cd02148 580332003569 putative FMN binding site [chemical binding]; other site 580332003570 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 580332003571 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 580332003572 putative substrate translocation pore; other site 580332003573 asparagine synthase family amidotransferase; Region: trio_amidotrans; TIGR03104 580332003574 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 580332003575 active site 580332003576 dimer interface [polypeptide binding]; other site 580332003577 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 580332003578 Ligand Binding Site [chemical binding]; other site 580332003579 Molecular Tunnel; other site 580332003580 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 580332003581 EamA-like transporter family; Region: EamA; cl01037 580332003582 EamA-like transporter family; Region: EamA; cl01037 580332003583 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 580332003584 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332003585 dimer interface [polypeptide binding]; other site 580332003586 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 580332003587 putative CheW interface [polypeptide binding]; other site 580332003588 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 580332003589 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 580332003590 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332003591 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct...; Region: Trunc_globin; cd00454 580332003592 apolar tunnel; other site 580332003593 heme binding site [chemical binding]; other site 580332003594 dimerization interface [polypeptide binding]; other site 580332003595 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 580332003596 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 580332003597 GTP/Mg2+ binding site [chemical binding]; other site 580332003598 G4 box; other site 580332003599 G5 box; other site 580332003600 G1 box; other site 580332003601 Switch I region; other site 580332003602 G2 box; other site 580332003603 G3 box; other site 580332003604 Switch II region; other site 580332003605 Fumarate hydratase (Fumerase); Region: Fumerase; cl00851 580332003606 Fumarase C-terminus; Region: Fumerase_C; cl00795 580332003607 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14969 580332003608 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 580332003609 Walker A motif; other site 580332003610 ATP binding site [chemical binding]; other site 580332003611 Walker B motif; other site 580332003612 arginine finger; other site 580332003613 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 580332003614 YbaB/EbfC DNA-binding family; Region: YbaB_DNA_bd; cl00494 580332003615 recombination protein RecR; Reviewed; Region: recR; PRK00076 580332003616 RecR protein; Region: RecR; pfam02132 580332003617 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 580332003618 putative active site [active] 580332003619 putative metal-binding site [ion binding]; other site 580332003620 tetramer interface [polypeptide binding]; other site 580332003621 23S rRNA pseudouridylate synthase B; Provisional; Region: PRK10700 580332003622 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 580332003623 RNA binding surface [nucleotide binding]; other site 580332003624 PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like. This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to...; Region: PseudoU_synth_RluB; cd02556 580332003625 probable active site [active] 580332003626 cyclase homology domain; Region: CHD; cd07302 580332003627 nucleotidyl binding site; other site 580332003628 metal binding site [ion binding]; metal-binding site 580332003629 dimer interface [polypeptide binding]; other site 580332003630 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 580332003631 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 580332003632 active site 580332003633 ATP binding site [chemical binding]; other site 580332003634 substrate binding site [chemical binding]; other site 580332003635 activation loop (A-loop); other site 580332003636 L-aspartate oxidase; Provisional; Region: PRK09077 580332003637 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332003638 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 580332003639 RNA polymerase sigma factor RpoE; Region: RpoE_Sigma70; TIGR02939 580332003640 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 580332003641 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 580332003642 DNA binding residues [nucleotide binding] 580332003643 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 580332003644 Negative regulator of sigma E activity [Signal transduction mechanisms]; Region: RseB; COG3026 580332003645 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 580332003646 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; cl01178 580332003647 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 580332003648 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 580332003649 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 580332003650 protein binding site [polypeptide binding]; other site 580332003651 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 580332003652 protein binding site [polypeptide binding]; other site 580332003653 GTP-binding protein LepA; Provisional; Region: PRK05433 580332003654 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 580332003655 G1 box; other site 580332003656 putative GEF interaction site [polypeptide binding]; other site 580332003657 GTP/Mg2+ binding site [chemical binding]; other site 580332003658 Switch I region; other site 580332003659 G2 box; other site 580332003660 G3 box; other site 580332003661 Switch II region; other site 580332003662 G4 box; other site 580332003663 G5 box; other site 580332003664 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 580332003665 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 580332003666 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 580332003667 signal peptidase I; Provisional; Region: PRK10861 580332003668 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 580332003669 Catalytic site [active] 580332003670 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 580332003671 ribonuclease III; Reviewed; Region: rnc; PRK00102 580332003672 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 580332003673 dimerization interface [polypeptide binding]; other site 580332003674 active site 580332003675 metal binding site [ion binding]; metal-binding site 580332003676 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 580332003677 dsRNA binding site [nucleotide binding]; other site 580332003678 GTPase Era; Reviewed; Region: era; PRK00089 580332003679 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 580332003680 G1 box; other site 580332003681 GTP/Mg2+ binding site [chemical binding]; other site 580332003682 Switch I region; other site 580332003683 G2 box; other site 580332003684 Switch II region; other site 580332003685 G3 box; other site 580332003686 G4 box; other site 580332003687 G5 box; other site 580332003688 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 580332003689 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 580332003690 Recombination protein O N terminal; Region: RecO_N; cl15812 580332003691 Recombination protein O C terminal; Region: RecO_C; pfam02565 580332003692 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in the...; Region: PNPsynthase; cd00003 580332003693 active site 580332003694 hydrophilic channel; other site 580332003695 dimerization interface [polypeptide binding]; other site 580332003696 catalytic residues [active] 580332003697 active site lid [active] 580332003698 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 580332003699 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 580332003700 enoyl-CoA hydratase; Validated; Region: PRK08788 580332003701 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 580332003702 substrate binding site [chemical binding]; other site 580332003703 oxyanion hole (OAH) forming residues; other site 580332003704 trimer interface [polypeptide binding]; other site 580332003705 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 580332003706 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 580332003707 dimer interface [polypeptide binding]; other site 580332003708 phosphorylation site [posttranslational modification] 580332003709 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 580332003710 ATP binding site [chemical binding]; other site 580332003711 Mg2+ binding site [ion binding]; other site 580332003712 G-X-G motif; other site 580332003713 Response regulator receiver domain; Region: Response_reg; pfam00072 580332003714 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 580332003715 active site 580332003716 phosphorylation site [posttranslational modification] 580332003717 intermolecular recognition site; other site 580332003718 dimerization interface [polypeptide binding]; other site 580332003719 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 580332003720 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 580332003721 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 580332003722 active site 580332003723 phosphorylation site [posttranslational modification] 580332003724 intermolecular recognition site; other site 580332003725 dimerization interface [polypeptide binding]; other site 580332003726 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332003727 Zn2+ binding site [ion binding]; other site 580332003728 Mg2+ binding site [ion binding]; other site 580332003729 ZipA C-terminal domain. ZipA, a membrane-anchored protein, is one of at least nine essential gene products necessary for assembly of the septal ring which mediates cell division in E.coli. ZipA and FtsA directly bind FtsZ, a homolog of eukaryotic...; Region: ZipA; cl12038 580332003730 FtsZ protein binding site [polypeptide binding]; other site 580332003731 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 580332003732 NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction...; Region: LIGANc; cd00114 580332003733 nucleotide binding pocket [chemical binding]; other site 580332003734 K-X-D-G motif; other site 580332003735 catalytic site [active] 580332003736 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 580332003737 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 580332003738 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 580332003739 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 580332003740 Dimer interface [polypeptide binding]; other site 580332003741 BRCT sequence motif; other site 580332003742 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 580332003743 active site 580332003744 tetramer interface; other site 580332003745 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 580332003746 active site 580332003747 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 580332003748 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 580332003749 active site 580332003750 catalytic residues [active] 580332003751 metal binding site [ion binding]; metal-binding site 580332003752 Ion channel; Region: Ion_trans_2; cl11596 580332003753 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 580332003754 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332003755 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 580332003756 Response regulator receiver domain; Region: Response_reg; pfam00072 580332003757 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 580332003758 active site 580332003759 phosphorylation site [posttranslational modification] 580332003760 intermolecular recognition site; other site 580332003761 dimerization interface [polypeptide binding]; other site 580332003762 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332003763 metal binding site [ion binding]; metal-binding site 580332003764 active site 580332003765 I-site; other site 580332003766 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 580332003767 Response regulator receiver domain; Region: Response_reg; pfam00072 580332003768 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 580332003769 active site 580332003770 phosphorylation site [posttranslational modification] 580332003771 intermolecular recognition site; other site 580332003772 dimerization interface [polypeptide binding]; other site 580332003773 HDOD domain; Region: HDOD; pfam08668 580332003774 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 580332003775 Zn2+ binding site [ion binding]; other site 580332003776 Mg2+ binding site [ion binding]; other site 580332003777 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 580332003778 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 580332003779 active site 580332003780 phosphorylation site [posttranslational modification] 580332003781 intermolecular recognition site; other site 580332003782 dimerization interface [polypeptide binding]; other site 580332003783 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332003784 Zn2+ binding site [ion binding]; other site 580332003785 Mg2+ binding site [ion binding]; other site 580332003786 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 580332003787 octamerization interface [polypeptide binding]; other site 580332003788 diferric-oxygen binding site [ion binding]; other site 580332003789 sensory histidine kinase AtoS; Provisional; Region: PRK11360 580332003790 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 580332003791 ATP binding site [chemical binding]; other site 580332003792 Mg2+ binding site [ion binding]; other site 580332003793 G-X-G motif; other site 580332003794 HPP family; Region: HPP; pfam04982 580332003795 FOG: CBS domain [General function prediction only]; Region: COG0517 580332003796 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the HPP motif domain. These proteins are integral membrane proteins with four transmembrane spanning helices. The function of these proteins is...; Region: CBS_pair_HPP_assoc; cd04600 580332003797 aconitate hydratase; Validated; Region: PRK09277 580332003798 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 580332003799 substrate binding site [chemical binding]; other site 580332003800 ligand binding site [chemical binding]; other site 580332003801 Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group...; Region: AcnA_IRP_Swivel; cd01580 580332003802 substrate binding site [chemical binding]; other site 580332003803 CHASE domain; Region: CHASE; cl01369 580332003804 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332003805 Zn2+ binding site [ion binding]; other site 580332003806 Mg2+ binding site [ion binding]; other site 580332003807 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 580332003808 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 580332003809 putative substrate translocation pore; other site 580332003810 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 580332003811 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 580332003812 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 580332003813 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 580332003814 Helix-turn-helix domains; Region: HTH; cl00088 580332003815 tRNA 2-selenouridine synthase; Provisional; Region: PRK11784 580332003816 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 580332003817 active site residue [active] 580332003818 selenophosphate synthetase; Provisional; Region: PRK00943 580332003819 Selenophosphate synthetase (SelD) catalyzes the conversion of selenium to selenophosphate which is required by a number of bacterial, archaeal and eukaryotic organisms for synthesis of Secys-tRNA, the precursor of selenocysteine in selenoenzymes. The...; Region: SelD; cd02195 580332003820 dimerization interface [polypeptide binding]; other site 580332003821 putative ATP binding site [chemical binding]; other site 580332003822 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 580332003823 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cl02529 580332003824 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 580332003825 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 580332003826 Ankyrin repeats (many copies); Region: Ank_5; pfam13857 580332003827 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332003828 Zn2+ binding site [ion binding]; other site 580332003829 Mg2+ binding site [ion binding]; other site 580332003830 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 580332003831 heme-binding site [chemical binding]; other site 580332003832 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332003833 metal binding site [ion binding]; metal-binding site 580332003834 active site 580332003835 I-site; other site 580332003836 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 580332003837 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332003838 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332003839 Protein of unknown function (DUF2721); Region: DUF2721; pfam11026 580332003840 Flavin Reductases; Region: FlaRed; cl00801 580332003841 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; cl00727 580332003842 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 580332003843 Major Facilitator Superfamily; Region: MFS_1; pfam07690 580332003844 putative substrate translocation pore; other site 580332003845 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 580332003846 Domain of unknown function (DUF1924); Region: DUF1924; pfam09086 580332003847 Dihaem cytochrome c; Region: DHC; pfam09626 580332003848 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 580332003849 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 580332003850 dimerization interface [polypeptide binding]; other site 580332003851 domain crossover interface; other site 580332003852 redox-dependent activation switch; other site 580332003853 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 580332003854 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332003855 putative diguanylate cyclase; Provisional; Region: PRK09776 580332003856 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 580332003857 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 580332003858 putative active site [active] 580332003859 heme pocket [chemical binding]; other site 580332003860 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 580332003861 putative active site [active] 580332003862 heme pocket [chemical binding]; other site 580332003863 GAF domain; Region: GAF_2; pfam13185 580332003864 PAS fold; Region: PAS_4; pfam08448 580332003865 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 580332003866 putative active site [active] 580332003867 heme pocket [chemical binding]; other site 580332003868 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 580332003869 dimer interface [polypeptide binding]; other site 580332003870 phosphorylation site [posttranslational modification] 580332003871 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 580332003872 ATP binding site [chemical binding]; other site 580332003873 Mg2+ binding site [ion binding]; other site 580332003874 G-X-G motif; other site 580332003875 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 580332003876 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 580332003877 dimer interface [polypeptide binding]; other site 580332003878 phosphorylation site [posttranslational modification] 580332003879 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 580332003880 ATP binding site [chemical binding]; other site 580332003881 Mg2+ binding site [ion binding]; other site 580332003882 G-X-G motif; other site 580332003883 Response regulator receiver domain; Region: Response_reg; pfam00072 580332003884 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 580332003885 active site 580332003886 phosphorylation site [posttranslational modification] 580332003887 intermolecular recognition site; other site 580332003888 dimerization interface [polypeptide binding]; other site 580332003889 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 580332003890 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 580332003891 active site 580332003892 phosphorylation site [posttranslational modification] 580332003893 intermolecular recognition site; other site 580332003894 dimerization interface [polypeptide binding]; other site 580332003895 PAS domain S-box; Region: sensory_box; TIGR00229 580332003896 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 580332003897 putative active site [active] 580332003898 heme pocket [chemical binding]; other site 580332003899 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332003900 Zn2+ binding site [ion binding]; other site 580332003901 Mg2+ binding site [ion binding]; other site 580332003902 DNA repair protein RadA; Provisional; Region: PRK11823 580332003903 Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of...; Region: Sms; cd01121 580332003904 Walker A motif/ATP binding site; other site 580332003905 ATP binding site [chemical binding]; other site 580332003906 Walker B motif; other site 580332003907 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 580332003908 Cation efflux family; Region: Cation_efflux; cl00316 580332003909 Protein of unknown function, DUF599; Region: DUF599; cl01575 580332003910 Uncharacterized membrane-anchored protein conserved in bacteria [Function unknown]; Region: COG4705 580332003911 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 580332003912 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 580332003913 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 580332003914 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 580332003915 2-haloalkanoic acid dehalogenase, type II; Region: HAD_type_II; TIGR01428 580332003916 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 580332003917 motif II; other site 580332003918 EamA-like transporter family; Region: EamA; cl01037 580332003919 EamA-like transporter family; Region: EamA; cl01037 580332003920 ATPase, P-type (transporting), HAD superfamily, subfamily IC; Region: ATPase_P-type; TIGR01494 580332003921 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 580332003922 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 580332003923 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 580332003924 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 580332003925 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 580332003926 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 580332003927 dimer interface [polypeptide binding]; other site 580332003928 active site 580332003929 metal binding site [ion binding]; metal-binding site 580332003930 glutathione binding site [chemical binding]; other site 580332003931 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 580332003932 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 580332003933 active site 580332003934 catalytic tetrad [active] 580332003935 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 580332003936 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14189 580332003937 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 580332003938 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 580332003939 homodimer interface [polypeptide binding]; other site 580332003940 NADP binding site [chemical binding]; other site 580332003941 substrate binding site [chemical binding]; other site 580332003942 Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers; Region: pyrophosphatase; cd00412 580332003943 dimer interface [polypeptide binding]; other site 580332003944 substrate binding site [chemical binding]; other site 580332003945 metal binding sites [ion binding]; metal-binding site 580332003946 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN; cd02933 580332003947 FMN binding site [chemical binding]; other site 580332003948 active site 580332003949 substrate binding site [chemical binding]; other site 580332003950 catalytic residue [active] 580332003951 YceI-like domain; Region: YceI; cl01001 580332003952 YceI-like domain; Region: YceI; cl01001 580332003953 Pirin-related protein [General function prediction only]; Region: COG1741 580332003954 Cupin domain; Region: Cupin_2; cl09118 580332003955 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 580332003956 Transcriptional regulator [Transcription]; Region: LysR; COG0583 580332003957 Helix-turn-helix domains; Region: HTH; cl00088 580332003958 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 580332003959 putative effector binding pocket; other site 580332003960 dimerization interface [polypeptide binding]; other site 580332003961 TPR repeat; Region: TPR_11; pfam13414 580332003962 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 580332003963 binding surface 580332003964 TPR motif; other site 580332003965 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; cl15394 580332003966 Cytochrome c; Region: Cytochrom_C; cl11414 580332003967 Inorganic pyrophosphatase [Energy production and conversion]; Region: OVP1; cl11452 580332003968 membrane-bound proton-translocating pyrophosphatase; Validated; Region: hppA; PRK00733 580332003969 Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to PFK family that includes ATP- and pyrophosphate (PPi)- dependent phosphofructokinases; Region: PFK; cl00204 580332003970 active site 580332003971 ADP/pyrophosphate binding site [chemical binding]; other site 580332003972 dimerization interface [polypeptide binding]; other site 580332003973 allosteric effector site; other site 580332003974 fructose-1,6-bisphosphate binding site; other site 580332003975 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 580332003976 Domain of unknown function (DUF336); Region: DUF336; cl01249 580332003977 adenylate kinase; Reviewed; Region: adk; PRK00279 580332003978 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 580332003979 AMP-binding site [chemical binding]; other site 580332003980 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 580332003981 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 580332003982 Ligand binding site; other site 580332003983 oligomer interface; other site 580332003984 Trm112p-like protein; Region: Trm112p; cl01066 580332003985 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 580332003986 tetraacyldisaccharide 4'-kinase; Region: lpxK; TIGR00682 580332003987 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 580332003988 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 580332003989 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 580332003990 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 580332003991 generic binding surface II; other site 580332003992 generic binding surface I; other site 580332003993 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl15769 580332003994 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 580332003995 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 580332003996 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 580332003997 inhibitor-cofactor binding pocket; inhibition site 580332003998 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332003999 catalytic residue [active] 580332004000 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332004001 dimer interface [polypeptide binding]; other site 580332004002 putative CheW interface [polypeptide binding]; other site 580332004003 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 580332004004 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 580332004005 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 580332004006 Ligand binding site; other site 580332004007 Putative Catalytic site; other site 580332004008 DXD motif; other site 580332004009 putative formyltransferase; Provisional; Region: PRK06988 580332004010 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 580332004011 active site 580332004012 substrate binding site [chemical binding]; other site 580332004013 cosubstrate binding site; other site 580332004014 catalytic site [active] 580332004015 Carboxy-terminal domain of Formyltransferase and similar domains; Region: FMT_C_like; cl14785 580332004016 NAD-dependent epimerase/dehydratase family protein; Provisional; Region: PRK11908 580332004017 Arna decarboxylase_like, extended (e) SDRs; Region: Arna_like_SDR_e; cd05257 580332004018 NAD binding site [chemical binding]; other site 580332004019 substrate binding site [chemical binding]; other site 580332004020 active site 580332004021 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD; Provisional; Region: PRK15394 580332004022 Catalytic domain of Escherichia coli 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD and other bacterial homologs; Region: CE4_ArnD; cd10939 580332004023 putative active site [active] 580332004024 putative catalytic site [active] 580332004025 putative Zn binding site [ion binding]; other site 580332004026 HDOD domain; Region: HDOD; pfam08668 580332004027 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 580332004028 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332004029 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 580332004030 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332004031 Domain of unknown function DUF302; Region: DUF302; cl01364 580332004032 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 ADP-ribose...; Region: Macro_Appr_pase_like; cd02908 580332004033 putative ADP-ribose binding site [chemical binding]; other site 580332004034 putative active site [active] 580332004035 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 580332004036 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332004037 metabolite-proton symporter; Region: 2A0106; TIGR00883 580332004038 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 580332004039 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 580332004040 ATP binding site [chemical binding]; other site 580332004041 Mg2+ binding site [ion binding]; other site 580332004042 G-X-G motif; other site 580332004043 MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL. EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second...; Region: MutL_Trans_MutL; cd03482 580332004044 ATP binding site [chemical binding]; other site 580332004045 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 580332004046 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 580332004047 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 580332004048 N-terminal plug; other site 580332004049 ligand-binding site [chemical binding]; other site 580332004050 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 580332004051 4Fe-4S binding domain; Region: Fer4_5; pfam12801 580332004052 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 580332004053 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 580332004054 Gram-negative bacterial tonB protein; Region: TonB; cl10048 580332004055 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 580332004056 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 580332004057 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 580332004058 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; cl15379 580332004059 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332004060 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 580332004061 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; cl00566 580332004062 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 580332004063 MASE1; Region: MASE1; pfam05231 580332004064 PAS fold; Region: PAS_3; pfam08447 580332004065 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 580332004066 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 580332004067 PAS domain; Region: PAS_9; pfam13426 580332004068 putative active site [active] 580332004069 heme pocket [chemical binding]; other site 580332004070 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332004071 metal binding site [ion binding]; metal-binding site 580332004072 active site 580332004073 I-site; other site 580332004074 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 580332004075 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 580332004076 DNA internalization-related competence protein ComEC/Rec2; Region: ComEC_Rec2; TIGR00361 580332004077 Competence protein; Region: Competence; cl00471 580332004078 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 580332004079 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; cl01261 580332004080 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 580332004081 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 580332004082 Walker A/P-loop; other site 580332004083 ATP binding site [chemical binding]; other site 580332004084 Q-loop/lid; other site 580332004085 ABC transporter signature motif; other site 580332004086 Walker B; other site 580332004087 D-loop; other site 580332004088 H-loop/switch region; other site 580332004089 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 580332004090 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 580332004091 FtsX-like permease family; Region: FtsX; cl15850 580332004092 Sulfatase; Region: Sulfatase; cl10460 580332004093 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 580332004094 Mechanosensitive ion channel; Region: MS_channel; pfam00924 580332004095 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 580332004096 ligand binding site [chemical binding]; other site 580332004097 flexible hinge region; other site 580332004098 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 580332004099 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 580332004100 tRNA(Ile)-lysidine synthetase; Provisional; Region: tilS; PRK10660 580332004101 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 580332004102 Ligand Binding Site [chemical binding]; other site 580332004103 TilS substrate binding domain; Region: TilS; pfam09179 580332004104 B3/4 domain; Region: B3_4; cl11458 580332004105 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 580332004106 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 580332004107 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 580332004108 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 580332004109 DctM-like transporters; Region: DctM; pfam06808 580332004110 Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside...; Region: NDPk_I; cd04413 580332004111 active site 580332004112 multimer interface [polypeptide binding]; other site 580332004113 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 580332004114 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 580332004115 FeS/SAM binding site; other site 580332004116 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 580332004117 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 580332004118 binding surface 580332004119 TPR motif; other site 580332004120 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 580332004121 binding surface 580332004122 TPR motif; other site 580332004123 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 580332004124 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 580332004125 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 580332004126 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 580332004127 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 580332004128 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 580332004129 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: HisRS-like_core; cd00773 580332004130 dimer interface [polypeptide binding]; other site 580332004131 motif 1; other site 580332004132 active site 580332004133 motif 2; other site 580332004134 motif 3; other site 580332004135 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 580332004136 anticodon binding site; other site 580332004137 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 580332004138 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 580332004139 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 580332004140 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 580332004141 Trp docking motif [polypeptide binding]; other site 580332004142 active site 580332004143 GTP-binding protein Der; Reviewed; Region: PRK00093 580332004144 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 580332004145 G1 box; other site 580332004146 GTP/Mg2+ binding site [chemical binding]; other site 580332004147 Switch I region; other site 580332004148 G2 box; other site 580332004149 Switch II region; other site 580332004150 G3 box; other site 580332004151 G4 box; other site 580332004152 G5 box; other site 580332004153 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 580332004154 G1 box; other site 580332004155 GTP/Mg2+ binding site [chemical binding]; other site 580332004156 Switch I region; other site 580332004157 G2 box; other site 580332004158 G3 box; other site 580332004159 Switch II region; other site 580332004160 G4 box; other site 580332004161 G5 box; other site 580332004162 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of...; Region: Sm_like; cl00259 580332004163 Sm1 motif; other site 580332004164 D1 - D2 interaction site; other site 580332004165 D3 - B interaction site; other site 580332004166 Hfq - Hfq interaction site; other site 580332004167 RNA binding pocket [nucleotide binding]; other site 580332004168 Sm2 motif; other site 580332004169 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 580332004170 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 580332004171 HflX GTPase family; Region: HflX; cd01878 580332004172 G1 box; other site 580332004173 GTP/Mg2+ binding site [chemical binding]; other site 580332004174 Switch I region; other site 580332004175 G2 box; other site 580332004176 G3 box; other site 580332004177 Switch II region; other site 580332004178 G4 box; other site 580332004179 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 580332004180 Band_7_HflK: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfK (High frequency of lysogenization K). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflK; cd03404 580332004181 HflK protein; Region: hflK; TIGR01933 580332004182 HflC protein; Region: hflC; TIGR01932 580332004183 Band_7_HflC: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfC (High frequency of lysogenization C). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflC; cd03405 580332004184 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; cl01275 580332004185 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: PRK12421 580332004186 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: HisRS-like_core; cd00773 580332004187 dimer interface [polypeptide binding]; other site 580332004188 motif 1; other site 580332004189 active site 580332004190 motif 2; other site 580332004191 motif 3; other site 580332004192 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 580332004193 Adenylosuccinate synthetase (AdSS) catalyzes the first step in the de novo biosynthesis of AMP. IMP and L-aspartate are conjugated in a two-step reaction accompanied by the hydrolysis of GTP to GDP in the presence of Mg2+. In the first step, the...; Region: AdSS; cd03108 580332004194 GDP-binding site [chemical binding]; other site 580332004195 ACT binding site; other site 580332004196 IMP binding site; other site 580332004197 ribonuclease R; Region: RNase_R; TIGR02063 580332004198 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 580332004199 RNB domain; Region: RNB; pfam00773 580332004200 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important...; Region: S1_RNase_R; cd04471 580332004201 RNA binding site [nucleotide binding]; other site 580332004202 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 580332004203 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 580332004204 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 580332004205 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 580332004206 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 580332004207 P-loop; other site 580332004208 Magnesium ion binding site [ion binding]; other site 580332004209 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 580332004210 Magnesium ion binding site [ion binding]; other site 580332004211 Protein of unknown function (DUF1161); Region: DUF1161; pfam06649 580332004212 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 580332004213 ligand binding site [chemical binding]; other site 580332004214 Protein of unknown function (DUF3025); Region: DUF3025; pfam11227 580332004215 MltA-interacting protein MipA; Region: MipA; cl01504 580332004216 squalene-associated FAD-dependent desaturase; Region: HpnE; TIGR03467 580332004217 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 580332004218 active site lid residues [active] 580332004219 substrate binding pocket [chemical binding]; other site 580332004220 catalytic residues [active] 580332004221 substrate-Mg2+ binding site; other site 580332004222 aspartate-rich region 1; other site 580332004223 aspartate-rich region 2; other site 580332004224 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 580332004225 active site lid residues [active] 580332004226 substrate binding pocket [chemical binding]; other site 580332004227 catalytic residues [active] 580332004228 substrate-Mg2+ binding site; other site 580332004229 aspartate-rich region 1; other site 580332004230 aspartate-rich region 2; other site 580332004231 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332004232 HemK family putative methylases; Region: hemK_fam; TIGR00536 580332004233 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 580332004234 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 580332004235 metal binding site [ion binding]; metal-binding site 580332004236 dimer interface [polypeptide binding]; other site 580332004237 Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine...; Region: ArsC_Yffb; cd03035 580332004238 ArsC family; Region: ArsC; pfam03960 580332004239 putative catalytic residues [active] 580332004240 pilus retraction protein PilT; Region: pilT_fam; TIGR01420 580332004241 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332004242 Walker A motif; other site 580332004243 ATP binding site [chemical binding]; other site 580332004244 Walker B motif; other site 580332004245 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 580332004246 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (also called THP succinyltransferase): THDP N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA; Region: LbH_THP_succinylT; cd03350 580332004247 active site 580332004248 substrate binding site [chemical binding]; other site 580332004249 trimer interface [polypeptide binding]; other site 580332004250 CoA binding site [chemical binding]; other site 580332004251 succinyldiaminopimelate transaminase; Region: DapC_gpp; TIGR03538 580332004252 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 580332004253 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332004254 homodimer interface [polypeptide binding]; other site 580332004255 catalytic residue [active] 580332004256 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 580332004257 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 580332004258 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 580332004259 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 580332004260 fructose-bisphosphate aldolase; Provisional; Region: PRK09250 580332004261 Class I fructose-1,6-bisphosphate (FBP) aldolases of the archaeal type (DhnA homologs); Region: DhnA; cd00958 580332004262 putative active site; other site 580332004263 catalytic residue [active] 580332004264 Bacterial Ig-like domain (group 2); Region: Big_2; cl02708 580332004265 Kelch motif; Region: Kelch_1; cl02701 580332004266 kelch-like protein; Provisional; Region: PHA03098 580332004267 Kelch motif; Region: Kelch_1; cl02701 580332004268 Kelch motif; Region: Kelch_1; cl02701 580332004269 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 580332004270 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332004271 ATP-grasp domain; Region: ATP-grasp_4; cl03087 580332004272 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 580332004273 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_9; cd07245 580332004274 dimer interface [polypeptide binding]; other site 580332004275 putative metal binding site [ion binding]; other site 580332004276 Predicted ATPase [General function prediction only]; Region: COG1485 580332004277 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 580332004278 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 580332004279 substrate binding pocket [chemical binding]; other site 580332004280 membrane-bound complex binding site; other site 580332004281 hinge residues; other site 580332004282 PAS fold; Region: PAS_4; pfam08448 580332004283 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 580332004284 putative active site [active] 580332004285 heme pocket [chemical binding]; other site 580332004286 GAF domain; Region: GAF_2; pfam13185 580332004287 GAF domain; Region: GAF; cl15785 580332004288 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 580332004289 PAS domain; Region: PAS_9; pfam13426 580332004290 putative active site [active] 580332004291 heme pocket [chemical binding]; other site 580332004292 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332004293 metal binding site [ion binding]; metal-binding site 580332004294 active site 580332004295 I-site; other site 580332004296 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 580332004297 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 580332004298 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 580332004299 active site 580332004300 catalytic tetrad [active] 580332004301 The Class III extradiol dioxygenase, 4,5-DOPA Dioxygenase, catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine; Region: 45_DOPA_Dioxygenase; cd07363 580332004302 putative active site [active] 580332004303 metal binding site [ion binding]; metal-binding site 580332004304 Uncharacterized conserved protein [Function unknown]; Region: COG3287 580332004305 FIST N domain; Region: FIST; cl10701 580332004306 FIST C domain; Region: FIST_C; pfam10442 580332004307 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 580332004308 PAS domain; Region: PAS_9; pfam13426 580332004309 putative active site [active] 580332004310 heme pocket [chemical binding]; other site 580332004311 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332004312 metal binding site [ion binding]; metal-binding site 580332004313 active site 580332004314 I-site; other site 580332004315 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 580332004316 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 580332004317 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 580332004318 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large; Region: ABC_SMC_barmotin; cd03278 580332004319 Walker A/P-loop; other site 580332004320 ATP binding site [chemical binding]; other site 580332004321 Q-loop/lid; other site 580332004322 fzo-like conserved region; Region: Fzo_mitofusin; pfam04799 580332004323 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; cl05797 580332004324 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large; Region: ABC_SMC_barmotin; cd03278 580332004325 ABC transporter signature motif; other site 580332004326 Walker B; other site 580332004327 D-loop; other site 580332004328 H-loop/switch region; other site 580332004329 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 580332004330 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 580332004331 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 580332004332 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a key...; Region: CBS_pair_IMPDH; cd04601 580332004333 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of the guanine...; Region: IMPDH; cd00381 580332004334 active site 580332004335 GMP synthase; Reviewed; Region: guaA; PRK00074 580332004336 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 580332004337 AMP/PPi binding site [chemical binding]; other site 580332004338 candidate oxyanion hole; other site 580332004339 catalytic triad [active] 580332004340 potential glutamine specificity residues [chemical binding]; other site 580332004341 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 580332004342 ATP Binding subdomain [chemical binding]; other site 580332004343 Ligand Binding sites [chemical binding]; other site 580332004344 Dimerization subdomain; other site 580332004345 MASE1; Region: MASE1; pfam05231 580332004346 hypothetical protein; Provisional; Region: PRK13560 580332004347 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 580332004348 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 580332004349 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332004350 metal binding site [ion binding]; metal-binding site 580332004351 active site 580332004352 I-site; other site 580332004353 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 580332004354 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cl00065 580332004355 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cl00065 580332004356 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 580332004357 Protein of unknown function (DUF3281); Region: DUF3281; pfam11685 580332004358 FecR protein; Region: FecR; pfam04773 580332004359 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 580332004360 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 580332004361 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 580332004362 metal-binding site [ion binding] 580332004363 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 580332004364 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 580332004365 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 580332004366 L-ribulose-5-phosphate 4-epimerase; Reviewed; Region: araD; PRK08193 580332004367 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II); Region: Aldolase_II; cl00214 580332004368 intersubunit interface [polypeptide binding]; other site 580332004369 active site 580332004370 Zn2+ binding site [ion binding]; other site 580332004371 Adenine/guanine phosphoribosyltransferases and related PRPP-binding proteins [Nucleotide transport and metabolism]; Region: Apt; COG0503 580332004372 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 580332004373 active site 580332004374 methylthioribose-1-phosphate isomerase; Reviewed; Region: mtnA; PRK05720 580332004375 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]; Region: COG0182; cl00348 580332004376 ribosome maturation protein RimP; Reviewed; Region: PRK00092 580332004377 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of...; Region: Sm_like; cl00259 580332004378 YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix...; Region: YlxS_C; cd01734 580332004379 Sm1 motif; other site 580332004380 predicted subunit interaction site [polypeptide binding]; other site 580332004381 RNA binding pocket [nucleotide binding]; other site 580332004382 Sm2 motif; other site 580332004383 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 580332004384 NusA N-terminal domain; Region: NusA_N; pfam08529 580332004385 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 580332004386 RNA binding site [nucleotide binding]; other site 580332004387 homodimer interface [polypeptide binding]; other site 580332004388 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 580332004389 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 580332004390 G-X-X-G motif; other site 580332004391 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 580332004392 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 580332004393 translation initiation factor IF-2; Validated; Region: infB; PRK05306 580332004394 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 580332004395 translation initiation factor IF-2; Region: IF-2; TIGR00487 580332004396 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 580332004397 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 580332004398 G1 box; other site 580332004399 putative GEF interaction site [polypeptide binding]; other site 580332004400 GTP/Mg2+ binding site [chemical binding]; other site 580332004401 Switch I region; other site 580332004402 G2 box; other site 580332004403 G3 box; other site 580332004404 Switch II region; other site 580332004405 G4 box; other site 580332004406 G5 box; other site 580332004407 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 580332004408 Translation-initiation factor 2; Region: IF-2; pfam11987 580332004409 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 580332004410 Ribosome-binding factor A; Region: RBFA; cl00542 580332004411 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 580332004412 PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific...; Region: PseudoU_synth_EcTruB; cd02573 580332004413 RNA binding site [nucleotide binding]; other site 580332004414 active site 580332004415 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 580332004416 16S/18S rRNA binding site [nucleotide binding]; other site 580332004417 S13e-L30e interaction site [polypeptide binding]; other site 580332004418 25S rRNA binding site [nucleotide binding]; other site 580332004419 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 580332004420 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 580332004421 RNase E interface [polypeptide binding]; other site 580332004422 trimer interface [polypeptide binding]; other site 580332004423 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 580332004424 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 580332004425 RNase E interface [polypeptide binding]; other site 580332004426 trimer interface [polypeptide binding]; other site 580332004427 active site 580332004428 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 580332004429 putative nucleic acid binding region [nucleotide binding]; other site 580332004430 G-X-X-G motif; other site 580332004431 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 580332004432 RNA binding site [nucleotide binding]; other site 580332004433 domain interface; other site 580332004434 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 580332004435 macrolide transporter subunit MacA; Provisional; Region: PRK11578 580332004436 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 580332004437 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 580332004438 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 580332004439 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 580332004440 Walker A/P-loop; other site 580332004441 ATP binding site [chemical binding]; other site 580332004442 Q-loop/lid; other site 580332004443 ABC transporter signature motif; other site 580332004444 Walker B; other site 580332004445 D-loop; other site 580332004446 H-loop/switch region; other site 580332004447 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 580332004448 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 580332004449 FtsX-like permease family; Region: FtsX; cl15850 580332004450 Family-5 Uracil-DNA glycosylases (UDG), found in thermophilic organisms; Region: UDG_F5_TTUDGB_like; cd10031 580332004451 Fe-S cluster binding site [ion binding]; other site 580332004452 DNA binding site [nucleotide binding] 580332004453 active site 580332004454 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 580332004455 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 580332004456 GIY-YIG motif/motif A; other site 580332004457 active site 580332004458 catalytic site [active] 580332004459 putative DNA binding site [nucleotide binding]; other site 580332004460 metal binding site [ion binding]; metal-binding site 580332004461 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 580332004462 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 580332004463 DsrC like protein; Region: DsrC; cl01101 580332004464 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 580332004465 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 580332004466 global nitrogen regulator NtcA, cyanobacterial; Region: NtcA_cyano; TIGR03697 580332004467 ligand binding site [chemical binding]; other site 580332004468 flexible hinge region; other site 580332004469 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 580332004470 putative switch regulator; other site 580332004471 non-specific DNA interactions [nucleotide binding]; other site 580332004472 DNA binding site [nucleotide binding] 580332004473 sequence specific DNA binding site [nucleotide binding]; other site 580332004474 putative cAMP binding site [chemical binding]; other site 580332004475 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 580332004476 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 580332004477 dimer interface [polypeptide binding]; other site 580332004478 putative anticodon binding site; other site 580332004479 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 580332004480 motif 1; other site 580332004481 active site 580332004482 motif 2; other site 580332004483 motif 3; other site 580332004484 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332004485 AAA domain; Region: AAA_23; pfam13476 580332004486 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 580332004487 AAA domain; Region: AAA_21; pfam13304 580332004488 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332004489 ABC transporter signature motif; other site 580332004490 Walker B; other site 580332004491 D-loop; other site 580332004492 H-loop/switch region; other site 580332004493 peptide chain release factor 2; Validated; Region: prfB; PRK00578 580332004494 RF-1 domain; Region: RF-1; cl02875 580332004495 RF-1 domain; Region: RF-1; cl02875 580332004496 MgtC family; Region: MgtC; pfam02308 580332004497 Predicted membrane protein [Function unknown]; Region: COG3174 580332004498 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 580332004499 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 580332004500 DHH family; Region: DHH; pfam01368 580332004501 DHHA1 domain; Region: DHHA1; pfam02272 580332004502 aspartate kinase; Reviewed; Region: PRK06635 580332004503 AAK_AKii-LysC-BS: Amino Acid Kinase Superfamily (AAK), AKii; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, and the lysine plus threonine-sensitive...; Region: AAK_AKii-LysC-BS; cd04261 580332004504 putative nucleotide binding site [chemical binding]; other site 580332004505 putative catalytic residues [active] 580332004506 putative Mg ion binding site [ion binding]; other site 580332004507 putative aspartate binding site [chemical binding]; other site 580332004508 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins; Region: ACT_AKii-LysC-BS-like_1; cd04913 580332004509 putative allosteric regulatory site; other site 580332004510 ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains; Region: ACT_AKii-LysC-BS-like_2; cd04936 580332004511 putative allosteric regulatory residue; other site 580332004512 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 580332004513 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 580332004514 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 580332004515 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332004516 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 580332004517 RNA/DNA hybrid binding site [nucleotide binding]; other site 580332004518 active site 580332004519 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 580332004520 DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; Region: DNA_pol_III_epsilon_Ecoli_like; cd06131 580332004521 active site 580332004522 catalytic site [active] 580332004523 substrate binding site [chemical binding]; other site 580332004524 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 580332004525 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 580332004526 HI0933-like protein; Region: HI0933_like; pfam03486 580332004527 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332004528 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332004529 LemA family; Region: LemA; cl00742 580332004530 Repair protein; Region: Repair_PSII; cl01535 580332004531 Repair protein; Region: Repair_PSII; cl01535 580332004532 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 580332004533 putative active site [active] 580332004534 putative metal binding residues [ion binding]; other site 580332004535 signature motif; other site 580332004536 putative triphosphate binding site [ion binding]; other site 580332004537 CHAD domain; Region: CHAD; cl10506 580332004538 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 580332004539 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 580332004540 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332004541 Family description; Region: UvrD_C_2; cl15862 580332004542 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 580332004543 classical (c) SDRs; Region: SDR_c; cd05233 580332004544 NAD(P) binding site [chemical binding]; other site 580332004545 active site 580332004546 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 580332004547 Maf-like protein; Region: Maf; pfam02545 580332004548 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 580332004549 active site 580332004550 dimer interface [polypeptide binding]; other site 580332004551 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 580332004552 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 580332004553 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 580332004554 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 580332004555 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 580332004556 dimer interface [polypeptide binding]; other site 580332004557 active site 580332004558 CoA binding pocket [chemical binding]; other site 580332004559 Acyl transferase domain; Region: Acyl_transf_1; cl08282 580332004560 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 580332004561 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 580332004562 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 580332004563 NAD(P) binding site [chemical binding]; other site 580332004564 homotetramer interface [polypeptide binding]; other site 580332004565 homodimer interface [polypeptide binding]; other site 580332004566 active site 580332004567 Phosphopantetheine attachment site; Region: PP-binding; cl09936 580332004568 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 580332004569 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 580332004570 dimer interface [polypeptide binding]; other site 580332004571 active site 580332004572 ADCL_like: 4-Amino-4-deoxychorismate lyase: is a member of the fold-type IV of PLP dependent enzymes that converts 4-amino-4-deoxychorismate (ADC) to p-aminobenzoate and pyruvate. Based on the information available from the crystal structure, most...; Region: ADCL_like; cd01559 580332004573 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332004574 catalytic residue [active] 580332004575 YceG-like family; Region: YceG; pfam02618 580332004576 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 580332004577 dimerization interface [polypeptide binding]; other site 580332004578 thymidylate kinase; Validated; Region: tmk; PRK00698 580332004579 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 580332004580 TMP-binding site; other site 580332004581 ATP-binding site [chemical binding]; other site 580332004582 DNA polymerase III subunit delta'; Validated; Region: PRK06964 580332004583 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332004584 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 580332004585 active site 580332004586 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 580332004587 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 580332004588 active site 580332004589 HIGH motif; other site 580332004590 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 580332004591 active site 580332004592 KMSKS motif; other site 580332004593 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 580332004594 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 580332004595 acetyl coenzyme A synthetase (ADP forming), alpha domain; Region: AcCoA-syn-alpha; TIGR02717 580332004596 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332004597 CoA-ligase; Region: Ligase_CoA; cl02894 580332004598 ATP-grasp domain; Region: ATP-grasp_4; cl03087 580332004599 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 580332004600 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 580332004601 Adenylyl- / guanylyl cyclase, catalytic domain; Region: CYCc; smart00044 580332004602 cyclase homology domain; Region: CHD; cd07302 580332004603 nucleotidyl binding site; other site 580332004604 metal binding site [ion binding]; metal-binding site 580332004605 dimer interface [polypeptide binding]; other site 580332004606 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 580332004607 Coenzyme A binding pocket [chemical binding]; other site 580332004608 GAF domain; Region: GAF; cl15785 580332004609 GAF domain; Region: GAF_2; pfam13185 580332004610 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332004611 metal binding site [ion binding]; metal-binding site 580332004612 active site 580332004613 I-site; other site 580332004614 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 580332004615 Di-iron ligands [ion binding]; other site 580332004616 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 580332004617 Transposase; Region: DDE_Tnp_ISL3; pfam01610 580332004618 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 580332004619 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 580332004620 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cl00243 580332004621 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 580332004622 RNA binding site [nucleotide binding]; other site 580332004623 Predicted transcription regulator containing HTH domain [Transcription]; Region: COG5499 580332004624 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 580332004625 non-specific DNA binding site [nucleotide binding]; other site 580332004626 salt bridge; other site 580332004627 sequence-specific DNA binding site [nucleotide binding]; other site 580332004628 Uncharacterized protein conserved in bacteria (DUF2136); Region: DUF2136; cl01912 580332004629 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 580332004630 octamerization interface [polypeptide binding]; other site 580332004631 diferric-oxygen binding site [ion binding]; other site 580332004632 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 580332004633 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 580332004634 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 580332004635 ligand binding site [chemical binding]; other site 580332004636 flexible hinge region; other site 580332004637 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332004638 metal binding site [ion binding]; metal-binding site 580332004639 active site 580332004640 I-site; other site 580332004641 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 580332004642 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 580332004643 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332004644 metal binding site [ion binding]; metal-binding site 580332004645 active site 580332004646 I-site; other site 580332004647 HDOD domain; Region: HDOD; pfam08668 580332004648 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 580332004649 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 580332004650 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 580332004651 octamerization interface [polypeptide binding]; other site 580332004652 diferric-oxygen binding site [ion binding]; other site 580332004653 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing...; Region: PRX_BCP; cd03017 580332004654 catalytic triad [active] 580332004655 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 580332004656 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 580332004657 Glycine-zipper containing OmpA-like membrane domain; Region: Gly-zipper_OmpA; pfam13436 580332004658 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 580332004659 cyclase homology domain; Region: CHD; cd07302 580332004660 nucleotidyl binding site; other site 580332004661 metal binding site [ion binding]; metal-binding site 580332004662 dimer interface [polypeptide binding]; other site 580332004663 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 580332004664 TM-ABC transporter signature motif; other site 580332004665 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 580332004666 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 580332004667 Walker A/P-loop; other site 580332004668 ATP binding site [chemical binding]; other site 580332004669 Q-loop/lid; other site 580332004670 ABC transporter signature motif; other site 580332004671 Walker B; other site 580332004672 D-loop; other site 580332004673 H-loop/switch region; other site 580332004674 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 580332004675 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 580332004676 Walker A/P-loop; other site 580332004677 ATP binding site [chemical binding]; other site 580332004678 Q-loop/lid; other site 580332004679 ABC transporter signature motif; other site 580332004680 Walker B; other site 580332004681 D-loop; other site 580332004682 H-loop/switch region; other site 580332004683 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 580332004684 TM-ABC transporter signature motif; other site 580332004685 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 580332004686 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_2; cd06335 580332004687 putative ligand binding site [chemical binding]; other site 580332004688 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 580332004689 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 580332004690 PAS domain; Region: PAS_9; pfam13426 580332004691 putative active site [active] 580332004692 heme pocket [chemical binding]; other site 580332004693 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332004694 metal binding site [ion binding]; metal-binding site 580332004695 active site 580332004696 I-site; other site 580332004697 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 580332004698 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 580332004699 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 580332004700 active site 580332004701 phosphorylation site [posttranslational modification] 580332004702 intermolecular recognition site; other site 580332004703 dimerization interface [polypeptide binding]; other site 580332004704 CheB methylesterase; Region: CheB_methylest; pfam01339 580332004705 CheD chemotactic sensory transduction; Region: CheD; cl00810 580332004706 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 580332004707 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 580332004708 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 580332004709 S-adenosylmethionine binding site [chemical binding]; other site 580332004710 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 580332004711 CHASE3 domain; Region: CHASE3; cl05000 580332004712 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 580332004713 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 580332004714 dimerization interface [polypeptide binding]; other site 580332004715 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332004716 dimer interface [polypeptide binding]; other site 580332004717 putative CheW interface [polypeptide binding]; other site 580332004718 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 580332004719 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 580332004720 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 580332004721 putative binding surface; other site 580332004722 active site 580332004723 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 580332004724 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 580332004725 ATP binding site [chemical binding]; other site 580332004726 Mg2+ binding site [ion binding]; other site 580332004727 G-X-G motif; other site 580332004728 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 580332004729 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 580332004730 anti sigma factor interaction site; other site 580332004731 regulatory phosphorylation site [posttranslational modification]; other site 580332004732 Response regulator receiver domain; Region: Response_reg; pfam00072 580332004733 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 580332004734 active site 580332004735 phosphorylation site [posttranslational modification] 580332004736 intermolecular recognition site; other site 580332004737 dimerization interface [polypeptide binding]; other site 580332004738 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332004739 dimer interface [polypeptide binding]; other site 580332004740 putative CheW interface [polypeptide binding]; other site 580332004741 PAS domain S-box; Region: sensory_box; TIGR00229 580332004742 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 580332004743 putative active site [active] 580332004744 heme pocket [chemical binding]; other site 580332004745 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 580332004746 Histidine kinase; Region: HisKA_3; pfam07730 580332004747 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 580332004748 ATP binding site [chemical binding]; other site 580332004749 Mg2+ binding site [ion binding]; other site 580332004750 G-X-G motif; other site 580332004751 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 580332004752 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 580332004753 active site 580332004754 phosphorylation site [posttranslational modification] 580332004755 intermolecular recognition site; other site 580332004756 dimerization interface [polypeptide binding]; other site 580332004757 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 580332004758 DNA binding residues [nucleotide binding] 580332004759 dimerization interface [polypeptide binding]; other site 580332004760 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 580332004761 hypothetical protein; Provisional; Region: PRK13560 580332004762 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 580332004763 GAF domain; Region: GAF_2; pfam13185 580332004764 GAF domain; Region: GAF; cl15785 580332004765 Histidine kinase; Region: HisKA_3; pfam07730 580332004766 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 580332004767 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 580332004768 ATP binding site [chemical binding]; other site 580332004769 Mg2+ binding site [ion binding]; other site 580332004770 G-X-G motif; other site 580332004771 Ca2+/Na+ antiporter [Inorganic ion transport and metabolism]; Region: ECM27; COG0530 580332004772 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 580332004773 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 580332004774 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 580332004775 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 580332004776 Peptidase family M23; Region: Peptidase_M23; pfam01551 580332004777 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 580332004778 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 580332004779 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 580332004780 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 580332004781 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 580332004782 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 580332004783 Cadherin repeat-like domain; Region: CA_like; cl15786 580332004784 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 580332004785 Ca2+ binding site [ion binding]; other site 580332004786 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 580332004787 Cadherin repeat-like domain; Region: CA_like; cl15786 580332004788 VCBS repeat; Region: VCBS_repeat; TIGR01965 580332004789 VCBS repeat; Region: VCBS_repeat; TIGR01965 580332004790 VCBS repeat; Region: VCBS_repeat; TIGR01965 580332004791 VCBS repeat; Region: VCBS_repeat; TIGR01965 580332004792 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 580332004793 Cadherin-like repeat domain of alpha dystroglycan; Region: Dystroglycan_repeat; cd11303 580332004794 Cadherin repeat-like domain; Region: CA_like; cl15786 580332004795 Periplasmic component of the Tol biopolymer transport system [Intracellular trafficking and secretion]; Region: TolB; COG0823 580332004796 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332004797 Walker A/P-loop; other site 580332004798 ATP binding site [chemical binding]; other site 580332004799 ABC transporter; Region: ABC_tran; pfam00005 580332004800 Q-loop/lid; other site 580332004801 ABC transporter signature motif; other site 580332004802 Walker B; other site 580332004803 D-loop; other site 580332004804 H-loop/switch region; other site 580332004805 Transposase IS200 like; Region: Y1_Tnp; cl00848 580332004806 Protein of unknown function (DUF497); Region: DUF497; cl01108 580332004807 Domain of unknown function (DUF4415); Region: DUF4415; cl01401 580332004808 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 580332004809 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 580332004810 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332004811 Walker A/P-loop; other site 580332004812 ATP binding site [chemical binding]; other site 580332004813 Q-loop/lid; other site 580332004814 ABC transporter signature motif; other site 580332004815 Walker B; other site 580332004816 D-loop; other site 580332004817 H-loop/switch region; other site 580332004818 ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria; Region: ybbN; cd02956 580332004819 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 580332004820 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 580332004821 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 580332004822 SLBB domain; Region: SLBB; pfam10531 580332004823 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; cl11211 580332004824 bidirectional hydrogenase complex protein HoxU; Validated; Region: PRK07569 580332004825 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 580332004826 catalytic loop [active] 580332004827 iron binding site [ion binding]; other site 580332004828 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; cl11210 580332004829 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl15792 580332004830 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 580332004831 Endopeptidases that belong to the bidirectional NAD-linked hydrogenase group. This group of endopeptidases are highly specific carboxyl-terminal protease (HoxW protease) which releases a 24-amino-acid peptide from HoxH prior to progression of subunit...; Region: H2MP_NAD-link-bidir; cd06066 580332004832 nickel binding site [ion binding]; other site 580332004833 Protein of unknown function (DUF1311); Region: DUF1311; cl01530 580332004834 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 580332004835 non-specific DNA binding site [nucleotide binding]; other site 580332004836 salt bridge; other site 580332004837 sequence-specific DNA binding site [nucleotide binding]; other site 580332004838 Phage derived protein Gp49-like (DUF891); Region: Gp49; cl01470 580332004839 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 580332004840 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 580332004841 4Fe-4S binding domain; Region: Fer4; cl02805 580332004842 Ni,Fe-hydrogenase I small subunit [Energy production and conversion]; Region: HyaA; COG1740 580332004843 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl15792 580332004844 HupF/HypC family; Region: HupF_HypC; cl00394 580332004845 Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD...; Region: H2MP_MemB-H2up; cd06062 580332004846 putative substrate-binding site; other site 580332004847 nickel binding site [ion binding]; other site 580332004848 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 580332004849 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 580332004850 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 580332004851 Putative transcriptional regulators (Ypuh-like); Region: DUF387; cl00612 580332004852 ScpA/B protein; Region: ScpA_ScpB; cl00598 580332004853 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 580332004854 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 580332004855 active site 580332004856 HIGH motif; other site 580332004857 dimer interface [polypeptide binding]; other site 580332004858 KMSKS motif; other site 580332004859 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 580332004860 active site 580332004861 putative substrate binding region [chemical binding]; other site 580332004862 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 580332004863 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 580332004864 The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information...; Region: TGS; cl15768 580332004865 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 580332004866 putative coenzyme Q binding site [chemical binding]; other site 580332004867 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 580332004868 SmpB-tmRNA interface; other site 580332004869 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 580332004870 Copper resistance protein D; Region: CopD; cl00563 580332004871 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 580332004872 RNA/DNA hybrid binding site [nucleotide binding]; other site 580332004873 active site 580332004874 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 580332004875 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 580332004876 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 580332004877 UDP-N-acetylglucosamine O-acyltransferase (UDP-GlcNAc acyltransferase): Proteins in this family catalyze the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-GlcNAc. It is the first enzyme in the lipid A biosynthetic...; Region: LbH_UDP-GlcNAc_AT; cd03351 580332004878 active site 580332004879 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 580332004880 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 580332004881 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 580332004882 UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD): The enzyme catalyzes the transfer of 3-hydroxymyristic acid or 3-hydroxy-arachidic acid, depending on the organism, from the acyl carrier protein (ACP) to UDP-3-O-acyl-glucosamine to produce UDP-2; Region: LbH_LpxD; cd03352 580332004883 trimer interface [polypeptide binding]; other site 580332004884 active site 580332004885 UDP-GlcNAc binding site [chemical binding]; other site 580332004886 lipid binding site [chemical binding]; lipid-binding site 580332004887 periplasmic chaperone; Provisional; Region: PRK10780 580332004888 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 580332004889 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 580332004890 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 580332004891 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 580332004892 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 580332004893 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 580332004894 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 580332004895 Surface antigen; Region: Bac_surface_Ag; cl03097 580332004896 zinc metallopeptidase RseP; Provisional; Region: PRK10779 580332004897 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 580332004898 active site 580332004899 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 580332004900 protein binding site [polypeptide binding]; other site 580332004901 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 580332004902 protein binding site [polypeptide binding]; other site 580332004903 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 580332004904 putative substrate binding region [chemical binding]; other site 580332004905 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 580332004906 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 580332004907 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 580332004908 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 580332004909 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 580332004910 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 580332004911 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 580332004912 catalytic residue [active] 580332004913 putative FPP diphosphate binding site; other site 580332004914 putative FPP binding hydrophobic cleft; other site 580332004915 dimer interface [polypeptide binding]; other site 580332004916 putative IPP diphosphate binding site; other site 580332004917 ribosome recycling factor; Reviewed; Region: frr; PRK00083 580332004918 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are 'recycled' and ready for another round of...; Region: RRF; cd00520 580332004919 hinge region; other site 580332004920 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 580332004921 putative nucleotide binding site [chemical binding]; other site 580332004922 uridine monophosphate binding site [chemical binding]; other site 580332004923 homohexameric interface [polypeptide binding]; other site 580332004924 elongation factor Ts; Provisional; Region: tsf; PRK09377 580332004925 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 580332004926 Elongation factor TS; Region: EF_TS; pfam00889 580332004927 Elongation factor TS; Region: EF_TS; pfam00889 580332004928 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 580332004929 rRNA interaction site [nucleotide binding]; other site 580332004930 S8 interaction site; other site 580332004931 putative laminin-1 binding site; other site 580332004932 Flagellar protein YcgR; Region: YcgR_2; pfam12945 580332004933 PilZ domain; Region: PilZ; cl01260 580332004934 Nitrogen regulatory protein P-II; Region: P-II; cl00412 580332004935 Nitrogen regulatory protein P-II; Region: P-II; smart00938 580332004936 NAD synthetase; Provisional; Region: PRK13981 580332004937 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 580332004938 multimer interface [polypeptide binding]; other site 580332004939 active site 580332004940 catalytic triad [active] 580332004941 protein interface 1 [polypeptide binding]; other site 580332004942 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 580332004943 homodimer interface [polypeptide binding]; other site 580332004944 NAD binding pocket [chemical binding]; other site 580332004945 ATP binding pocket [chemical binding]; other site 580332004946 Mg binding site [ion binding]; other site 580332004947 active-site loop [active] 580332004948 RmuC family; Region: RmuC; pfam02646 580332004949 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 580332004950 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 580332004951 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 580332004952 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 580332004953 G1 box; other site 580332004954 putative GEF interaction site [polypeptide binding]; other site 580332004955 GTP/Mg2+ binding site [chemical binding]; other site 580332004956 Switch I region; other site 580332004957 G2 box; other site 580332004958 G3 box; other site 580332004959 Switch II region; other site 580332004960 G4 box; other site 580332004961 G5 box; other site 580332004962 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to...; Region: Translation_Factor_II_like; cl02787 580332004963 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 580332004964 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 580332004965 PAS domain S-box; Region: sensory_box; TIGR00229 580332004966 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 580332004967 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 580332004968 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332004969 metal binding site [ion binding]; metal-binding site 580332004970 active site 580332004971 I-site; other site 580332004972 NMT1-like family; Region: NMT1_2; cl15260 580332004973 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 580332004974 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 580332004975 DEAD-like helicases superfamily; Region: DEXDc; smart00487 580332004976 ATP binding site [chemical binding]; other site 580332004977 Mg++ binding site [ion binding]; other site 580332004978 motif III; other site 580332004979 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 580332004980 nucleotide binding region [chemical binding]; other site 580332004981 ATP-binding site [chemical binding]; other site 580332004982 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 580332004983 active site 580332004984 PII uridylyl-transferase; Provisional; Region: PRK03059 580332004985 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 580332004986 metal binding triad; other site 580332004987 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 580332004988 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 580332004989 ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains; Region: ACT_UUR-like_1; cd04900 580332004990 C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains; Region: ACT_ACR-UUR-like_2; cd04899 580332004991 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl00284 580332004992 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 580332004993 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 580332004994 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 580332004995 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 580332004996 GAF domain; Region: GAF_2; pfam13185 580332004997 GAF domain; Region: GAF; cl15785 580332004998 PAS domain S-box; Region: sensory_box; TIGR00229 580332004999 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 580332005000 putative active site [active] 580332005001 heme pocket [chemical binding]; other site 580332005002 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332005003 metal binding site [ion binding]; metal-binding site 580332005004 active site 580332005005 I-site; other site 580332005006 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 580332005007 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 580332005008 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 580332005009 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 580332005010 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 580332005011 anthranilate dioxygenase reductase; Provisional; Region: antC; PRK11872 580332005012 catalytic loop [active] 580332005013 iron binding site [ion binding]; other site 580332005014 Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport...; Region: FNR_like; cl06868 580332005015 FAD binding pocket [chemical binding]; other site 580332005016 conserved FAD binding motif [chemical binding]; other site 580332005017 phosphate binding motif [ion binding]; other site 580332005018 beta-alpha-beta structure motif; other site 580332005019 NAD binding pocket [chemical binding]; other site 580332005020 siroheme synthase; Provisional; Region: cysG; PRK10637 580332005021 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332005022 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 580332005023 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 580332005024 Domain of unknown function (DUF4202); Region: DUF4202; pfam13875 580332005025 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 580332005026 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332005027 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 580332005028 catalytic triad [active] 580332005029 Polysulphide reductase, NrfD; Region: NrfD; cl01295 580332005030 Formate-dependent nitrite reductase, membrane component [Inorganic ion transport and metabolism]; Region: NrfD; COG3301 580332005031 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 580332005032 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 580332005033 4Fe-4S binding domain; Region: Fer4; cl02805 580332005034 cytochrome c nitrate reductase, small subunit; Region: cytochr_NrfH; TIGR03153 580332005035 putative glutamate synthase (NADPH) small subunit; Provisional; Region: PRK12771 580332005036 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332005037 4Fe-4S binding domain; Region: Fer4; cl02805 580332005038 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 580332005039 Cysteine-rich domain; Region: CCG; pfam02754 580332005040 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; cl00959 580332005041 DsrC like protein; Region: DsrC; cl01101 580332005042 DsrE/DsrF-like family; Region: DrsE; cl00672 580332005043 DsrE/DsrF-like family; Region: DrsE; cl00672 580332005044 DsrE/DsrF-like family; Region: DrsE; cl00672 580332005045 sulfite reductase, dissimilatory-type beta subunit; Region: dsrB; TIGR02066 580332005046 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 580332005047 sulfite reductase, dissimilatory-type alpha subunit; Region: dsrA; TIGR02064 580332005048 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 580332005049 CRISPR/Cas system-associated RAMP superfamily protein Cas6; Region: Cas6-I-III; cd09733 580332005050 DsrC like protein; Region: DsrC; cl01101 580332005051 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 580332005052 CPxP motif; other site 580332005053 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 580332005054 CPxP motif; other site 580332005055 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cl00184 580332005056 active site 580332005057 iron coordination sites [ion binding]; other site 580332005058 substrate binding pocket [chemical binding]; other site 580332005059 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 580332005060 DsrE/DsrF-like family; Region: DrsE; cl00672 580332005061 Predicted transporter component [General function prediction only]; Region: COG2391 580332005062 Sulphur transport; Region: Sulf_transp; cl01018 580332005063 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 580332005064 Thermus thermophilus SoxB and related proteins, N-terminal metallophosphatase domain; Region: MPP_SoxB_N; cd07411 580332005065 active site 580332005066 metal binding site [ion binding]; metal-binding site 580332005067 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 580332005068 Cytochrome c [Energy production and conversion]; Region: COG3258 580332005069 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 580332005070 Predicted secreted protein [Function unknown]; Region: COG5501 580332005071 Superoxide reductase-like (SORL) domain; present in a family of mononuclear non-heme iron proteins that includes superoxide reductase and desulfoferrodoxin. Superoxide reductase-like proteins scavenge superoxide anion radicals as a defense mechanism...; Region: SORL; cl00014 580332005072 Cytochrome c; Region: Cytochrom_C; cl11414 580332005073 Predicted transmembrane transcriptional regulator (anti-sigma factor) [Transcription]; Region: COG5662 580332005074 DsrE/DsrF-like family; Region: DrsE; cl00672 580332005075 RNA polymerase sigma factor RpoE; Provisional; Region: PRK09652 580332005076 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 580332005077 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 580332005078 DNA binding residues [nucleotide binding] 580332005079 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 580332005080 dimerization domain [polypeptide binding]; other site 580332005081 dimer interface [polypeptide binding]; other site 580332005082 catalytic residues [active] 580332005083 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 580332005084 DsrE/DsrF-like family; Region: DrsE; cl00672 580332005085 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 580332005086 CPxP motif; other site 580332005087 high affinity sulphate transporter 1; Region: sulP; TIGR00815 580332005088 Sulfate transporter family; Region: Sulfate_transp; cl15842 580332005089 Sulfate transporter family; Region: Sulfate_transp; cl15842 580332005090 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 580332005091 DMSO reductase anchor subunit (DmsC); Region: DmsC; cl04869 580332005092 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 580332005093 4Fe-4S binding domain; Region: Fer4; cl02805 580332005094 anaerobic dimethyl sulfoxide reductase, A subunit, DmsA/YnfE family; Region: dmsA_ynfE; TIGR02166 580332005095 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 580332005096 molybdopterin cofactor binding site; other site 580332005097 The MopB_2 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to...; Region: MopB_2; cd02763 580332005098 putative molybdopterin cofactor binding site [chemical binding]; other site 580332005099 The MopB_CT_2 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is...; Region: MopB_CT_2; cd02783 580332005100 putative molybdopterin cofactor binding site; other site 580332005101 sulfate adenylyltransferase; Reviewed; Region: sat; PRK04149 580332005102 ATP-sulfurylase; Region: ATPS; cd00517 580332005103 active site 580332005104 HXXH motif; other site 580332005105 flexible loop; other site 580332005106 adenosine phosphosulphate reductase, beta subunit; Region: aprB; TIGR02060 580332005107 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 580332005108 Adenosine-5'-phosphosulfate reductase beta subunit; Region: APS-reductase_C; pfam12139 580332005109 adenylylsulfate reductase subunit alpha; Validated; Region: PRK06854 580332005110 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 580332005111 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 580332005112 Tetratricopeptide repeat; Region: TPR_12; pfam13424 580332005113 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 580332005114 Tetratricopeptide repeat; Region: TPR_12; pfam13424 580332005115 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis...; Region: HIT_like; cl00228 580332005116 nucleotide binding site/active site [active] 580332005117 HIT family signature motif; other site 580332005118 catalytic residue [active] 580332005119 Domain of unknown function (DUF4279); Region: DUF4279; pfam14106 580332005120 Member of the Rhodanese Homology Domain superfamily, subgroup 1. This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins; Region: RHOD_1; cd01522 580332005121 active site residue [active] 580332005122 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 580332005123 active site 580332005124 metal binding site [ion binding]; metal-binding site 580332005125 homotetramer interface [polypeptide binding]; other site 580332005126 GAF domain; Region: GAF_2; pfam13185 580332005127 GAF domain; Region: GAF; cl15785 580332005128 Histidine kinase; Region: HisKA_3; pfam07730 580332005129 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 580332005130 ATP binding site [chemical binding]; other site 580332005131 Mg2+ binding site [ion binding]; other site 580332005132 G-X-G motif; other site 580332005133 transcriptional regulator NarL; Provisional; Region: PRK10651 580332005134 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 580332005135 active site 580332005136 phosphorylation site [posttranslational modification] 580332005137 intermolecular recognition site; other site 580332005138 dimerization interface [polypeptide binding]; other site 580332005139 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 580332005140 DNA binding residues [nucleotide binding] 580332005141 dimerization interface [polypeptide binding]; other site 580332005142 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 580332005143 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 580332005144 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 580332005145 DNA binding residues [nucleotide binding] 580332005146 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 580332005147 IHF - DNA interface [nucleotide binding]; other site 580332005148 IHF dimer interface [polypeptide binding]; other site 580332005149 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 580332005150 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 580332005151 putative tRNA-binding site [nucleotide binding]; other site 580332005152 B3/4 domain; Region: B3_4; cl11458 580332005153 tRNA synthetase B5 domain; Region: B5; cl08394 580332005154 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 580332005155 dimer interface [polypeptide binding]; other site 580332005156 motif 1; other site 580332005157 motif 3; other site 580332005158 motif 2; other site 580332005159 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 580332005160 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 580332005161 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 580332005162 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 580332005163 dimer interface [polypeptide binding]; other site 580332005164 motif 1; other site 580332005165 active site 580332005166 motif 2; other site 580332005167 motif 3; other site 580332005168 ribosomal protein L20; Region: rpl20; CHL00068 580332005169 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 580332005170 23S rRNA binding site [nucleotide binding]; other site 580332005171 L21 binding site [polypeptide binding]; other site 580332005172 L13 binding site [polypeptide binding]; other site 580332005173 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 580332005174 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 580332005175 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 580332005176 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 580332005177 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 580332005178 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 580332005179 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 580332005180 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 580332005181 active site 580332005182 dimer interface [polypeptide binding]; other site 580332005183 motif 1; other site 580332005184 motif 2; other site 580332005185 motif 3; other site 580332005186 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 580332005187 anticodon binding site; other site 580332005188 Permease; Region: Permease; cl00510 580332005189 CHASE2 domain; Region: CHASE2; cl01732 580332005190 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 580332005191 cyclase homology domain; Region: CHD; cd07302 580332005192 nucleotidyl binding site; other site 580332005193 metal binding site [ion binding]; metal-binding site 580332005194 dimer interface [polypeptide binding]; other site 580332005195 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 580332005196 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 580332005197 mce related protein; Region: MCE; pfam02470 580332005198 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332005199 Q-loop/lid; other site 580332005200 ABC transporter signature motif; other site 580332005201 Walker B; other site 580332005202 D-loop; other site 580332005203 replicative DNA helicase; Provisional; Region: PRK07004 580332005204 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 580332005205 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 580332005206 Walker A motif; other site 580332005207 ATP binding site [chemical binding]; other site 580332005208 Walker B motif; other site 580332005209 DNA binding loops [nucleotide binding] 580332005210 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 580332005211 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 580332005212 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 580332005213 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 580332005214 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 580332005215 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 580332005216 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 580332005217 FtsX-like permease family; Region: FtsX; cl15850 580332005218 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 580332005219 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 580332005220 Walker A/P-loop; other site 580332005221 ATP binding site [chemical binding]; other site 580332005222 Q-loop/lid; other site 580332005223 ABC transporter signature motif; other site 580332005224 Walker B; other site 580332005225 D-loop; other site 580332005226 H-loop/switch region; other site 580332005227 Lysophospholipase L1-like subgroup of SGNH-hydrolases. The best characterized member in this family is TesA, an E. coli periplasmic protein with thioesterase, esterase, arylesterase, protease and lysophospholipase activity; Region: Lysophospholipase_L1_like; cd01822 580332005228 active site 580332005229 catalytic triad [active] 580332005230 oxyanion hole [active] 580332005231 switch loop; other site 580332005232 Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones]; Region: COG1331 580332005233 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 580332005234 catalytic residues [active] 580332005235 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 580332005236 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 580332005237 tandem repeat interface [polypeptide binding]; other site 580332005238 oligomer interface [polypeptide binding]; other site 580332005239 active site residues [active] 580332005240 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 580332005241 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 580332005242 motif II; other site 580332005243 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional; Region: PRK11760 580332005244 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 580332005245 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 580332005246 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 580332005247 RNA binding surface [nucleotide binding]; other site 580332005248 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 580332005249 active site 580332005250 ribonuclease E; Reviewed; Region: rne; PRK10811 580332005251 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 580332005252 homodimer interface [polypeptide binding]; other site 580332005253 oligonucleotide binding site [chemical binding]; other site 580332005254 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 580332005255 The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Region: NR_LBD; cl11397 580332005256 ligand binding site [chemical binding]; other site 580332005257 Surface antigen; Region: Bac_surface_Ag; cl03097 580332005258 Low molecular weight phosphatase family; Region: LMWPc; cd00115 580332005259 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 580332005260 active site 580332005261 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 580332005262 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 580332005263 ATP binding site [chemical binding]; other site 580332005264 Mg2+ binding site [ion binding]; other site 580332005265 G-X-G motif; other site 580332005266 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 580332005267 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 580332005268 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 580332005269 active site 580332005270 metal binding site [ion binding]; metal-binding site 580332005271 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 580332005272 excinuclease ABC subunit B; Provisional; Region: PRK05298 580332005273 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 580332005274 ATP binding site [chemical binding]; other site 580332005275 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 580332005276 nucleotide binding region [chemical binding]; other site 580332005277 ATP-binding site [chemical binding]; other site 580332005278 Ultra-violet resistance protein B; Region: UvrB; pfam12344 580332005279 UvrB/uvrC motif; Region: UVR; pfam02151 580332005280 Phage derived protein Gp49-like (DUF891); Region: Gp49; cl01470 580332005281 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 580332005282 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing...; Region: PRX_BCP; cd03017 580332005283 catalytic triad [active] 580332005284 Cytochrome c; Region: Cytochrom_C; cl11414 580332005285 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 580332005286 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 580332005287 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 580332005288 fructokinase; Reviewed; Region: PRK09557 580332005289 PAS domain S-box; Region: sensory_box; TIGR00229 580332005290 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332005291 metal binding site [ion binding]; metal-binding site 580332005292 active site 580332005293 I-site; other site 580332005294 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 580332005295 putative active site [active] 580332005296 dimerization interface [polypeptide binding]; other site 580332005297 putative tRNAtyr binding site [nucleotide binding]; other site 580332005298 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 580332005299 Domain of unknown function (DUF427); Region: DUF427; cl00998 580332005300 TIGR03440 family protein; Region: unchr_TIGR03440 580332005301 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; cl15394 580332005302 probable methyltransferase; Region: TIGR03438 580332005303 Uncharacterized conserved protein (DUF2260); Region: DUF2260; pfam10017 580332005304 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 580332005305 Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]; Region: MalY; COG1168 580332005306 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 580332005307 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332005308 homodimer interface [polypeptide binding]; other site 580332005309 catalytic residue [active] 580332005310 Response regulator receiver domain; Region: Response_reg; pfam00072 580332005311 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 580332005312 active site 580332005313 phosphorylation site [posttranslational modification] 580332005314 intermolecular recognition site; other site 580332005315 dimerization interface [polypeptide binding]; other site 580332005316 Response regulator receiver domain; Region: Response_reg; pfam00072 580332005317 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 580332005318 active site 580332005319 phosphorylation site [posttranslational modification] 580332005320 intermolecular recognition site; other site 580332005321 dimerization interface [polypeptide binding]; other site 580332005322 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the GGDEF (DiGuanylate-Cyclase (DGC)) domain. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain and...; Region: CBS_pair_GGDEF_assoc; cd04598 580332005323 sensory histidine kinase AtoS; Provisional; Region: PRK11360 580332005324 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 580332005325 phosphorylation site [posttranslational modification] 580332005326 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 580332005327 ATP binding site [chemical binding]; other site 580332005328 Mg2+ binding site [ion binding]; other site 580332005329 G-X-G motif; other site 580332005330 Putative glycerate kinase [Carbohydrate transport and metabolism]; Region: GckA; COG2379 580332005331 Domain of unknown function (DUF4147); Region: DUF4147; pfam13660 580332005332 MOFRL family; Region: MOFRL; pfam05161 580332005333 aspartate aminotransferase; Provisional; Region: PRK05764 580332005334 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 580332005335 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332005336 homodimer interface [polypeptide binding]; other site 580332005337 catalytic residue [active] 580332005338 HDOD domain; Region: HDOD; pfam08668 580332005339 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 580332005340 AsmA-like C-terminal region; Region: AsmA_2; cl15864 580332005341 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 580332005342 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 580332005343 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 580332005344 binding surface 580332005345 TPR motif; other site 580332005346 Cytochrome C biogenesis protein; Region: CcmH; cl01179 580332005347 TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c...; Region: TlpA_like_DsbE; cd03010 580332005348 catalytic residues [active] 580332005349 central insert; other site 580332005350 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 580332005351 CcmE; Region: CcmE; cl00994 580332005352 Heme exporter protein D (CcmD); Region: CcmD; cl11475 580332005353 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 580332005354 CcmB protein; Region: CcmB; cl01016 580332005355 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13538 580332005356 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332005357 Walker A/P-loop; other site 580332005358 ATP binding site [chemical binding]; other site 580332005359 Q-loop/lid; other site 580332005360 ABC transporter signature motif; other site 580332005361 Walker B; other site 580332005362 D-loop; other site 580332005363 H-loop/switch region; other site 580332005364 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06997 580332005365 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 580332005366 NAD binding site [chemical binding]; other site 580332005367 homotetramer interface [polypeptide binding]; other site 580332005368 homodimer interface [polypeptide binding]; other site 580332005369 substrate binding site [chemical binding]; other site 580332005370 active site 580332005371 SurA N-terminal domain; Region: SurA_N_3; cl07813 580332005372 periplasmic folding chaperone; Provisional; Region: PRK10788 580332005373 PPIC-type PPIASE domain; Region: Rotamase; cl08278 580332005374 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 580332005375 IHF dimer interface [polypeptide binding]; other site 580332005376 IHF - DNA interface [nucleotide binding]; other site 580332005377 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 580332005378 Found in ATP-dependent protease La (LON); Region: LON; smart00464 580332005379 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 580332005380 Walker A motif; other site 580332005381 ATP binding site [chemical binding]; other site 580332005382 Walker B motif; other site 580332005383 arginine finger; other site 580332005384 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 580332005385 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 580332005386 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 580332005387 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 580332005388 Walker A motif; other site 580332005389 ATP binding site [chemical binding]; other site 580332005390 Walker B motif; other site 580332005391 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 580332005392 Clp protease; Region: CLP_protease; pfam00574 580332005393 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 580332005394 oligomer interface [polypeptide binding]; other site 580332005395 active site residues [active] 580332005396 trigger factor; Provisional; Region: tig; PRK01490 580332005397 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 580332005398 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 580332005399 This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of...; Region: GT1_Glycogen_Phosphorylase; cd04300 580332005400 homodimer interface [polypeptide binding]; other site 580332005401 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 580332005402 active site pocket [active] 580332005403 Alpha-amylase/alpha-mannosidase [Carbohydrate transport and metabolism]; Region: COG1449 580332005404 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 580332005405 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 580332005406 ligand binding site; other site 580332005407 oligomer interface; other site 580332005408 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and...; Region: LbH_G1P_AT_C; cd04651 580332005409 dimer interface [polypeptide binding]; other site 580332005410 N-terminal domain interface [polypeptide binding]; other site 580332005411 sulfate 1 binding site; other site 580332005412 glycogen synthase; Provisional; Region: glgA; PRK00654 580332005413 This family is most closely related to the GT1 family of glycosyltransferases. Glycogen synthase catalyzes the formation and elongation of the alpha-1,4-glucose backbone using ADP-glucose, the second and key step of glycogen biosynthesis. This family...; Region: GT1_Glycogen_synthase_DULL1_like; cd03791 580332005414 ADP-binding pocket [chemical binding]; other site 580332005415 homodimer interface [polypeptide binding]; other site 580332005416 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 580332005417 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 580332005418 active site 580332005419 dimer interface [polypeptide binding]; other site 580332005420 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 580332005421 dimer interface [polypeptide binding]; other site 580332005422 active site 580332005423 glycogen branching enzyme; Provisional; Region: PRK05402 580332005424 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 580332005425 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 580332005426 active site 580332005427 catalytic site [active] 580332005428 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; cl02706 580332005429 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 580332005430 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 580332005431 Cu(I) binding site [ion binding]; other site 580332005432 Domain of unknown function (DUF4292); Region: DUF4292; pfam14125 580332005433 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 580332005434 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 580332005435 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 580332005436 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 580332005437 Right handed beta helix region; Region: Beta_helix; pfam13229 580332005438 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 580332005439 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 580332005440 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 580332005441 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 580332005442 Response regulator receiver domain; Region: Response_reg; pfam00072 580332005443 active site 580332005444 phosphorylation site [posttranslational modification] 580332005445 intermolecular recognition site; other site 580332005446 dimerization interface [polypeptide binding]; other site 580332005447 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 580332005448 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 580332005449 PAS domain; Region: PAS_9; pfam13426 580332005450 putative active site [active] 580332005451 heme pocket [chemical binding]; other site 580332005452 PAS domain S-box; Region: sensory_box; TIGR00229 580332005453 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 580332005454 putative active site [active] 580332005455 heme pocket [chemical binding]; other site 580332005456 Histidine kinase; Region: HisKA_3; pfam07730 580332005457 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 580332005458 ATP binding site [chemical binding]; other site 580332005459 Mg2+ binding site [ion binding]; other site 580332005460 G-X-G motif; other site 580332005461 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 580332005462 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 580332005463 active site 580332005464 phosphorylation site [posttranslational modification] 580332005465 intermolecular recognition site; other site 580332005466 dimerization interface [polypeptide binding]; other site 580332005467 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 580332005468 DNA binding residues [nucleotide binding] 580332005469 dimerization interface [polypeptide binding]; other site 580332005470 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 580332005471 general secretion pathway protein G; Region: typeII_sec_gspG; TIGR01710 580332005472 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 580332005473 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 580332005474 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 580332005475 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 580332005476 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 580332005477 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 580332005478 binding surface 580332005479 TPR motif; other site 580332005480 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 580332005481 Secretin and TonB N terminus short domain; Region: STN; cl06624 580332005482 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 580332005483 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 580332005484 Cohesin domain, interaction parter of dockerin; Region: cohesin_like; cd08546 580332005485 dockerin binding interface; other site 580332005486 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 580332005487 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 580332005488 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 580332005489 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 580332005490 Walker A motif; other site 580332005491 ATP binding site [chemical binding]; other site 580332005492 Walker B motif; other site 580332005493 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 580332005494 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 580332005495 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 580332005496 general secretion pathway protein G; Region: typeII_sec_gspG; TIGR01710 580332005497 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 580332005498 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 580332005499 Yhdh and yhfp-like putative quinone oxidoreductases; Region: MDR_yhdh_yhfp; cd05280 580332005500 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 580332005501 NADP binding site [chemical binding]; other site 580332005502 dimer interface [polypeptide binding]; other site 580332005503 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 580332005504 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 580332005505 E3 interaction surface; other site 580332005506 lipoyl attachment site [posttranslational modification]; other site 580332005507 e3 binding domain; Region: E3_binding; pfam02817 580332005508 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 580332005509 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 580332005510 Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of...; Region: TPP_E1_OGDC_like; cd02016 580332005511 TPP-binding site [chemical binding]; other site 580332005512 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 580332005513 Escherichia coli (Ec) citrate synthase (CS) GltA_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS...; Region: EcCS_like; cd06114 580332005514 dimer interface [polypeptide binding]; other site 580332005515 Citrate synthase; Region: Citrate_synt; pfam00285 580332005516 active site 580332005517 citrylCoA binding site [chemical binding]; other site 580332005518 NADH binding [chemical binding]; other site 580332005519 cationic pore residues; other site 580332005520 oxalacetate/citrate binding site [chemical binding]; other site 580332005521 coenzyme A binding site [chemical binding]; other site 580332005522 catalytic triad [active] 580332005523 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 580332005524 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 580332005525 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 580332005526 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK07057 580332005527 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332005528 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 580332005529 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. E. coli SQR, a member of this subfamily, reduces the...; Region: SQR_TypeC_SdhD; cd03494 580332005530 SdhC subunit interface [polypeptide binding]; other site 580332005531 proximal heme binding site [chemical binding]; other site 580332005532 cardiolipin binding site; other site 580332005533 Iron-sulfur protein interface; other site 580332005534 proximal quinone binding site [chemical binding]; other site 580332005535 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the...; Region: SQR_TypeC_SdhC; cd03499 580332005536 Iron-sulfur protein interface; other site 580332005537 proximal quinone binding site [chemical binding]; other site 580332005538 SdhD (CybS) interface [polypeptide binding]; other site 580332005539 proximal heme binding site [chemical binding]; other site 580332005540 malate dehydrogenase; Provisional; Region: PRK05442 580332005541 Chloroplast-like malate dehydrogenases; Region: MDH_choloroplast_like; cd01338 580332005542 NAD(P) binding site [chemical binding]; other site 580332005543 dimer interface [polypeptide binding]; other site 580332005544 malate binding site [chemical binding]; other site 580332005545 Memo (mediator of ErbB2-driven cell motility) is co-precipitated with the C terminus of ErbB2, a protein involved in cell motility; Region: MEMO_like; cd07361 580332005546 putative ligand binding pocket/active site [active] 580332005547 putative metal binding site [ion binding]; other site 580332005548 AMMECR1; Region: AMMECR1; cl00911 580332005549 Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones]; Region: PflA; COG1180 580332005550 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 580332005551 FeS/SAM binding site; other site 580332005552 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 580332005553 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332005554 Zn2+ binding site [ion binding]; other site 580332005555 Mg2+ binding site [ion binding]; other site 580332005556 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl00503 580332005557 Chalcone-flavanone isomerase; Region: Chalcone; cl03589 580332005558 acetyl-CoA acetyltransferase; Provisional; Region: PRK09052 580332005559 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 580332005560 dimer interface [polypeptide binding]; other site 580332005561 active site 580332005562 Protein of unknown function DUF86; Region: DUF86; cl01031 580332005563 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 580332005564 active site 580332005565 NTP binding site [chemical binding]; other site 580332005566 metal binding triad [ion binding]; metal-binding site 580332005567 antibiotic binding site [chemical binding]; other site 580332005568 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 580332005569 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 580332005570 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332005571 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 580332005572 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 580332005573 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 580332005574 substrate binding site [chemical binding]; other site 580332005575 oxyanion hole (OAH) forming residues; other site 580332005576 trimer interface [polypeptide binding]; other site 580332005577 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 580332005578 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 580332005579 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 580332005580 AMP-binding enzyme; Region: AMP-binding; cl15778 580332005581 short chain dehydrogenase; Provisional; Region: PRK08278 580332005582 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332005583 NAD(P) binding site [chemical binding]; other site 580332005584 active site 580332005585 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 580332005586 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 580332005587 active site 580332005588 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 580332005589 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 580332005590 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 580332005591 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 580332005592 Copper binding periplasmic protein CusF; Region: CusF_Ec; cl02363 580332005593 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 580332005594 Copper binding periplasmic protein CusF; Region: CusF_Ec; cl02363 580332005595 Mycolic acid cyclopropane synthetase; Region: CMAS; pfam02353 580332005596 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 580332005597 S-adenosylmethionine binding site [chemical binding]; other site 580332005598 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor...; Region: Ribosomal_L24e_L24; cl00909 580332005599 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 580332005600 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 580332005601 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 580332005602 Short C-terminal domain; Region: SHOCT; cl01373 580332005603 Cytochrome c; Region: Cytochrom_C; cl11414 580332005604 Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_1; cd02432 580332005605 Protein of unknown function (DUF1211); Region: DUF1211; cl01421 580332005606 ferredoxin-NADP+ reductase; Region: PLN02852 580332005607 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332005608 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 580332005609 4Fe-4S binding domain; Region: Fer4_5; pfam12801 580332005610 Cytochrome c; Region: Cytochrom_C; cl11414 580332005611 Cytochrome c; Region: Cytochrom_C; cl11414 580332005612 Cytochrome c [Energy production and conversion]; Region: COG3258 580332005613 Cytochrome c; Region: Cytochrom_C; cl11414 580332005614 Transcriptional regulator; Region: Transcrip_reg; cl00361 580332005615 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 580332005616 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 580332005617 ATP binding site [chemical binding]; other site 580332005618 putative Mg++ binding site [ion binding]; other site 580332005619 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 580332005620 nucleotide binding region [chemical binding]; other site 580332005621 ATP-binding site [chemical binding]; other site 580332005622 RQC domain; Region: RQC; cl09632 580332005623 HRDC domain; Region: HRDC; cl02578 580332005624 phosphoglucomutase; Region: PLN02307 580332005625 Phosphoglucomutase 1 (PGM1) catalyzes the bidirectional interconversion of glucose-1-phosphate (G-1-P) and glucose-6-phosphate (G-6-P) via a glucose 1,6-diphosphate intermediate, an important metabolic step in prokaryotes and eukaryotes. In one direction; Region: PGM1; cd03085 580332005626 substrate binding site [chemical binding]; other site 580332005627 dimer interface [polypeptide binding]; other site 580332005628 active site 580332005629 metal binding site [ion binding]; metal-binding site 580332005630 Septum formation initiator; Region: DivIC; cl11433 580332005631 enolase; Provisional; Region: eno; PRK00077 580332005632 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 580332005633 dimer interface [polypeptide binding]; other site 580332005634 metal binding site [ion binding]; metal-binding site 580332005635 substrate binding pocket [chemical binding]; other site 580332005636 NeuB family; Region: NeuB; cl00496 580332005637 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 580332005638 CTP synthetase; Validated; Region: pyrG; PRK05380 580332005639 CTP synthetase (CTPs) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer nascent...; Region: CTGs; cd03113 580332005640 Catalytic site [active] 580332005641 active site 580332005642 UTP binding site [chemical binding]; other site 580332005643 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 580332005644 active site 580332005645 putative oxyanion hole; other site 580332005646 catalytic triad [active] 580332005647 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 580332005648 active site 580332005649 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 580332005650 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 580332005651 N-acetyl-D-glucosamine binding site [chemical binding]; other site 580332005652 catalytic residue [active] 580332005653 Protein of unknown function (DUF4063); Region: DUF4063; pfam13272 580332005654 Baseplate J-like protein; Region: Baseplate_J; cl01294 580332005655 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 580332005656 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 580332005657 Bacteriophage protein of unknown function (DUF646); Region: DUF646; cl12124 580332005658 Phage tail sheath protein; Region: Phage_sheath_1; cl01389 580332005659 Phage-related protein [Function unknown]; Region: COG4695; cl01923 580332005660 Phage portal protein; Region: Phage_portal; pfam04860 580332005661 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5410 580332005662 Terminase-like family; Region: Terminase_6; pfam03237 580332005663 Phage-related terminase [General function prediction only]; Region: COG5362; cl02216 580332005664 Uncharacterized conserved protein (DUF2280); Region: DUF2280; cl02353 580332005665 Endodeoxyribonuclease RusA; Region: RusA; cl01885 580332005666 Protein of unknown function (DUF1367); Region: DUF1367; pfam07105 580332005667 Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]; Region: HepA; COG0553 580332005668 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332005669 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 580332005670 type 2 lantibiotic biosynthesis protein LanM; Region: lanti_2_LanM; TIGR03897 580332005671 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 580332005672 KTSC domain; Region: KTSC; pfam13619 580332005673 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 580332005674 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 580332005675 putative active site [active] 580332005676 putative NTP binding site [chemical binding]; other site 580332005677 putative nucleic acid binding site [nucleotide binding]; other site 580332005678 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 580332005679 cofactor binding site; other site 580332005680 DNA binding site [nucleotide binding] 580332005681 substrate interaction site [chemical binding]; other site 580332005682 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 580332005683 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 580332005684 Active Sites [active] 580332005685 Phage protein Gp37/Gp68; Region: Gp37_Gp68; cl15384 580332005686 Protein of unknown function (DUF1643); Region: DUF1643; cl01787 580332005687 Protein of unknown function (DUF3268); Region: DUF3268; pfam11672 580332005688 Protein of unknown function (DUF4031); Region: DUF4031; pfam13223 580332005689 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 580332005690 dimer interface [polypeptide binding]; other site 580332005691 ssDNA binding site [nucleotide binding]; other site 580332005692 tetramer (dimer of dimers) interface [polypeptide binding]; other site 580332005693 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 580332005694 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 580332005695 catalytic residues [active] 580332005696 catalytic nucleophile [active] 580332005697 Recombinase; Region: Recombinase; pfam07508 580332005698 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 580332005699 pyruvate carboxylase; Region: pyruv_carbox; TIGR01235 580332005700 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 580332005701 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 580332005702 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 580332005703 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 580332005704 Nitrogen regulatory protein P-II; Region: P-II; cl00412 580332005705 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 580332005706 PQ loop repeat; Region: PQ-loop; cl12056 580332005707 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 580332005708 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 580332005709 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332005710 Zn2+ binding site [ion binding]; other site 580332005711 Mg2+ binding site [ion binding]; other site 580332005712 acetyl-CoA synthetase; Provisional; Region: PRK00174 580332005713 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 580332005714 AMP-binding enzyme; Region: AMP-binding; cl15778 580332005715 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 580332005716 murein transglycosylase C; Provisional; Region: mltC; PRK11671 580332005717 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 580332005718 N-acetyl-D-glucosamine binding site [chemical binding]; other site 580332005719 catalytic residue [active] 580332005720 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 580332005721 putative peptidoglycan binding site; other site 580332005722 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 580332005723 putative peptidoglycan binding site; other site 580332005724 YqjK-like protein; Region: YqjK; pfam13997 580332005725 Protein of unknown function (DUF1469); Region: DUF1469; cl12095 580332005726 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 580332005727 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 580332005728 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 580332005729 Walker A/P-loop; other site 580332005730 ATP binding site [chemical binding]; other site 580332005731 Q-loop/lid; other site 580332005732 ABC transporter signature motif; other site 580332005733 Walker B; other site 580332005734 D-loop; other site 580332005735 H-loop/switch region; other site 580332005736 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 580332005737 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 580332005738 Walker A/P-loop; other site 580332005739 ATP binding site [chemical binding]; other site 580332005740 Q-loop/lid; other site 580332005741 ABC transporter signature motif; other site 580332005742 Walker B; other site 580332005743 D-loop; other site 580332005744 H-loop/switch region; other site 580332005745 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 580332005746 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 580332005747 dimer interface [polypeptide binding]; other site 580332005748 conserved gate region; other site 580332005749 putative PBP binding loops; other site 580332005750 ABC-ATPase subunit interface; other site 580332005751 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 580332005752 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 580332005753 dimer interface [polypeptide binding]; other site 580332005754 conserved gate region; other site 580332005755 putative PBP binding loops; other site 580332005756 ABC-ATPase subunit interface; other site 580332005757 Predicted dinucleotide-binding enzymes [General function prediction only]; Region: COG2085 580332005758 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332005759 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 580332005760 DsbA family, FrnE subfamily; FrnE is a DsbA-like protein containing a CXXC motif. It is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins; Region: DsbA_FrnE; cd03024 580332005761 catalytic residues [active] 580332005762 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 580332005763 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 580332005764 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; cl00397 580332005765 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 580332005766 Coenzyme A binding pocket [chemical binding]; other site 580332005767 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 580332005768 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 580332005769 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 580332005770 nucleoside/Zn binding site; other site 580332005771 dimer interface [polypeptide binding]; other site 580332005772 catalytic motif [active] 580332005773 Haemolysin-III related; Region: HlyIII; cl03831 580332005774 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing...; Region: PRX_BCP; cd03017 580332005775 catalytic triad [active] 580332005776 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 580332005777 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 580332005778 putative active site [active] 580332005779 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332005780 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 580332005781 GST_N family, unknown subfamily 3; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_3; cd03049 580332005782 putative C-terminal domain interface [polypeptide binding]; other site 580332005783 putative GSH binding site (G-site) [chemical binding]; other site 580332005784 putative dimer interface [polypeptide binding]; other site 580332005785 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 580332005786 dimer interface [polypeptide binding]; other site 580332005787 N-terminal domain interface [polypeptide binding]; other site 580332005788 putative substrate binding pocket (H-site) [chemical binding]; other site 580332005789 methionine sulfoxide reductase B; Provisional; Region: PRK00222; cl15841 580332005790 SelR domain; Region: SelR; pfam01641 580332005791 Intracellular septation protein A; Region: IspA; cl01098 580332005792 YCII-related domain; Region: YCII; cl00999 580332005793 peptidyl-prolyl cis-trans isomerase, EpsD family; Region: cis_trans_EpsD; TIGR02925 580332005794 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 580332005795 PPIC-type PPIASE domain; Region: Rotamase; cl08278 580332005796 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 580332005797 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 580332005798 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 580332005799 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 580332005800 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 580332005801 MASE1; Region: MASE1; pfam05231 580332005802 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 580332005803 PAS domain; Region: PAS_9; pfam13426 580332005804 putative active site [active] 580332005805 heme pocket [chemical binding]; other site 580332005806 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332005807 metal binding site [ion binding]; metal-binding site 580332005808 active site 580332005809 I-site; other site 580332005810 Dna-J like membrane chaperone protein; Provisional; Region: djlA; PRK09430 580332005811 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 580332005812 putative metal binding site [ion binding]; other site 580332005813 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 580332005814 HSP70 interaction site [polypeptide binding]; other site 580332005815 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 580332005816 Catalytic domain of Protein Kinases; Region: PKc; cd00180 580332005817 active site 580332005818 ATP binding site [chemical binding]; other site 580332005819 substrate binding site [chemical binding]; other site 580332005820 activation loop (A-loop); other site 580332005821 HDOD domain; Region: HDOD; pfam08668 580332005822 GAF domain; Region: GAF; cl15785 580332005823 GAF domain; Region: GAF_2; pfam13185 580332005824 PAS domain S-box; Region: sensory_box; TIGR00229 580332005825 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 580332005826 putative active site [active] 580332005827 heme pocket [chemical binding]; other site 580332005828 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 580332005829 putative active site [active] 580332005830 heme pocket [chemical binding]; other site 580332005831 RNase II stability modulator; Provisional; Region: PRK10060 580332005832 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 580332005833 putative active site [active] 580332005834 heme pocket [chemical binding]; other site 580332005835 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332005836 metal binding site [ion binding]; metal-binding site 580332005837 active site 580332005838 I-site; other site 580332005839 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 580332005840 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 580332005841 PAS domain; Region: PAS_9; pfam13426 580332005842 putative active site [active] 580332005843 heme pocket [chemical binding]; other site 580332005844 KTSC domain; Region: KTSC; pfam13619 580332005845 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 580332005846 active site residue [active] 580332005847 FOG: CBS domain [General function prediction only]; Region: COG0517 580332005848 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_10; cd04623 580332005849 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 580332005850 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 580332005851 PAS fold; Region: PAS_4; pfam08448 580332005852 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 580332005853 PAS domain; Region: PAS_9; pfam13426 580332005854 putative active site [active] 580332005855 heme pocket [chemical binding]; other site 580332005856 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332005857 metal binding site [ion binding]; metal-binding site 580332005858 active site 580332005859 I-site; other site 580332005860 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 580332005861 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 580332005862 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 580332005863 dimerization interface [polypeptide binding]; other site 580332005864 ATP binding site [chemical binding]; other site 580332005865 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 580332005866 dimerization interface [polypeptide binding]; other site 580332005867 ATP binding site [chemical binding]; other site 580332005868 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 580332005869 putative active site [active] 580332005870 catalytic triad [active] 580332005871 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 580332005872 putative substrate binding site [chemical binding]; other site 580332005873 putative ATP binding site [chemical binding]; other site 580332005874 Protein of unknown function (DUF2937); Region: DUF2937; pfam11157 580332005875 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 580332005876 Uncharacterized ACR, COG1993; Region: DUF190; cl00872 580332005877 CrcB-like protein; Region: CRCB; cl09114 580332005878 Flagellin N-methylase; Region: FliB; cl00497 580332005879 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 580332005880 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 580332005881 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 580332005882 FeS/SAM binding site; other site 580332005883 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 580332005884 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 580332005885 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 580332005886 dimerization interface [polypeptide binding]; other site 580332005887 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332005888 dimer interface [polypeptide binding]; other site 580332005889 putative CheW interface [polypeptide binding]; other site 580332005890 PilZ domain; Region: PilZ; cl01260 580332005891 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 580332005892 putative substrate translocation pore; other site 580332005893 metabolite-proton symporter; Region: 2A0106; TIGR00883 580332005894 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 580332005895 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 580332005896 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 580332005897 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 580332005898 RNA binding surface [nucleotide binding]; other site 580332005899 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 580332005900 active site 580332005901 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 580332005902 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_4; cd04511 580332005903 nudix motif; other site 580332005904 Cytochrome c; Region: Cytochrom_C; cl11414 580332005905 FecR protein; Region: FecR; pfam04773 580332005906 Helix-turn-helix domains; Region: HTH; cl00088 580332005907 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 580332005908 IHF - DNA interface [nucleotide binding]; other site 580332005909 IHF dimer interface [polypeptide binding]; other site 580332005910 Peptidase family M48; Region: Peptidase_M48; cl12018 580332005911 CHASE2 domain; Region: CHASE2; cl01732 580332005912 Adenylyl- / guanylyl cyclase, catalytic domain; Region: CYCc; smart00044 580332005913 cyclase homology domain; Region: CHD; cd07302 580332005914 nucleotidyl binding site; other site 580332005915 metal binding site [ion binding]; metal-binding site 580332005916 dimer interface [polypeptide binding]; other site 580332005917 VacJ like lipoprotein; Region: VacJ; cl01073 580332005918 Peptidase family M48; Region: Peptidase_M48; cl12018 580332005919 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 580332005920 YceI-like domain; Region: YceI; cl01001 580332005921 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 580332005922 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 580332005923 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 580332005924 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 580332005925 NADP binding site [chemical binding]; other site 580332005926 homopentamer interface [polypeptide binding]; other site 580332005927 substrate binding site [chemical binding]; other site 580332005928 active site 580332005929 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 580332005930 RfaE encodes a bifunctional ADP-heptose synthase involved in the biosynthesis of the lipopolysaccharide (LPS) core precursor ADP-L-glycero-D-manno-heptose. LPS plays an important role in maintaining the structural integrity of the bacterial outer...; Region: RfaE_like; cd01172 580332005931 putative ribose interaction site [chemical binding]; other site 580332005932 putative ADP binding site [chemical binding]; other site 580332005933 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase contains two...; Region: OMP_decarboxylase_like; cd04725 580332005934 active site 580332005935 dimer interface [polypeptide binding]; other site 580332005936 tetratricopeptide repeat protein; Provisional; Region: PRK11788 580332005937 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 580332005938 binding surface 580332005939 TPR motif; other site 580332005940 Protein of unknown function (DUF1049); Region: DUF1049; cl01539 580332005941 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 580332005942 IHF dimer interface [polypeptide binding]; other site 580332005943 IHF - DNA interface [nucleotide binding]; other site 580332005944 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 580332005945 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 580332005946 RNA binding site [nucleotide binding]; other site 580332005947 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 580332005948 RNA binding site [nucleotide binding]; other site 580332005949 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec3; cd05688 580332005950 RNA binding site [nucleotide binding]; other site 580332005951 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec4; cd05689 580332005952 RNA binding site [nucleotide binding]; other site 580332005953 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec5; cd05690 580332005954 RNA binding site [nucleotide binding]; other site 580332005955 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec6; cd05691 580332005956 RNA binding site [nucleotide binding]; other site 580332005957 bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidine monophosphate kinase; Provisional; Region: PRK11860 580332005958 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 580332005959 hinge; other site 580332005960 active site 580332005961 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 580332005962 CMP-binding site; other site 580332005963 The sites determining sugar specificity; other site 580332005964 cyclohexadienyl dehydrogenase; Validated; Region: PRK07502 580332005965 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332005966 3-deoxy-7-phosphoheptulonate synthase; Reviewed; Region: PRK08673 580332005967 NeuB family; Region: NeuB; cl00496 580332005968 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 580332005969 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 580332005970 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332005971 homodimer interface [polypeptide binding]; other site 580332005972 catalytic residue [active] 580332005973 Chorismate mutase type II; Region: CM_2; cl00693 580332005974 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 580332005975 Prephenate dehydratase; Region: PDT; pfam00800 580332005976 C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme; Region: ACT_CM-PDT; cd04905 580332005977 putative L-Phe binding site [chemical binding]; other site 580332005978 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 580332005979 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332005980 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 580332005981 L-serine binding site [chemical binding]; other site 580332005982 ACT domain interface; other site 580332005983 Phosphoserine aminotransferase (PSAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major group in this CD corresponds to phosphoserine aminotransferase (PSAT). PSAT is active as...; Region: PSAT_like; cd00611 580332005984 homodimer interface [polypeptide binding]; other site 580332005985 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 580332005986 substrate-cofactor binding pocket; other site 580332005987 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332005988 catalytic residue [active] 580332005989 DNA gyrase subunit A; Validated; Region: PRK05560 580332005990 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA...; Region: TOP4c; cd00187 580332005991 CAP-like domain; other site 580332005992 active site 580332005993 primary dimer interface [polypeptide binding]; other site 580332005994 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 580332005995 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 580332005996 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 580332005997 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 580332005998 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 580332005999 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 580332006000 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 580332006001 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 580332006002 S-adenosylmethionine binding site [chemical binding]; other site 580332006003 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 580332006004 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 580332006005 motif II; other site 580332006006 cyclase homology domain; Region: CHD; cd07302 580332006007 nucleotidyl binding site; other site 580332006008 metal binding site [ion binding]; metal-binding site 580332006009 dimer interface [polypeptide binding]; other site 580332006010 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 580332006011 octamerization interface [polypeptide binding]; other site 580332006012 diferric-oxygen binding site [ion binding]; other site 580332006013 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 580332006014 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 580332006015 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 580332006016 Walker A motif; other site 580332006017 ATP binding site [chemical binding]; other site 580332006018 Walker B motif; other site 580332006019 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 580332006020 Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism]; Region: GalM; COG2017 580332006021 active site 580332006022 phosphate binding residues; other site 580332006023 catalytic residues [active] 580332006024 elongation factor P; Validated; Region: PRK00529 580332006025 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 580332006026 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 580332006027 RNA binding site [nucleotide binding]; other site 580332006028 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 580332006029 RNA binding site [nucleotide binding]; other site 580332006030 Uncharacterized protein conserved in bacteria (DUF2331); Region: DUF2331; cl01823 580332006031 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 580332006032 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 580332006033 FtsX-like permease family; Region: FtsX; cl15850 580332006034 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 580332006035 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 580332006036 FtsX-like permease family; Region: FtsX; cl15850 580332006037 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 580332006038 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 580332006039 Walker A/P-loop; other site 580332006040 ATP binding site [chemical binding]; other site 580332006041 Q-loop/lid; other site 580332006042 ABC transporter signature motif; other site 580332006043 Walker B; other site 580332006044 D-loop; other site 580332006045 H-loop/switch region; other site 580332006046 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 580332006047 Ribosomal protein L19e. L19e is found in the large ribosomal subunit of eukaryotes and archaea. L19e is distinct from the ribosomal subunit L19, which is found in prokaryotes. It consists of two small globular domains connected by an extended segment; Region: Ribosomal_L19e; cl00232 580332006048 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 580332006049 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 580332006050 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332006051 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 580332006052 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 580332006053 type IV pilus modification protein PilV; Region: type_IV_pilV; TIGR02523 580332006054 PilX N-terminal; Region: PilX_N; pfam14341 580332006055 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 580332006056 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 580332006057 LytB protein; Region: LYTB; cl00507 580332006058 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 580332006059 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 580332006060 lipoprotein signal peptidase; Provisional; Region: PRK14787 580332006061 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 580332006062 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 580332006063 active site 580332006064 HIGH motif; other site 580332006065 nucleotide binding site [chemical binding]; other site 580332006066 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 580332006067 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 580332006068 active site 580332006069 KMSKS motif; other site 580332006070 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 580332006071 tRNA binding surface [nucleotide binding]; other site 580332006072 anticodon binding site; other site 580332006073 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 580332006074 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 580332006075 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 580332006076 active site 580332006077 Riboflavin kinase; Region: Flavokinase; cl03312 580332006078 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 580332006079 octamerization interface [polypeptide binding]; other site 580332006080 diferric-oxygen binding site [ion binding]; other site 580332006081 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 580332006082 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 580332006083 Predicted amidohydrolase [General function prediction only]; Region: COG0388 580332006084 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 580332006085 putative active site [active] 580332006086 catalytic triad [active] 580332006087 dimer interface [polypeptide binding]; other site 580332006088 TIGR02099 family protein; Region: TIGR02099 580332006089 AsmA-like C-terminal region; Region: AsmA_2; cl15864 580332006090 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 580332006091 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 580332006092 metal binding triad; other site 580332006093 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 580332006094 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 580332006095 metal binding triad; other site 580332006096 Heme NO binding associated; Region: HNOBA; pfam07701 580332006097 Adenylyl- / guanylyl cyclase, catalytic domain; Region: CYCc; smart00044 580332006098 cyclase homology domain; Region: CHD; cd07302 580332006099 nucleotidyl binding site; other site 580332006100 metal binding site [ion binding]; metal-binding site 580332006101 dimer interface [polypeptide binding]; other site 580332006102 BCAT_beta_family: Branched-chain aminotransferase catalyses the transamination of the branched-chain amino acids leusine, isoleucine and valine to their respective alpha-keto acids, alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and...; Region: BCAT_beta_family; cd01557 580332006103 homodimer interface [polypeptide binding]; other site 580332006104 substrate-cofactor binding pocket; other site 580332006105 catalytic residue [active] 580332006106 Zinc-finger domain; Region: zf-CHCC; cl01821 580332006107 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 580332006108 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 580332006109 putative active site [active] 580332006110 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 580332006111 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 580332006112 active site 580332006113 substrate binding site [chemical binding]; other site 580332006114 metal binding site [ion binding]; metal-binding site 580332006115 Response regulator receiver domain; Region: Response_reg; pfam00072 580332006116 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl09944 580332006117 active site 580332006118 phosphorylation site [posttranslational modification] 580332006119 intermolecular recognition site; other site 580332006120 dimerization interface [polypeptide binding]; other site 580332006121 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 580332006122 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of...; Region: AlaRS_core; cd00673 580332006123 motif 1; other site 580332006124 active site 580332006125 motif 2; other site 580332006126 motif 3; other site 580332006127 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 580332006128 DHHA1 domain; Region: DHHA1; pfam02272 580332006129 RecX family; Region: RecX; cl00936 580332006130 recombinase A; Provisional; Region: recA; PRK09354 580332006131 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 580332006132 hexamer interface [polypeptide binding]; other site 580332006133 Walker A motif; other site 580332006134 ATP binding site [chemical binding]; other site 580332006135 Walker B motif; other site 580332006136 Competence-damaged protein; Region: CinA; cl00666 580332006137 O-succinylhomoserine sulfhydrylase; Validated; Region: PRK08133 580332006138 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 580332006139 homodimer interface [polypeptide binding]; other site 580332006140 substrate-cofactor binding pocket; other site 580332006141 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332006142 catalytic residue [active] 580332006143 amidophosphoribosyltransferase; Provisional; Region: PRK09246 580332006144 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 580332006145 active site 580332006146 tetramer interface [polypeptide binding]; other site 580332006147 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 580332006148 active site 580332006149 Colicin V production protein; Region: Colicin_V; cl00567 580332006150 Sporulation related domain; Region: SPOR; cl10051 580332006151 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional; Region: PRK10846 580332006152 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 580332006153 hypothetical protein; Provisional; Region: PRK09272 580332006154 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 580332006155 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 580332006156 tryptophan synthase subunit alpha; Provisional; Region: trpA; PRK13111 580332006157 Ttryptophan synthase (TRPS) alpha subunit (TSA). TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are both...; Region: Tryptophan_synthase_alpha; cd04724 580332006158 substrate binding site [chemical binding]; other site 580332006159 active site 580332006160 catalytic residues [active] 580332006161 heterodimer interface [polypeptide binding]; other site 580332006162 Tryptophan synthase-beta: Trptophan synthase is a bifunctional enzyme that catalyses the last two steps in the biosynthesis of L-tryptophan via its alpha and beta reactions. In the alpha reaction, indole 3-glycerol phosphate is cleaved reversibly to...; Region: Trp-synth_B; cd06446 580332006163 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 580332006164 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332006165 catalytic residue [active] 580332006166 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are monomeric; Region: PRAI; cd00405 580332006167 active site 580332006168 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 580332006169 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 580332006170 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 580332006171 PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1); Region: PseudoU_synth_EcTruA; cd02570 580332006172 dimerization interface 3.5A [polypeptide binding]; other site 580332006173 active site 580332006174 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 580332006175 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 580332006176 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 580332006177 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 580332006178 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 580332006179 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332006180 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 580332006181 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 580332006182 tartrate dehydrogenase; Provisional; Region: PRK08194 580332006183 Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate...; Region: IPMI_Swivel; cd01577 580332006184 substrate binding site [chemical binding]; other site 580332006185 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 580332006186 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 580332006187 substrate binding site [chemical binding]; other site 580332006188 ligand binding site [chemical binding]; other site 580332006189 2-isopropylmalate synthase; Validated; Region: PRK03739 580332006190 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 580332006191 active site 580332006192 catalytic residues [active] 580332006193 metal binding site [ion binding]; metal-binding site 580332006194 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 580332006195 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 580332006196 Helix-turn-helix domains; Region: HTH; cl00088 580332006197 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 580332006198 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 580332006199 putative substrate translocation pore; other site 580332006200 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 580332006201 dimer interface [polypeptide binding]; other site 580332006202 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 580332006203 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 580332006204 chaperone protein DnaJ; Provisional; Region: PRK10767 580332006205 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 580332006206 HSP70 interaction site [polypeptide binding]; other site 580332006207 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 580332006208 substrate binding site [polypeptide binding]; other site 580332006209 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 580332006210 Zn binding sites [ion binding]; other site 580332006211 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 580332006212 dimer interface [polypeptide binding]; other site 580332006213 LemA family; Region: LemA; cl00742 580332006214 E3 Ubiquitin ligase; Region: GIDE; pfam12483 580332006215 Protein of unknown function, DUF482; Region: DUF482; pfam04339 580332006216 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 580332006217 Domain of unknown function (DUF3393); Region: DUF3393; pfam11873 580332006218 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 580332006219 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 580332006220 N-acetyl-D-glucosamine binding site [chemical binding]; other site 580332006221 catalytic residue [active] 580332006222 ABC transporter ATPase component; Reviewed; Region: PRK11147 580332006223 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC...; Region: ABC_cobalt_CbiO_domain1; cd03225 580332006224 Walker A/P-loop; other site 580332006225 ATP binding site [chemical binding]; other site 580332006226 Q-loop/lid; other site 580332006227 ABC transporter signature motif; other site 580332006228 Walker B; other site 580332006229 D-loop; other site 580332006230 H-loop/switch region; other site 580332006231 ABC transporter; Region: ABC_tran_2; pfam12848 580332006232 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 580332006233 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing...; Region: PRX_BCP; cd03017 580332006234 catalytic triad [active] 580332006235 alanine racemase; Reviewed; Region: dadX; PRK03646 580332006236 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 580332006237 active site 580332006238 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 580332006239 substrate binding site [chemical binding]; other site 580332006240 catalytic residues [active] 580332006241 dimer interface [polypeptide binding]; other site 580332006242 lysophospholipid transporter LplT; Provisional; Region: PRK11195 580332006243 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 580332006244 Peptidase family M23; Region: Peptidase_M23; pfam01551 580332006245 Conserved hypothetical protein (DUF2461); Region: DUF2461; cl02374 580332006246 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 580332006247 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; cl15379 580332006248 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332006249 Lecithin:cholesterol acyltransferase; Region: LACT; pfam02450 580332006250 Bacterial capsule synthesis protein PGA_cap; Region: PGA_cap; smart00854 580332006251 CapA and related proteins, metallophosphatase domain; Region: MPP_CapA; cd07381 580332006252 putative active site [active] 580332006253 putative metal binding site [ion binding]; other site 580332006254 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 580332006255 Ligand Binding Site [chemical binding]; other site 580332006256 AAA domain; Region: AAA_32; pfam13654 580332006257 lon-related putative ATP-dependent protease; Region: lon_rel; TIGR00764 580332006258 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 580332006259 RaiA ('ribosome-associated inhibitor A', also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site; Region: RaiA; cd00552 580332006260 30S subunit binding site; other site 580332006261 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2187 580332006262 Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits; Region: GntK; cd02021 580332006263 AAA domain; Region: AAA_33; pfam13671 580332006264 ATP-binding site [chemical binding]; other site 580332006265 Gluconate-6-phosphate binding site [chemical binding]; other site 580332006266 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 580332006267 Walker A motif; other site 580332006268 ATP binding site [chemical binding]; other site 580332006269 Walker B motif; other site 580332006270 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 580332006271 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332006272 Zn2+ binding site [ion binding]; other site 580332006273 Mg2+ binding site [ion binding]; other site 580332006274 MASE1; Region: MASE1; pfam05231 580332006275 CHASE domain; Region: CHASE; cl01369 580332006276 hypothetical protein; Provisional; Region: PRK13560 580332006277 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 580332006278 putative active site [active] 580332006279 heme pocket [chemical binding]; other site 580332006280 PAS domain; Region: PAS_9; pfam13426 580332006281 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 580332006282 putative active site [active] 580332006283 heme pocket [chemical binding]; other site 580332006284 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332006285 metal binding site [ion binding]; metal-binding site 580332006286 active site 580332006287 I-site; other site 580332006288 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 580332006289 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 580332006290 putative active site [active] 580332006291 putative metal binding site [ion binding]; other site 580332006292 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 580332006293 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 580332006294 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 580332006295 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 580332006296 type IV pilus modification protein PilV; Region: type_IV_pilV; TIGR02523 580332006297 Type II transport protein GspH; Region: GspH; pfam12019 580332006298 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 580332006299 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 580332006300 Histidine kinase; Region: HisKA_3; pfam07730 580332006301 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 580332006302 ATP binding site [chemical binding]; other site 580332006303 Mg2+ binding site [ion binding]; other site 580332006304 G-X-G motif; other site 580332006305 Lysophospholipase L1-like subgroup of SGNH-hydrolases. The best characterized member in this family is TesA, an E. coli periplasmic protein with thioesterase, esterase, arylesterase, protease and lysophospholipase activity; Region: Lysophospholipase_L1_like; cd01822 580332006306 active site 580332006307 catalytic triad [active] 580332006308 oxyanion hole [active] 580332006309 switch loop; other site 580332006310 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 580332006311 PAS fold; Region: PAS_3; pfam08447 580332006312 putative active site [active] 580332006313 heme pocket [chemical binding]; other site 580332006314 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332006315 metal binding site [ion binding]; metal-binding site 580332006316 active site 580332006317 I-site; other site 580332006318 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 580332006319 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 580332006320 active site 580332006321 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 580332006322 dimer interface [polypeptide binding]; other site 580332006323 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 580332006324 HEAT repeats; Region: HEAT_2; pfam13646 580332006325 Uncharacterized protein family UPF0047; Region: UPF0047; cl00439 580332006326 Domain of unknown function (DUF336); Region: DUF336; cl01249 580332006327 multidrug efflux protein; Reviewed; Region: PRK01766 580332006328 MatE; Region: MatE; cl10513 580332006329 MatE; Region: MatE; cl10513 580332006330 DoxX; Region: DoxX; cl00976 580332006331 Bacterial protein of unknown function (DUF934); Region: DUF934; cl01526 580332006332 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 580332006333 Domain of unknown function (DUF4160); Region: DUF4160; pfam13711 580332006334 Protein of unknown function (DUF2442); Region: DUF2442; pfam10387 580332006335 Methyltransferase domain; Region: Methyltransf_31; pfam13847 580332006336 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 580332006337 S-adenosylmethionine binding site [chemical binding]; other site 580332006338 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]; Region: COG3593 580332006339 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332006340 Walker A/P-loop; other site 580332006341 ATP binding site [chemical binding]; other site 580332006342 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332006343 ABC transporter signature motif; other site 580332006344 Walker B; other site 580332006345 D-loop; other site 580332006346 H-loop/switch region; other site 580332006347 Restriction endonuclease; Region: Mrr_cat; cl00516 580332006348 Superfamily I DNA and RNA helicases [General function prediction only]; Region: COG3972 580332006349 Family description; Region: UvrD_C_2; cl15862 580332006350 aminomethyltransferase; Region: PLN02319 580332006351 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 580332006352 sequence-specific DNA binding site [nucleotide binding]; other site 580332006353 salt bridge; other site 580332006354 Plasmid maintenance system killer protein; Region: Plasmid_killer; cl01422 580332006355 PAS domain S-box; Region: sensory_box; TIGR00229 580332006356 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 580332006357 putative active site [active] 580332006358 heme pocket [chemical binding]; other site 580332006359 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 580332006360 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 580332006361 Catalytic site [active] 580332006362 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 580332006363 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 580332006364 cyclase homology domain; Region: CHD; cd07302 580332006365 nucleotidyl binding site; other site 580332006366 metal binding site [ion binding]; metal-binding site 580332006367 dimer interface [polypeptide binding]; other site 580332006368 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14464 580332006369 Membrane protein of unknown function; Region: DUF360; cl00850 580332006370 DEDDy 3'-5' exonuclease domain of WRN and similar proteins; Region: WRN_exo; cd06141 580332006371 catalytic site [active] 580332006372 putative active site [active] 580332006373 putative substrate binding site [chemical binding]; other site 580332006374 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 580332006375 Clp amino terminal domain; Region: Clp_N; pfam02861 580332006376 Clp amino terminal domain; Region: Clp_N; pfam02861 580332006377 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 580332006378 Walker A motif; other site 580332006379 ATP binding site [chemical binding]; other site 580332006380 Walker B motif; other site 580332006381 arginine finger; other site 580332006382 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 580332006383 Walker A motif; other site 580332006384 ATP binding site [chemical binding]; other site 580332006385 Walker B motif; other site 580332006386 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 580332006387 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK06978 580332006388 Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with...; Region: QPRTase; cd01572 580332006389 dimerization interface [polypeptide binding]; other site 580332006390 active site 580332006391 zinc-ribbon domain; Region: zinc_ribbon_5; cl11777 580332006392 thioredoxin 2; Provisional; Region: PRK10996 580332006393 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 580332006394 catalytic residues [active] 580332006395 Methyltransferase domain; Region: Methyltransf_31; pfam13847 580332006396 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 580332006397 S-adenosylmethionine binding site [chemical binding]; other site 580332006398 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 580332006399 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 580332006400 Membrane transport protein; Region: Mem_trans; cl09117 580332006401 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 580332006402 binding surface 580332006403 TPR motif; other site 580332006404 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 580332006405 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 580332006406 binding surface 580332006407 TPR motif; other site 580332006408 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 580332006409 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 580332006410 FecR protein; Region: FecR; pfam04773 580332006411 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 580332006412 binding surface 580332006413 TPR motif; other site 580332006414 Tetratricopeptide repeat; Region: TPR_16; pfam13432 580332006415 Uncharacterized protein conserved in bacteria (DUF2320); Region: DUF2320; cl12051 580332006416 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332006417 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 580332006418 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 580332006419 active site 580332006420 phosphorylation site [posttranslational modification] 580332006421 intermolecular recognition site; other site 580332006422 dimerization interface [polypeptide binding]; other site 580332006423 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 580332006424 DNA binding residues [nucleotide binding] 580332006425 dimerization interface [polypeptide binding]; other site 580332006426 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 580332006427 PAS domain; Region: PAS_9; pfam13426 580332006428 putative active site [active] 580332006429 heme pocket [chemical binding]; other site 580332006430 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 580332006431 Histidine kinase; Region: HisKA_3; pfam07730 580332006432 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 580332006433 ATP binding site [chemical binding]; other site 580332006434 Mg2+ binding site [ion binding]; other site 580332006435 G-X-G motif; other site 580332006436 Protein of unknown function (DUF535); Region: DUF535; cl01128 580332006437 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 580332006438 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants, cyanobacteria; Region: Thr-synth_2; cd01560 580332006439 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332006440 catalytic residue [active] 580332006441 homoserine dehydrogenase; Provisional; Region: PRK06349 580332006442 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332006443 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 580332006444 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 580332006445 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 580332006446 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 580332006447 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332006448 homodimer interface [polypeptide binding]; other site 580332006449 catalytic residue [active] 580332006450 Xcc1710_like family, specific to proteobacteria. Xcc1710 is a hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913, similar to Mth938, a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome; Region: Xcc1710_like; cd05560 580332006451 MoxR-like ATPases [General function prediction only]; Region: COG0714 580332006452 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 580332006453 Walker A motif; other site 580332006454 ATP binding site [chemical binding]; other site 580332006455 Walker B motif; other site 580332006456 arginine finger; other site 580332006457 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 580332006458 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 580332006459 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 580332006460 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 580332006461 Domain of unknown function (DUF4129); Region: DUF4129; pfam13559 580332006462 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 580332006463 active site 580332006464 Response regulator receiver domain; Region: Response_reg; pfam00072 580332006465 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 580332006466 active site 580332006467 phosphorylation site [posttranslational modification] 580332006468 intermolecular recognition site; other site 580332006469 dimerization interface [polypeptide binding]; other site 580332006470 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332006471 metal binding site [ion binding]; metal-binding site 580332006472 active site 580332006473 I-site; other site 580332006474 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 580332006475 dimerization interface [polypeptide binding]; other site 580332006476 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 580332006477 PAS domain; Region: PAS_9; pfam13426 580332006478 putative active site [active] 580332006479 heme pocket [chemical binding]; other site 580332006480 PAS domain S-box; Region: sensory_box; TIGR00229 580332006481 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 580332006482 putative active site [active] 580332006483 heme pocket [chemical binding]; other site 580332006484 PAS domain S-box; Region: sensory_box; TIGR00229 580332006485 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 580332006486 putative active site [active] 580332006487 heme pocket [chemical binding]; other site 580332006488 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 580332006489 PAS domain; Region: PAS_9; pfam13426 580332006490 putative active site [active] 580332006491 heme pocket [chemical binding]; other site 580332006492 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332006493 metal binding site [ion binding]; metal-binding site 580332006494 active site 580332006495 I-site; other site 580332006496 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 580332006497 Fe-S cluster binding site [ion binding]; other site 580332006498 active site 580332006499 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 580332006500 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 580332006501 Coenzyme A binding pocket [chemical binding]; other site 580332006502 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 580332006503 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 580332006504 homotrimer interaction site [polypeptide binding]; other site 580332006505 zinc binding site [ion binding]; other site 580332006506 CDP-binding sites; other site 580332006507 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 580332006508 substrate binding site; other site 580332006509 dimer interface; other site 580332006510 GAF domain; Region: GAF_2; pfam13185 580332006511 GAF domain; Region: GAF; cl15785 580332006512 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332006513 Zn2+ binding site [ion binding]; other site 580332006514 Mg2+ binding site [ion binding]; other site 580332006515 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 580332006516 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 580332006517 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 580332006518 ATP binding site [chemical binding]; other site 580332006519 putative Mg++ binding site [ion binding]; other site 580332006520 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 580332006521 nucleotide binding region [chemical binding]; other site 580332006522 ATP-binding site [chemical binding]; other site 580332006523 TRCF domain; Region: TRCF; cl04088 580332006524 Domain of unknown function (DUF4258); Region: DUF4258; pfam14076 580332006525 Protein of unknown function (DUF2283); Region: DUF2283; cl02251 580332006526 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 580332006527 triphenylmethane reductase (TMR)-like proteins, NMRa-like, atypical (a) SDRs; Region: TMR_SDR_a; cd05269 580332006528 NADP binding site [chemical binding]; other site 580332006529 Helix-turn-helix domains; Region: HTH; cl00088 580332006530 Domain of unknown function (DUF4072); Region: DUF4072; pfam13284 580332006531 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 580332006532 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 580332006533 motif II; other site 580332006534 Galactose binding lectin domain; Region: Gal_Lectin; pfam02140 580332006535 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 580332006536 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; Region: NrdJ_Z; TIGR02504 580332006537 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 580332006538 active site 580332006539 dimer interface [polypeptide binding]; other site 580332006540 effector binding site; other site 580332006541 Membrane transport protein; Region: Mem_trans; cl09117 580332006542 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 580332006543 DEAD-like helicases superfamily; Region: DEXDc; smart00487 580332006544 ATP binding site [chemical binding]; other site 580332006545 Mg++ binding site [ion binding]; other site 580332006546 motif III; other site 580332006547 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 580332006548 nucleotide binding region [chemical binding]; other site 580332006549 ATP-binding site [chemical binding]; other site 580332006550 HI0933-like protein; Region: HI0933_like; pfam03486 580332006551 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332006552 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332006553 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 580332006554 Invasion gene expression up-regulator, SirB; Region: SirB; cl01184 580332006555 Protein of unknown function (DUF2798); Region: DUF2798; pfam11391 580332006556 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 580332006557 Iron-sulphur cluster assembly; Region: Fe-S_assembly; cl01123 580332006558 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 580332006559 catalytic loop [active] 580332006560 iron binding site [ion binding]; other site 580332006561 chaperone protein HscA; Provisional; Region: hscA; PRK05183 580332006562 co-chaperone HscB; Provisional; Region: hscB; PRK03578 580332006563 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 580332006564 HSP70 interaction site [polypeptide binding]; other site 580332006565 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 580332006566 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 580332006567 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 580332006568 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 580332006569 trimerization site [polypeptide binding]; other site 580332006570 active site 580332006571 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 580332006572 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 580332006573 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 580332006574 catalytic residue [active] 580332006575 Helix-turn-helix domains; Region: HTH; cl00088 580332006576 Rrf2 family protein; Region: rrf2_super; TIGR00738 580332006577 serine O-acetyltransferase; Region: cysE; TIGR01172 580332006578 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 580332006579 trimer interface [polypeptide binding]; other site 580332006580 active site 580332006581 substrate binding site [chemical binding]; other site 580332006582 CoA binding site [chemical binding]; other site 580332006583 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 580332006584 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 580332006585 IMPase, inositol monophosphatase and related domains. A family of Mg++ dependent phosphatases, inhibited by lithium, many of which may act on inositol monophosphate substrate. They dephosphorylate inositol phosphate to generate inositol, which may be...; Region: IMPase; cd01639 580332006586 active site 580332006587 dimerization interface [polypeptide binding]; other site 580332006588 Phosphate transporter family; Region: PHO4; cl00396 580332006589 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 580332006590 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 580332006591 MutS domain I; Region: MutS_I; pfam01624 580332006592 MutS domain II; Region: MutS_II; pfam05188 580332006593 MutS family domain IV; Region: MutS_IV; pfam05190 580332006594 MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal...; Region: ABC_MutS1; cd03284 580332006595 Walker A/P-loop; other site 580332006596 ATP binding site [chemical binding]; other site 580332006597 Q-loop/lid; other site 580332006598 ABC transporter signature motif; other site 580332006599 Walker B; other site 580332006600 D-loop; other site 580332006601 H-loop/switch region; other site 580332006602 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 580332006603 Uncharacterized conserved protein [Function unknown]; Region: COG0397; cl00428 580332006604 Uncharacterized ACR, YdiU/UPF0061 family; Region: UPF0061; pfam02696 580332006605 Protein of unknown function (DUF3301); Region: DUF3301; pfam11743 580332006606 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 580332006607 Protein of unknown function (DUF1697); Region: DUF1697; cl01557 580332006608 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332006609 Zn2+ binding site [ion binding]; other site 580332006610 Mg2+ binding site [ion binding]; other site 580332006611 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332006612 Zn2+ binding site [ion binding]; other site 580332006613 Mg2+ binding site [ion binding]; other site 580332006614 transcriptional regulator TraR; Provisional; Region: PRK13870 580332006615 Autoinducer binding domain; Region: Autoind_bind; pfam03472 580332006616 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 580332006617 DNA binding residues [nucleotide binding] 580332006618 dimerization interface [polypeptide binding]; other site 580332006619 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332006620 metal binding site [ion binding]; metal-binding site 580332006621 active site 580332006622 I-site; other site 580332006623 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 580332006624 Predicted proline hydroxylase [Posttranslational modification, protein turnover, chaperones]; Region: EGL-9; COG3751 580332006625 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 580332006626 Putative redox-active protein (C_GCAxxG_C_C); Region: C_GCAxxG_C_C; cl09920 580332006627 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 580332006628 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 580332006629 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 580332006630 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 580332006631 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332006632 ATP binding site [chemical binding]; other site 580332006633 Walker B motif; other site 580332006634 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GpsA; COG0240 580332006635 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332006636 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 580332006637 UDP-N-acetylglucosamine:LPS N-acetylglucosamine transferase [Cell envelope biogenesis, outer membrane]; Region: MurG; COG0707 580332006638 Glycosyl transferase family 1; Region: Glyco_trans_1_3; pfam13528 580332006639 Domain of unknown function (DUF1992); Region: DUF1992; cl08096 580332006640 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 580332006641 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 580332006642 Catalytic site [active] 580332006643 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 580332006644 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 580332006645 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing...; Region: PRX_BCP; cd03017 580332006646 catalytic triad [active] 580332006647 Uncharacterized conserved protein [Function unknown]; Region: COG2850 580332006648 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 580332006649 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]; Region: NlpB; COG3317 580332006650 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]; Region: NlpB; COG3317 580332006651 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 580332006652 dihydrodipicolinate synthase; Region: dapA; TIGR00674 580332006653 dimer interface [polypeptide binding]; other site 580332006654 active site 580332006655 catalytic residue [active] 580332006656 FeoA domain; Region: FeoA; cl00838 580332006657 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 580332006658 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 580332006659 G1 box; other site 580332006660 GTP/Mg2+ binding site [chemical binding]; other site 580332006661 Switch I region; other site 580332006662 G2 box; other site 580332006663 G3 box; other site 580332006664 Switch II region; other site 580332006665 G4 box; other site 580332006666 G5 box; other site 580332006667 Nucleoside recognition; Region: Gate; cl00486 580332006668 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 580332006669 Nucleoside recognition; Region: Gate; cl00486 580332006670 Polycystin cation channel protein; Provisional; Region: PLN03223 580332006671 YfaZ precursor; Region: YfaZ; pfam07437 580332006672 YccA-like proteins; Region: YccA_like; cd10433 580332006673 HopJ type III effector protein; Region: HopJ; pfam08888 580332006674 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 580332006675 active site residue [active] 580332006676 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 580332006677 TRAM domain; Region: TRAM; cl01282 580332006678 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 580332006679 S-adenosylmethionine binding site [chemical binding]; other site 580332006680 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 580332006681 active site 580332006682 catalytic site [active] 580332006683 substrate binding site [chemical binding]; other site 580332006684 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 580332006685 LexA repressor; Validated; Region: PRK00215 580332006686 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 580332006687 Catalytic site [active] 580332006688 Lipase (class 3). Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is 'interfacial activation,' the process of...; Region: Lipase_3; cd00519 580332006689 active site flap/lid [active] 580332006690 nucleophilic elbow; other site 580332006691 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 580332006692 Protein of unknown function (DUF3617); Region: DUF3617; pfam12276 580332006693 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 580332006694 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 580332006695 Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]; Region: TadD; COG5010 580332006696 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 580332006697 Peptidase family M48; Region: Peptidase_M48; cl12018 580332006698 Bacterial SH3 domain; Region: SH3_3; cl02551 580332006699 CHASE2 domain; Region: CHASE2; cl01732 580332006700 superoxide dismutase; Provisional; Region: PRK10543 580332006701 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 580332006702 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 580332006703 lipoyl synthase; Provisional; Region: PRK05481 580332006704 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 580332006705 FeS/SAM binding site; other site 580332006706 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 580332006707 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 580332006708 Walker A motif; other site 580332006709 ATP binding site [chemical binding]; other site 580332006710 DNA alkylation repair enzyme; Region: DNA_alkylation; pfam08713 580332006711 A new structural DNA glycosylase; Region: AlkD_like; cd06561 580332006712 active site 580332006713 RF-1 domain; Region: RF-1; cl02875 580332006714 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 580332006715 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 580332006716 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 580332006717 G1 box; other site 580332006718 putative GEF interaction site [polypeptide binding]; other site 580332006719 GTP/Mg2+ binding site [chemical binding]; other site 580332006720 Switch I region; other site 580332006721 G2 box; other site 580332006722 G3 box; other site 580332006723 Switch II region; other site 580332006724 G4 box; other site 580332006725 G5 box; other site 580332006726 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 580332006727 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 580332006728 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 580332006729 substrate binding pocket [chemical binding]; other site 580332006730 membrane-bound complex binding site; other site 580332006731 hinge residues; other site 580332006732 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 580332006733 cyclic-di-GMP phosphodiesterase; Provisional; Region: PRK11359 580332006734 putative active site [active] 580332006735 heme pocket [chemical binding]; other site 580332006736 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 580332006737 putative active site [active] 580332006738 heme pocket [chemical binding]; other site 580332006739 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 580332006740 putative active site [active] 580332006741 heme pocket [chemical binding]; other site 580332006742 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332006743 metal binding site [ion binding]; metal-binding site 580332006744 active site 580332006745 I-site; other site 580332006746 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 580332006747 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 580332006748 dimerization interface [polypeptide binding]; other site 580332006749 putative DNA binding site [nucleotide binding]; other site 580332006750 putative Zn2+ binding site [ion binding]; other site 580332006751 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_1; cd08894 580332006752 putative hydrophobic ligand binding site [chemical binding]; other site 580332006753 YCII-related domain; Region: YCII; cl00999 580332006754 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cl00161 580332006755 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 580332006756 hydrophobic ligand binding site; other site 580332006757 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 580332006758 hydrophobic ligand binding site; other site 580332006759 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cl00161 580332006760 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins; Region: SRPBCC_1; cd07818 580332006761 putative hydrophobic ligand binding site [chemical binding]; other site 580332006762 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 580332006763 dimer interface [polypeptide binding]; other site 580332006764 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 580332006765 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 580332006766 dimer interface [polypeptide binding]; other site 580332006767 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cl00161 580332006768 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 580332006769 dimer interface [polypeptide binding]; other site 580332006770 N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains; Region: SgaA_N_like; cd07247 580332006771 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 580332006772 Bacterial protein of unknown function (DUF924); Region: DUF924; cl01561 580332006773 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 580332006774 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 580332006775 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 580332006776 FeS/SAM binding site; other site 580332006777 Protein of unknown function (DUF4080); Region: DUF4080; pfam13311 580332006778 Karyopherin (importin) beta [Intracellular trafficking and secretion]; Region: KAP95; COG5215 580332006779 Helix-turn-helix domains; Region: HTH; cl00088 580332006780 putative transposase OrfB; Reviewed; Region: PHA02517 580332006781 HTH-like domain; Region: HTH_21; pfam13276 580332006782 Integrase core domain; Region: rve; cl01316 580332006783 Integrase core domain; Region: rve_3; cl15866 580332006784 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 580332006785 HDOD domain; Region: HDOD; pfam08668 580332006786 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 580332006787 octamerization interface [polypeptide binding]; other site 580332006788 diferric-oxygen binding site [ion binding]; other site 580332006789 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 580332006790 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 580332006791 PAS domain; Region: PAS_9; pfam13426 580332006792 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332006793 metal binding site [ion binding]; metal-binding site 580332006794 active site 580332006795 I-site; other site 580332006796 Protein of unknown function (DUF3014); Region: DUF3014; pfam11219 580332006797 norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial...; Region: vWA_norD_type; cd01454 580332006798 metal ion-dependent adhesion site (MIDAS); other site 580332006799 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332006800 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 580332006801 SEC-C motif; Region: SEC-C; pfam02810 580332006802 hypothetical protein; Provisional; Region: PRK01842 580332006803 FHIT (fragile histidine family): FHIT proteins, related to the HIT family carry a motif HxHxH/Qxx (x, is a hydrophobic amino acid), On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified into...; Region: FHIT; cd01275 580332006804 nucleotide binding site/active site [active] 580332006805 HIT family signature motif; other site 580332006806 catalytic residue [active] 580332006807 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 580332006808 Protein of unknown function (DUF1415); Region: DUF1415; cl01301 580332006809 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 580332006810 DEAD-like helicases superfamily; Region: DEXDc; smart00487 580332006811 ATP binding site [chemical binding]; other site 580332006812 Mg++ binding site [ion binding]; other site 580332006813 motif III; other site 580332006814 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 580332006815 nucleotide binding region [chemical binding]; other site 580332006816 ATP-binding site [chemical binding]; other site 580332006817 GTP-binding protein YchF; Reviewed; Region: PRK09601 580332006818 YchF GTPase; Region: YchF; cd01900 580332006819 G1 box; other site 580332006820 GTP/Mg2+ binding site [chemical binding]; other site 580332006821 Switch I region; other site 580332006822 G2 box; other site 580332006823 Switch II region; other site 580332006824 G3 box; other site 580332006825 G4 box; other site 580332006826 G5 box; other site 580332006827 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 580332006828 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 580332006829 putative active site [active] 580332006830 catalytic residue [active] 580332006831 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 580332006832 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 580332006833 5S rRNA interface [nucleotide binding]; other site 580332006834 CTC domain interface [polypeptide binding]; other site 580332006835 L16 interface [polypeptide binding]; other site 580332006836 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 580332006837 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 580332006838 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 580332006839 active site 580332006840 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 580332006841 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 580332006842 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 580332006843 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 580332006844 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 580332006845 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 580332006846 TPR motif; other site 580332006847 binding surface 580332006848 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 580332006849 TPR motif; other site 580332006850 binding surface 580332006851 TPR repeat; Region: TPR_11; pfam13414 580332006852 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 580332006853 binding surface 580332006854 TPR motif; other site 580332006855 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 580332006856 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 580332006857 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332006858 Walker A/P-loop; other site 580332006859 ATP binding site [chemical binding]; other site 580332006860 Q-loop/lid; other site 580332006861 ABC transporter signature motif; other site 580332006862 Walker B; other site 580332006863 D-loop; other site 580332006864 H-loop/switch region; other site 580332006865 ABC-2 type transporter; Region: ABC2_membrane; cl11417 580332006866 ABC-type uncharacterized transport system; Region: ABC_transp_aux; pfam09822 580332006867 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 580332006868 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 580332006869 DNA binding site [nucleotide binding] 580332006870 catalytic residue [active] 580332006871 H2TH interface [polypeptide binding]; other site 580332006872 putative catalytic residues [active] 580332006873 turnover-facilitating residue; other site 580332006874 intercalation triad [nucleotide binding]; other site 580332006875 8OG recognition residue [nucleotide binding]; other site 580332006876 putative reading head residues; other site 580332006877 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 580332006878 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 580332006879 PAS domain S-box; Region: sensory_box; TIGR00229 580332006880 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 580332006881 putative active site [active] 580332006882 heme pocket [chemical binding]; other site 580332006883 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332006884 metal binding site [ion binding]; metal-binding site 580332006885 active site 580332006886 I-site; other site 580332006887 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 580332006888 octamerization interface [polypeptide binding]; other site 580332006889 diferric-oxygen binding site [ion binding]; other site 580332006890 ferredoxin; Validated; Region: PRK07118 580332006891 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 580332006892 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 580332006893 active site 580332006894 (T/H)XGH motif; other site 580332006895 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 580332006896 S-adenosylmethionine binding site [chemical binding]; other site 580332006897 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 580332006898 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 580332006899 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 580332006900 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 580332006901 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 580332006902 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 580332006903 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332006904 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 580332006905 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332006906 Walker A/P-loop; other site 580332006907 ATP binding site [chemical binding]; other site 580332006908 Q-loop/lid; other site 580332006909 ABC transporter signature motif; other site 580332006910 Walker B; other site 580332006911 D-loop; other site 580332006912 H-loop/switch region; other site 580332006913 putative protein insertion permease FtsX; Region: ftsX; TIGR00439 580332006914 FtsX-like permease family; Region: FtsX; cl15850 580332006915 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 580332006916 octamerization interface [polypeptide binding]; other site 580332006917 diferric-oxygen binding site [ion binding]; other site 580332006918 Helix-turn-helix domains; Region: HTH; cl00088 580332006919 Rrf2 family protein; Region: rrf2_super; TIGR00738 580332006920 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct...; Region: Trunc_globin; cd00454 580332006921 apolar tunnel; other site 580332006922 heme binding site [chemical binding]; other site 580332006923 dimerization interface [polypeptide binding]; other site 580332006924 hypothetical protein; Provisional; Region: PRK05713 580332006925 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 580332006926 catalytic loop [active] 580332006927 iron binding site [ion binding]; other site 580332006928 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an N-terminal Iron-Sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible...; Region: FNR_N-term_Iron_sulfur_binding; cd06194 580332006929 FAD binding pocket [chemical binding]; other site 580332006930 FAD binding motif [chemical binding]; other site 580332006931 phosphate binding motif [ion binding]; other site 580332006932 beta-alpha-beta structure motif; other site 580332006933 NAD binding pocket [chemical binding]; other site 580332006934 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 580332006935 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 580332006936 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 580332006937 Protein of unknown function (DUF615); Region: DUF615; cl01147 580332006938 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 580332006939 PAS domain; Region: PAS_9; pfam13426 580332006940 putative active site [active] 580332006941 heme pocket [chemical binding]; other site 580332006942 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 580332006943 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 580332006944 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 580332006945 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 580332006946 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 580332006947 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 580332006948 Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires...; Region: DHOD_2_like; cd04738 580332006949 quinone interaction residues [chemical binding]; other site 580332006950 Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Region: PyrD; COG0167 580332006951 active site 580332006952 catalytic residues [active] 580332006953 FMN binding site [chemical binding]; other site 580332006954 substrate binding site [chemical binding]; other site 580332006955 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 580332006956 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 580332006957 GAF domain; Region: GAF; cl15785 580332006958 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 580332006959 dimer interface [polypeptide binding]; other site 580332006960 phosphorylation site [posttranslational modification] 580332006961 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 580332006962 ATP binding site [chemical binding]; other site 580332006963 Mg2+ binding site [ion binding]; other site 580332006964 G-X-G motif; other site 580332006965 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 580332006966 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 580332006967 active site 580332006968 phosphorylation site [posttranslational modification] 580332006969 intermolecular recognition site; other site 580332006970 dimerization interface [polypeptide binding]; other site 580332006971 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 580332006972 DNA binding site [nucleotide binding] 580332006973 potassium uptake protein; Region: kup; TIGR00794 580332006974 K+ potassium transporter; Region: K_trans; cl15781 580332006975 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 580332006976 electron transport complex protein RnfB; Provisional; Region: PRK05113 580332006977 Putative Fe-S cluster; Region: FeS; pfam04060 580332006978 4Fe-4S binding domain; Region: Fer4; cl02805 580332006979 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 580332006980 RnfC Barrel sandwich hybrid domain; Region: RnfC_N; pfam13375 580332006981 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 580332006982 SLBB domain; Region: SLBB; pfam10531 580332006983 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 580332006984 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 580332006985 FMN-binding domain; Region: FMN_bind; cl01081 580332006986 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 580332006987 endonuclease III; Provisional; Region: PRK10702 580332006988 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 580332006989 minor groove reading motif; other site 580332006990 helix-hairpin-helix signature motif; other site 580332006991 substrate binding pocket [chemical binding]; other site 580332006992 active site 580332006993 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 580332006994 Domain of unknown function (DUF1841); Region: DUF1841; pfam08897 580332006995 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; cl00920 580332006996 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 580332006997 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 580332006998 ketol-acid reductoisomerase; Provisional; Region: PRK05479 580332006999 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332007000 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 580332007001 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 580332007002 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 580332007003 putative valine binding site [chemical binding]; other site 580332007004 dimer interface [polypeptide binding]; other site 580332007005 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 580332007006 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06965 580332007007 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 580332007008 PYR/PP interface [polypeptide binding]; other site 580332007009 dimer interface [polypeptide binding]; other site 580332007010 TPP binding site [chemical binding]; other site 580332007011 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 580332007012 Thiamine pyrophosphate (TPP) family, Acetohydroxyacid synthase (AHAS) subfamily, TPP-binding module; composed of proteins similar to the large catalytic subunit of AHAS. AHAS catalyzes the condensation of two molecules of pyruvate to give the...; Region: TPP_AHAS; cd02015 580332007013 TPP-binding site [chemical binding]; other site 580332007014 dimer interface [polypeptide binding]; other site 580332007015 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 580332007016 RNA polymerase factor sigma-70; Validated; Region: PRK09047 580332007017 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 580332007018 DNA binding residues [nucleotide binding] 580332007019 Protein of unknown function (DUF3619); Region: DUF3619; pfam12279 580332007020 Protein of unknown function (DUF3106); Region: DUF3106; pfam11304 580332007021 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 580332007022 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 580332007023 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 580332007024 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 580332007025 multifunctional aminopeptidase A; Provisional; Region: PRK00913 580332007026 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 580332007027 interface (dimer of trimers) [polypeptide binding]; other site 580332007028 Substrate-binding/catalytic site; other site 580332007029 Zn-binding sites [ion binding]; other site 580332007030 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; cl01106 580332007031 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 580332007032 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 580332007033 HIGH motif; other site 580332007034 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 580332007035 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 580332007036 active site 580332007037 KMSKS motif; other site 580332007038 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 580332007039 tRNA binding surface [nucleotide binding]; other site 580332007040 anticodon binding site; other site 580332007041 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 580332007042 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 580332007043 CPxP motif; other site 580332007044 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 580332007045 active site residue [active] 580332007046 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 580332007047 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 580332007048 active site 580332007049 ATP binding site [chemical binding]; other site 580332007050 substrate binding site [chemical binding]; other site 580332007051 activation loop (A-loop); other site 580332007052 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 580332007053 ligand binding site [chemical binding]; other site 580332007054 flexible hinge region; other site 580332007055 Peptidase family M48; Region: Peptidase_M48; cl12018 580332007056 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 580332007057 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 580332007058 TPR motif; other site 580332007059 binding surface 580332007060 High-affinity nickel-transport protein; Region: NicO; cl00964 580332007061 HypE (Hydrogenase expression/formation protein). HypE is involved in Ni-Fe hydrogenase biosynthesis. HypE dehydrates its own carbamoyl moiety in an ATP-dependent process to yield the enzyme thiocyanate. The N-terminal domain of HypE is related to the...; Region: HypE; cd02197 580332007062 dimerization interface [polypeptide binding]; other site 580332007063 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 580332007064 ATP binding site [chemical binding]; other site 580332007065 Hydrogenase formation hypA family; Region: HypD; cl12072 580332007066 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypD; COG0409 580332007067 HupF/HypC family; Region: HupF_HypC; cl00394 580332007068 Acylphosphatase; Region: Acylphosphatase; cl00551 580332007069 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 580332007070 HypF finger; Region: zf-HYPF; pfam07503 580332007071 HypF finger; Region: zf-HYPF; pfam07503 580332007072 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 580332007073 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332007074 Hydrogenase expression/synthesis hypA family; Region: HypA; pfam01155 580332007075 hydrogenase nickel incorporation protein; Provisional; Region: hypA; cl00418 580332007076 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 580332007077 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 580332007078 dimerization interface [polypeptide binding]; other site 580332007079 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332007080 dimer interface [polypeptide binding]; other site 580332007081 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 580332007082 putative CheW interface [polypeptide binding]; other site 580332007083 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 580332007084 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 580332007085 tellurium resistance terB-like protein, subgroup 2; Region: terB_like_2; cd07313 580332007086 putative metal binding site [ion binding]; other site 580332007087 SlyX; Region: SlyX; cl01090 580332007088 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 580332007089 Fic/DOC family; Region: Fic; cl00960 580332007090 Flavin Reductases; Region: FlaRed; cl00801 580332007091 Restriction endonuclease; Region: Mrr_cat; cl00516 580332007092 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 580332007093 Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized proteins with a DEAD domain; Region: PLDc_Bfil_DEXD_like; cd09117 580332007094 homodimer interface [polypeptide binding]; other site 580332007095 putative active site [active] 580332007096 catalytic site [active] 580332007097 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 580332007098 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 580332007099 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 580332007100 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 580332007101 ATP binding site [chemical binding]; other site 580332007102 putative Mg++ binding site [ion binding]; other site 580332007103 Domain of unknown function (DUF3387); Region: DUF3387; pfam11867 580332007104 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 580332007105 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 580332007106 HsdM N-terminal domain; Region: HsdM_N; pfam12161 580332007107 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 580332007108 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332007109 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 580332007110 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 580332007111 non-specific DNA binding site [nucleotide binding]; other site 580332007112 salt bridge; other site 580332007113 sequence-specific DNA binding site [nucleotide binding]; other site 580332007114 Domain of unknown function (DUF955); Region: DUF955; cl01076 580332007115 Dodecin; Region: Dodecin; cl01328 580332007116 Fic family protein [Function unknown]; Region: COG3177 580332007117 Fic/DOC family N-terminal; Region: Fic_N; pfam13784 580332007118 Fic/DOC family; Region: Fic; cl00960 580332007119 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 580332007120 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 580332007121 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 580332007122 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 580332007123 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 580332007124 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 580332007125 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 580332007126 DNA binding residues [nucleotide binding] 580332007127 DNA primase; Validated; Region: dnaG; PRK05667 580332007128 CHC2 zinc finger; Region: zf-CHC2; cl15369 580332007129 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 580332007130 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 580332007131 active site 580332007132 metal binding site [ion binding]; metal-binding site 580332007133 interdomain interaction site; other site 580332007134 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 580332007135 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; cl07879 580332007136 GatB domain; Region: GatB_Yqey; cl11497 580332007137 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 580332007138 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 580332007139 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 580332007140 active site 580332007141 HIGH motif; other site 580332007142 dimer interface [polypeptide binding]; other site 580332007143 KMSKS motif; other site 580332007144 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 580332007145 Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]; Region: OapA; COG3061 580332007146 Peptidase family M23; Region: Peptidase_M23; pfam01551 580332007147 Uncharacterized protein family (UPF0075); Region: UPF0075; cl04217 580332007148 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 580332007149 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 580332007150 Axonemal dynein light chain; Region: Ax_dynein_light; pfam10211 580332007151 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 580332007152 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332007153 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 580332007154 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 580332007155 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 580332007156 23S rRNA interface [nucleotide binding]; other site 580332007157 L3 interface [polypeptide binding]; other site 580332007158 FGGY family of carbohydrate kinases; Region: FGGY; cl08364 580332007159 catalytic site [active] 580332007160 metal binding site [ion binding]; metal-binding site 580332007161 carbohydrate binding site [chemical binding]; other site 580332007162 FGGY family of carbohydrate kinases; Region: FGGY; cl08364 580332007163 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GlpA; COG0578 580332007164 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 580332007165 Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins; Region: GDPD; cd08556 580332007166 active site 580332007167 catalytic site [active] 580332007168 metal binding site [ion binding]; metal-binding site 580332007169 Esterase/lipase [General function prediction only]; Region: COG1647 580332007170 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 580332007171 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the GGDEF (DiGuanylate-Cyclase (DGC)) domain. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain and...; Region: CBS_pair_GGDEF_assoc; cd04598 580332007172 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332007173 metal binding site [ion binding]; metal-binding site 580332007174 active site 580332007175 I-site; other site 580332007176 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 580332007177 putative acyl-acceptor binding pocket; other site 580332007178 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 580332007179 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; cl00526 580332007180 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 580332007181 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_2; cd03814 580332007182 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 580332007183 active site 580332007184 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 580332007185 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 580332007186 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332007187 dimer interface [polypeptide binding]; other site 580332007188 putative CheW interface [polypeptide binding]; other site 580332007189 Zinc dependent phospholipase C; Region: Zn_dep_PLPC; cl03005 580332007190 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 580332007191 putative active site [active] 580332007192 OsmC-like protein; Region: OsmC; cl00767 580332007193 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 580332007194 diiron binding motif [ion binding]; other site 580332007195 Uncharacterized conserved protein [Function unknown]; Region: COG1656; cl09136 580332007196 Protein of unknown function (DUF433); Region: DUF433; cl01030 580332007197 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 580332007198 trimer interface [polypeptide binding]; other site 580332007199 eyelet of channel; other site 580332007200 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 580332007201 trimer interface [polypeptide binding]; other site 580332007202 eyelet of channel; other site 580332007203 phosphoenolpyruvate synthase; Validated; Region: PRK06464 580332007204 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 580332007205 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 580332007206 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 580332007207 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 580332007208 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 580332007209 FMN-binding domain; Region: FMN_bind; cl01081 580332007210 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 580332007211 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 580332007212 RnfC Barrel sandwich hybrid domain; Region: RnfC_N; pfam13375 580332007213 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 580332007214 SLBB domain; Region: SLBB; pfam10531 580332007215 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 580332007216 pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric; Region: pyruv_ox_red; TIGR02176 580332007217 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 580332007218 dimer interface [polypeptide binding]; other site 580332007219 PYR/PP interface [polypeptide binding]; other site 580332007220 TPP binding site [chemical binding]; other site 580332007221 substrate binding site [chemical binding]; other site 580332007222 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 580332007223 pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric; Region: pyruv_ox_red; TIGR02176 580332007224 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 580332007225 TPP-binding site [chemical binding]; other site 580332007226 4Fe-4S single cluster domain; Region: Fer4_15; pfam13459 580332007227 ferredoxin; Validated; Region: PRK07118 580332007228 Putative Fe-S cluster; Region: FeS; pfam04060 580332007229 Transcriptional regulator [Transcription]; Region: LysR; COG0583 580332007230 Helix-turn-helix domains; Region: HTH; cl00088 580332007231 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 580332007232 dimerization interface [polypeptide binding]; other site 580332007233 Kinase/pyrophosphorylase; Region: Kinase-PPPase; cl00780 580332007234 Sodium:solute symporter family; Region: SSF; cl00456 580332007235 Sodium:solute symporter family; Region: SSF; cl00456 580332007236 Domain of unknown function (DUF4212); Region: DUF4212; cl01781 580332007237 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 580332007238 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 580332007239 active site 580332007240 phosphorylation site [posttranslational modification] 580332007241 intermolecular recognition site; other site 580332007242 dimerization interface [polypeptide binding]; other site 580332007243 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 580332007244 DNA binding site [nucleotide binding] 580332007245 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 580332007246 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 580332007247 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 580332007248 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 580332007249 dimer interface [polypeptide binding]; other site 580332007250 phosphorylation site [posttranslational modification] 580332007251 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 580332007252 ATP binding site [chemical binding]; other site 580332007253 Mg2+ binding site [ion binding]; other site 580332007254 G-X-G motif; other site 580332007255 Cytochrome c; Region: Cytochrom_C; cl11414 580332007256 Fatty acid cis/trans isomerase (CTI); Region: CTI; pfam06934 580332007257 periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family; Region: napC_nirT; TIGR02161 580332007258 Protein of unknown function (DUF3374); Region: DUF3374; cl11904 580332007259 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 580332007260 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 580332007261 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 580332007262 Cytochrome c; Region: Cytochrom_C; cl11414 580332007263 Histidine kinase; Region: HisKA_3; pfam07730 580332007264 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 580332007265 ATP binding site [chemical binding]; other site 580332007266 Mg2+ binding site [ion binding]; other site 580332007267 G-X-G motif; other site 580332007268 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 580332007269 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 580332007270 active site 580332007271 phosphorylation site [posttranslational modification] 580332007272 intermolecular recognition site; other site 580332007273 dimerization interface [polypeptide binding]; other site 580332007274 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 580332007275 DNA binding residues [nucleotide binding] 580332007276 dimerization interface [polypeptide binding]; other site 580332007277 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 580332007278 Sodium:solute symporter family; Region: SSF; cl00456 580332007279 Protein of unknown function, DUF485; Region: DUF485; cl01231 580332007280 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 580332007281 active site 580332007282 catalytic site [active] 580332007283 substrate binding site [chemical binding]; other site 580332007284 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 580332007285 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 580332007286 ligand binding site [chemical binding]; other site 580332007287 flexible hinge region; other site 580332007288 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with either the CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain or the PB1 (Phox and Bem1p) domain; Region: CBS_pair_CAP-ED_DUF294_PBI_assoc2; cd04800 580332007289 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 580332007290 metal binding triad; other site 580332007291 Indole-3-glycerol phosphate synthase (IGPS); an enzyme in the tryptophan biosynthetic pathway, catalyzing the ring closure reaction of 1-(o-carboxyphenylamino)-1-deoxyribulose-5-phosphate (CdRP) to indole-3-glycerol phosphate (IGP), accompanied by the...; Region: IGPS; cd00331 580332007292 active site 580332007293 ribulose/triose binding site [chemical binding]; other site 580332007294 phosphate binding site [ion binding]; other site 580332007295 substrate (anthranilate) binding pocket [chemical binding]; other site 580332007296 product (indole) binding pocket [chemical binding]; other site 580332007297 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 580332007298 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 580332007299 putative catalytic cysteine [active] 580332007300 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 580332007301 E3 interaction surface; other site 580332007302 lipoyl attachment site [posttranslational modification]; other site 580332007303 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 580332007304 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332007305 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 580332007306 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 580332007307 Protein of unknown function (DUF4197); Region: DUF4197; pfam13852 580332007308 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 580332007309 Helix-turn-helix domains; Region: HTH; cl00088 580332007310 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 580332007311 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 580332007312 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 580332007313 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 580332007314 The ABCA subfamily mediates the transport of a variety of lipid compounds. Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency; Region: ABC_subfamily_A; cd03263 580332007315 Walker A/P-loop; other site 580332007316 ATP binding site [chemical binding]; other site 580332007317 Q-loop/lid; other site 580332007318 ABC transporter signature motif; other site 580332007319 Walker B; other site 580332007320 D-loop; other site 580332007321 H-loop/switch region; other site 580332007322 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 580332007323 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 580332007324 Walker A/P-loop; other site 580332007325 ATP binding site [chemical binding]; other site 580332007326 Q-loop/lid; other site 580332007327 ABC transporter signature motif; other site 580332007328 Walker B; other site 580332007329 D-loop; other site 580332007330 H-loop/switch region; other site 580332007331 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 580332007332 ABC-2 type transporter; Region: ABC2_membrane; cl11417 580332007333 ABC-2 type transporter; Region: ABC2_membrane; cl11417 580332007334 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 580332007335 PAS domain S-box; Region: sensory_box; TIGR00229 580332007336 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 580332007337 putative active site [active] 580332007338 heme pocket [chemical binding]; other site 580332007339 PAS domain S-box; Region: sensory_box; TIGR00229 580332007340 PAS domain S-box; Region: sensory_box; TIGR00229 580332007341 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 580332007342 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 580332007343 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 580332007344 PAS domain; Region: PAS_9; pfam13426 580332007345 putative active site [active] 580332007346 heme pocket [chemical binding]; other site 580332007347 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332007348 metal binding site [ion binding]; metal-binding site 580332007349 active site 580332007350 I-site; other site 580332007351 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 580332007352 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 580332007353 putative catalytic site [active] 580332007354 putative metal binding site [ion binding]; other site 580332007355 putative phosphate binding site [ion binding]; other site 580332007356 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 580332007357 interface (dimer of trimers) [polypeptide binding]; other site 580332007358 Substrate-binding/catalytic site; other site 580332007359 Zn-binding sites [ion binding]; other site 580332007360 Thymidylate synthase and pyrimidine hydroxymethylase: Thymidylate synthase (TS) and deoxycytidylate hydroxymethylase (dCMP-HMase) are homologs that catalyze analogous alkylation of C5 of pyrimidine nucleotides. Both enzymes are involved in the...; Region: TS_Pyrimidine_HMase; cd00351 580332007361 dimerization interface [polypeptide binding]; other site 580332007362 active site 580332007363 S23 ribosomal protein; Region: Ribosomal_S23p; cl05287 580332007364 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cd00209 580332007365 folate binding site [chemical binding]; other site 580332007366 NADP+ binding site [chemical binding]; other site 580332007367 Trehalose-6-phosphate synthase [Carbohydrate transport and metabolism]; Region: OtsA; COG0380 580332007368 Trehalose-6-Phosphate Synthase (TPS) is a glycosyltransferase that catalyses the synthesis of alpha,alpha-1,1-trehalose-6-phosphate from glucose-6-phosphate using a UDP-glucose donor. It is a key enzyme in the trehalose synthesis pathway. Trehalose is a...; Region: GT1_TPS; cd03788 580332007369 active site 580332007370 homotetramer interface [polypeptide binding]; other site 580332007371 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 580332007372 HAD-superfamily hydrolase, subfamily IIB; Region: HAD-SF-IIB; TIGR01484 580332007373 Glucoamylase and related glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: SGA1; COG3387 580332007374 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 580332007375 Ca2+/H+ antiporter [Inorganic ion transport and metabolism]; Region: ChaA; COG0387 580332007376 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 580332007377 Iron permease FTR1 family; Region: FTR1; cl00475 580332007378 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 580332007379 ferric uptake regulator; Provisional; Region: fur; PRK09462 580332007380 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 580332007381 metal binding site 2 [ion binding]; metal-binding site 580332007382 putative DNA binding helix; other site 580332007383 metal binding site 1 [ion binding]; metal-binding site 580332007384 dimer interface [polypeptide binding]; other site 580332007385 structural Zn2+ binding site [ion binding]; other site 580332007386 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 580332007387 Peptidase family U32; Region: Peptidase_U32; cl03113 580332007388 Collagenase; Region: DUF3656; pfam12392 580332007389 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 580332007390 dimerization interface [polypeptide binding]; other site 580332007391 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 580332007392 PAS domain; Region: PAS_9; pfam13426 580332007393 putative active site [active] 580332007394 heme pocket [chemical binding]; other site 580332007395 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332007396 metal binding site [ion binding]; metal-binding site 580332007397 active site 580332007398 I-site; other site 580332007399 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 580332007400 alpha-L-glutamate ligases, RimK family; Region: rimK_fam; TIGR00768 580332007401 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 580332007402 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 580332007403 catalytic residue [active] 580332007404 TlpA-like family, suppressor for copper sensitivity D protein (ScsD) and actinobacterial DsbE homolog subfamily; composed of ScsD, the DsbE homolog of Mycobacterium tuberculosis (MtbDsbE) and similar proteins, all containing a redox-active CXXC motif; Region: TlpA_like_ScsD_MtbDsbE; cd03011 580332007405 catalytic residues [active] 580332007406 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 580332007407 RNA binding surface [nucleotide binding]; other site 580332007408 arginine decarboxylase; Provisional; Region: PRK15029 580332007409 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl09944 580332007410 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 580332007411 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 580332007412 catalytic residue [active] 580332007413 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 580332007414 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 580332007415 trimer interface [polypeptide binding]; other site 580332007416 active site 580332007417 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 580332007418 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 580332007419 active site 580332007420 HIGH motif; other site 580332007421 KMSKS motif; other site 580332007422 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 580332007423 tRNA binding surface [nucleotide binding]; other site 580332007424 anticodon binding site; other site 580332007425 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 580332007426 dimer interface [polypeptide binding]; other site 580332007427 putative tRNA-binding site [nucleotide binding]; other site 580332007428 soluble pyridine nucleotide transhydrogenase; Provisional; Region: PRK05249 580332007429 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332007430 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 580332007431 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 580332007432 putative zinc finger/helix-turn-helix protein, YgiT family; Region: CxxCG_CxxCG_HTH; TIGR03830 580332007433 YokU-like protein; Region: YokU; cl15819 580332007434 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 580332007435 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 580332007436 octamerization interface [polypeptide binding]; other site 580332007437 diferric-oxygen binding site [ion binding]; other site 580332007438 ATP synthase subunit D; Region: ATP-synt_D; cl00613 580332007439 V-type ATP synthase subunit B; Provisional; Region: PRK04196 580332007440 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 580332007441 Walker A motif homologous position; other site 580332007442 Walker B motif; other site 580332007443 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 580332007444 V-type ATP synthase subunit A; Provisional; Region: PRK04192 580332007445 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 580332007446 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 580332007447 Walker A motif/ATP binding site; other site 580332007448 Walker B motif; other site 580332007449 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 580332007450 Plant ATP synthase F0; Region: YMF19; cl07975 580332007451 ATP synthase (F/14-kDa) subunit; Region: ATP-synt_F; cl00632 580332007452 ATP synthase subunit C; Region: ATP-synt_C; cl00466 580332007453 V-type ATP synthase subunit I; Validated; Region: PRK05771 580332007454 V-type ATP synthase subunit C; Provisional; Region: PRK01198; cl00660 580332007455 Archaeal/vacuolar-type H+-ATPase subunit C [Energy production and conversion]; Region: NtpC; COG1527 580332007456 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl15792 580332007457 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl15771 580332007458 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 580332007459 hydrogenase 4 subunit F; Validated; Region: PRK06458 580332007460 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 580332007461 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 580332007462 NADH dehydrogenase; Region: NADHdh; cl00469 580332007463 hydrogenase 4 subunit B; Validated; Region: PRK06521 580332007464 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 580332007465 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with a PAS domain, a GGDEF (DiGuanylate-Cyclase (DGC) domain, and a DUF1 domain downstream. PAS domains have been found to bind ligands, and to act...; Region: CBS_pair_PAS_GGDEF_DUF1_assoc; cd04611 580332007466 FOG: CBS domain [General function prediction only]; Region: COG0517 580332007467 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with a PAS domain, a GGDEF (DiGuanylate-Cyclase (DGC) domain, and a DUF1 domain downstream. PAS domains have been found to bind ligands, and to act...; Region: CBS_pair_PAS_GGDEF_DUF1_assoc; cd04611 580332007468 PAS fold; Region: PAS_4; pfam08448 580332007469 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 580332007470 putative active site [active] 580332007471 heme pocket [chemical binding]; other site 580332007472 PAS domain S-box; Region: sensory_box; TIGR00229 580332007473 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 580332007474 PAS domain S-box; Region: sensory_box; TIGR00229 580332007475 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 580332007476 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 580332007477 PAS domain; Region: PAS_9; pfam13426 580332007478 putative active site [active] 580332007479 heme pocket [chemical binding]; other site 580332007480 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332007481 metal binding site [ion binding]; metal-binding site 580332007482 active site 580332007483 I-site; other site 580332007484 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cl00047 580332007485 global nitrogen regulator NtcA, cyanobacterial; Region: NtcA_cyano; TIGR03697 580332007486 Helix-turn-helix domains; Region: HTH; cl00088 580332007487 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 580332007488 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 580332007489 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 580332007490 generic binding surface II; other site 580332007491 generic binding surface I; other site 580332007492 Dihaem cytochrome c; Region: DHC; pfam09626 580332007493 membrane-bound lytic transglycosylase F; Provisional; Region: PRK10859 580332007494 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 580332007495 substrate binding pocket [chemical binding]; other site 580332007496 membrane-bound complex binding site; other site 580332007497 hinge residues; other site 580332007498 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 580332007499 N-acetyl-D-glucosamine binding site [chemical binding]; other site 580332007500 catalytic residue [active] 580332007501 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 580332007502 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332007503 NAD(P) binding site [chemical binding]; other site 580332007504 active site 580332007505 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 580332007506 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 580332007507 FtsX-like permease family; Region: FtsX; cl15850 580332007508 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 580332007509 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 580332007510 Walker A/P-loop; other site 580332007511 ATP binding site [chemical binding]; other site 580332007512 Q-loop/lid; other site 580332007513 ABC transporter signature motif; other site 580332007514 Walker B; other site 580332007515 D-loop; other site 580332007516 H-loop/switch region; other site 580332007517 seryl-tRNA synthetase; Provisional; Region: PRK05431 580332007518 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 580332007519 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme bound...; Region: SerRS_core; cd00770 580332007520 dimer interface [polypeptide binding]; other site 580332007521 active site 580332007522 motif 1; other site 580332007523 motif 2; other site 580332007524 motif 3; other site 580332007525 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_3; pfam13366 580332007526 recombination factor protein RarA; Reviewed; Region: PRK13342 580332007527 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 580332007528 Walker A motif; other site 580332007529 ATP binding site [chemical binding]; other site 580332007530 Walker B motif; other site 580332007531 arginine finger; other site 580332007532 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 580332007533 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 580332007534 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 580332007535 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 580332007536 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332007537 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 580332007538 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 580332007539 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 580332007540 active site 580332007541 phosphorylation site [posttranslational modification] 580332007542 intermolecular recognition site; other site 580332007543 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 580332007544 DNA binding residues [nucleotide binding] 580332007545 dimerization interface [polypeptide binding]; other site 580332007546 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 580332007547 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 580332007548 dimer interface [polypeptide binding]; other site 580332007549 phosphorylation site [posttranslational modification] 580332007550 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 580332007551 ATP binding site [chemical binding]; other site 580332007552 Mg2+ binding site [ion binding]; other site 580332007553 G-X-G motif; other site 580332007554 Response regulator receiver domain; Region: Response_reg; pfam00072 580332007555 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 580332007556 active site 580332007557 phosphorylation site [posttranslational modification] 580332007558 intermolecular recognition site; other site 580332007559 dimerization interface [polypeptide binding]; other site 580332007560 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 580332007561 Cu(I) binding site [ion binding]; other site 580332007562 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 580332007563 AAA domain; Region: AAA_26; pfam13500 580332007564 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332007565 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332007566 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 580332007567 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 580332007568 S-adenosylmethionine binding site [chemical binding]; other site 580332007569 putative pimeloyl-BioC--CoA transferase BioH; Region: bioH; TIGR01738 580332007570 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 580332007571 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 580332007572 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 580332007573 KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS); Region: KBL_like; cd06454 580332007574 substrate-cofactor binding pocket; other site 580332007575 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332007576 catalytic residue [active] 580332007577 biotin synthase; Region: bioB; TIGR00433 580332007578 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 580332007579 FeS/SAM binding site; other site 580332007580 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 580332007581 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 580332007582 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 580332007583 active site 580332007584 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 580332007585 binding surface 580332007586 TPR motif; other site 580332007587 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 580332007588 binding surface 580332007589 TPR motif; other site 580332007590 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 580332007591 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332007592 Secretin and TonB N terminus short domain; Region: STN; cl06624 580332007593 Secretin N-terminal domain; Region: Secretin_N_2; pfam07655 580332007594 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 580332007595 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 580332007596 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 580332007597 Tfp pilus assembly protein, ATPase PilM [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilM; COG4972 580332007598 legume lectins; Region: lectin_L-type; cl14058 580332007599 homotetramer interaction site [polypeptide binding]; other site 580332007600 homodimer interaction site [polypeptide binding]; other site 580332007601 carbohydrate binding site [chemical binding]; other site 580332007602 metal binding site [ion binding]; metal-binding site 580332007603 Tfp pilus assembly protein PilV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilV; COG4967 580332007604 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 580332007605 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 580332007606 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 580332007607 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 580332007608 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 580332007609 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 580332007610 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 580332007611 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 580332007612 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 580332007613 Walker A motif; other site 580332007614 ATP binding site [chemical binding]; other site 580332007615 Walker B motif; other site 580332007616 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 580332007617 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 580332007618 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332007619 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 580332007620 Bacterial SH3 domain; Region: SH3_3; cl02551 580332007621 Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent...; Region: Translocase_SecB; cl00251 580332007622 SecA binding site; other site 580332007623 Preprotein binding site; other site 580332007624 Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the...; Region: GRX_GRXb_1_3_like; cd03418 580332007625 GSH binding site [chemical binding]; other site 580332007626 catalytic residues [active] 580332007627 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 580332007628 active site residue [active] 580332007629 O-Antigen ligase; Region: Wzy_C; cl04850 580332007630 Domain of unknown function (DUF3366); Region: DUF3366; pfam11846 580332007631 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 580332007632 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 580332007633 Protein export membrane protein; Region: SecD_SecF; cl14618 580332007634 Protein export membrane protein; Region: SecD_SecF; cl14618 580332007635 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 580332007636 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 580332007637 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 580332007638 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 580332007639 dimerization interface [polypeptide binding]; other site 580332007640 putative DNA binding site [nucleotide binding]; other site 580332007641 putative Zn2+ binding site [ion binding]; other site 580332007642 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 580332007643 Sulfatase; Region: Sulfatase; cl10460 580332007644 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 580332007645 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 580332007646 C-terminal peptidase (prc); Region: prc; TIGR00225 580332007647 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 580332007648 protein binding site [polypeptide binding]; other site 580332007649 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 580332007650 Catalytic dyad [active] 580332007651 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332007652 metal binding site [ion binding]; metal-binding site 580332007653 active site 580332007654 I-site; other site 580332007655 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 580332007656 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 580332007657 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 580332007658 NodB motif; other site 580332007659 active site 580332007660 catalytic site [active] 580332007661 metal binding site [ion binding]; metal-binding site 580332007662 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332007663 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332007664 ribonucleotide-diphosphate reductase subunit beta; Provisional; Region: nrdF2; PRK13966 580332007665 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 580332007666 dimer interface [polypeptide binding]; other site 580332007667 putative radical transfer pathway; other site 580332007668 diiron center [ion binding]; other site 580332007669 tyrosyl radical; other site 580332007670 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07207 580332007671 ATP cone domain; Region: ATP-cone; pfam03477 580332007672 Class I ribonucleotide reductase; Region: RNR_I; cd01679 580332007673 active site 580332007674 dimer interface [polypeptide binding]; other site 580332007675 catalytic residues [active] 580332007676 effector binding site; other site 580332007677 R2 peptide binding site; other site 580332007678 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 580332007679 amidase catalytic site [active] 580332007680 Zn binding residues [ion binding]; other site 580332007681 substrate binding site [chemical binding]; other site 580332007682 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 580332007683 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 580332007684 active site 580332007685 phosphorylation site [posttranslational modification] 580332007686 intermolecular recognition site; other site 580332007687 dimerization interface [polypeptide binding]; other site 580332007688 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 580332007689 Walker A motif; other site 580332007690 ATP binding site [chemical binding]; other site 580332007691 Walker B motif; other site 580332007692 arginine finger; other site 580332007693 Helix-turn-helix domains; Region: HTH; cl00088 580332007694 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 580332007695 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 580332007696 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 580332007697 dimer interface [polypeptide binding]; other site 580332007698 phosphorylation site [posttranslational modification] 580332007699 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 580332007700 ATP binding site [chemical binding]; other site 580332007701 Mg2+ binding site [ion binding]; other site 580332007702 G-X-G motif; other site 580332007703 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 580332007704 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 580332007705 4Fe-4S binding domain; Region: Fer4_5; pfam12801 580332007706 Major Facilitator Superfamily; Region: MFS_1; pfam07690 580332007707 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 580332007708 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 580332007709 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; cl15394 580332007710 Cytochrome c; Region: Cytochrom_C; cl11414 580332007711 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 580332007712 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 580332007713 Low-spin heme binding site [chemical binding]; other site 580332007714 D-pathway; other site 580332007715 Putative water exit pathway; other site 580332007716 Binuclear center (active site) [active] 580332007717 K-pathway; other site 580332007718 Putative proton exit pathway; other site 580332007719 Cytochrome c; Region: Cytochrom_C; cl11414 580332007720 Cytochrome c; Region: Cytochrom_C; cl11414 580332007721 Cytochrome c; Region: Cytochrom_C; cl11414 580332007722 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 580332007723 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 580332007724 catalytic residues [active] 580332007725 MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea; Region: MogA_MoaB; cd00886 580332007726 MPT binding site; other site 580332007727 trimer interface [polypeptide binding]; other site 580332007728 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 580332007729 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 580332007730 dimer interface [polypeptide binding]; other site 580332007731 putative functional site; other site 580332007732 putative MPT binding site; other site 580332007733 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 580332007734 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 580332007735 GTP binding site; other site 580332007736 Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa; Region: MobB; cd03116 580332007737 Walker A motif; other site 580332007738 MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoaE; cd00756 580332007739 MoaE homodimer interface [polypeptide binding]; other site 580332007740 MoaD interaction [polypeptide binding]; other site 580332007741 active site residues [active] 580332007742 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 580332007743 MoaE interaction surface [polypeptide binding]; other site 580332007744 MoeB interaction surface [polypeptide binding]; other site 580332007745 thiocarboxylated glycine; other site 580332007746 MoaC family, prokaryotic and eukaryotic. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine...; Region: MoaC_PE; cd01420 580332007747 trimer interface [polypeptide binding]; other site 580332007748 dimer interface [polypeptide binding]; other site 580332007749 putative active site [active] 580332007750 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 580332007751 ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD...; Region: ThiF_MoeB_HesA_family; cd00757 580332007752 ATP binding site [chemical binding]; other site 580332007753 substrate interface [chemical binding]; other site 580332007754 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 580332007755 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 580332007756 FeS/SAM binding site; other site 580332007757 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 580332007758 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 580332007759 Domain of unknown function DUF59; Region: DUF59; cl00941 580332007760 antiporter inner membrane protein; Provisional; Region: PRK11670 580332007761 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 580332007762 Walker A motif; other site 580332007763 NlpC/P60 family; Region: NLPC_P60; cl11438 580332007764 Transglycosylase SLT domain; Region: SLT_2; pfam13406 580332007765 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 580332007766 N-acetyl-D-glucosamine binding site [chemical binding]; other site 580332007767 catalytic residue [active] 580332007768 thioredoxin reductase; Provisional; Region: PRK10262 580332007769 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 580332007770 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 580332007771 Smr domain; Region: Smr; cl02619 580332007772 peroxidase; Provisional; Region: PRK15000 580332007773 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides; Region: PRX_Typ2cys; cd03015 580332007774 dimer interface [polypeptide binding]; other site 580332007775 decamer (pentamer of dimers) interface [polypeptide binding]; other site 580332007776 catalytic triad [active] 580332007777 peroxidatic and resolving cysteines [active] 580332007778 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 580332007779 octamerization interface [polypeptide binding]; other site 580332007780 diferric-oxygen binding site [ion binding]; other site 580332007781 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 580332007782 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 580332007783 MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic...; Region: ABCC_MsbA; cd03251 580332007784 Walker A/P-loop; other site 580332007785 ATP binding site [chemical binding]; other site 580332007786 Q-loop/lid; other site 580332007787 ABC transporter signature motif; other site 580332007788 Walker B; other site 580332007789 D-loop; other site 580332007790 H-loop/switch region; other site 580332007791 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 580332007792 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 580332007793 N-terminal plug; other site 580332007794 ligand-binding site [chemical binding]; other site 580332007795 Protein of unknown function (DUF972); Region: DUF972; pfam06156 580332007796 Cell division protein ZapA; Region: ZapA; cl01146 580332007797 EVE domain; Region: EVE; cl00728 580332007798 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 580332007799 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 580332007800 4Fe-4S binding domain; Region: Fer4_5; pfam12801 580332007801 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 580332007802 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 580332007803 Walker A/P-loop; other site 580332007804 ATP binding site [chemical binding]; other site 580332007805 Q-loop/lid; other site 580332007806 ABC transporter signature motif; other site 580332007807 Walker B; other site 580332007808 D-loop; other site 580332007809 H-loop/switch region; other site 580332007810 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 580332007811 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 580332007812 Walker A/P-loop; other site 580332007813 ATP binding site [chemical binding]; other site 580332007814 Q-loop/lid; other site 580332007815 ABC transporter signature motif; other site 580332007816 Walker B; other site 580332007817 D-loop; other site 580332007818 H-loop/switch region; other site 580332007819 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 580332007820 TM-ABC transporter signature motif; other site 580332007821 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 580332007822 TM-ABC transporter signature motif; other site 580332007823 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 580332007824 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 580332007825 dimerization interface [polypeptide binding]; other site 580332007826 ligand binding site [chemical binding]; other site 580332007827 Cytochrome c; Region: Cytochrom_C; cl11414 580332007828 Cytochrome c; Region: Cytochrom_C; cl11414 580332007829 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 580332007830 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 580332007831 P-loop; other site 580332007832 Magnesium ion binding site [ion binding]; other site 580332007833 Dehydratase family; Region: ILVD_EDD; cl00340 580332007834 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 580332007835 Domain of unknown function DUF21; Region: DUF21; pfam01595 580332007836 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 580332007837 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in...; Region: CBS_pair_CorC_HlyC_assoc; cd04590 580332007838 Transporter associated domain; Region: CorC_HlyC; cl08393 580332007839 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 580332007840 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 580332007841 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 580332007842 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 580332007843 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 580332007844 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 580332007845 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 580332007846 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 580332007847 CoA-binding site [chemical binding]; other site 580332007848 ATP-binding [chemical binding]; other site 580332007849 Protein of unknown function (DUF1342); Region: DUF1342; cl01892 580332007850 Domain of unknown function (DUF329); Region: DUF329; cl01144 580332007851 hypothetical protein; Provisional; Region: PRK08999 580332007852 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 580332007853 active site 580332007854 8-oxo-dGMP binding site [chemical binding]; other site 580332007855 nudix motif; other site 580332007856 metal binding site [ion binding]; metal-binding site 580332007857 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 580332007858 thiamine phosphate binding site [chemical binding]; other site 580332007859 active site 580332007860 pyrophosphate binding site [ion binding]; other site 580332007861 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 580332007862 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 580332007863 Walker A motif; other site 580332007864 ATP binding site [chemical binding]; other site 580332007865 Walker B motif; other site 580332007866 Ornithine acetyltransferase (OAT) family; also referred to as ArgJ. OAT catalyzes the first and fifth steps in arginine biosynthesis, coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group in...; Region: OAT; cd02152 580332007867 heterotetramer interface [polypeptide binding]; other site 580332007868 active site pocket [active] 580332007869 cleavage site 580332007870 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 580332007871 ligand binding site [chemical binding]; other site 580332007872 flexible hinge region; other site 580332007873 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 580332007874 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332007875 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 580332007876 SEC-C motif; Region: SEC-C; pfam02810 580332007877 Peptidase family M23; Region: Peptidase_M23; pfam01551 580332007878 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 580332007879 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 580332007880 cell division protein FtsZ; Validated; Region: PRK09330 580332007881 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 580332007882 nucleotide binding site [chemical binding]; other site 580332007883 SulA interaction site; other site 580332007884 cell division protein FtsA; Region: ftsA; TIGR01174 580332007885 Cell division protein FtsA; Region: FtsA; cl11496 580332007886 Cell division protein FtsA; Region: FtsA; cl11496 580332007887 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 580332007888 Cell division protein FtsQ; Region: FtsQ; pfam03799 580332007889 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 580332007890 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 580332007891 ATP-grasp domain; Region: ATP-grasp_4; cl03087 580332007892 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 580332007893 FAD binding domain; Region: FAD_binding_4; pfam01565 580332007894 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 580332007895 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 580332007896 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 580332007897 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 580332007898 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 580332007899 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 580332007900 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 580332007901 active site 580332007902 homodimer interface [polypeptide binding]; other site 580332007903 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 580332007904 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK02006 580332007905 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332007906 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 580332007907 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 580332007908 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 580332007909 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 580332007910 Mg++ binding site [ion binding]; other site 580332007911 putative catalytic motif [active] 580332007912 putative substrate binding site [chemical binding]; other site 580332007913 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 580332007914 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 580332007915 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 580332007916 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 580332007917 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 580332007918 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 580332007919 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 580332007920 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 580332007921 peptidoglycan synthase FtsI; Provisional; Region: PRK15105 580332007922 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 580332007923 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 580332007924 Septum formation initiator; Region: DivIC; cl11433 580332007925 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 580332007926 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332007927 cell division protein MraZ; Reviewed; Region: PRK00326 580332007928 MraZ protein; Region: MraZ; pfam02381 580332007929 MraZ protein; Region: MraZ; pfam02381 580332007930 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 580332007931 ligand binding site [chemical binding]; other site 580332007932 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 580332007933 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 580332007934 transcriptional regulator PhoU; Provisional; Region: PRK11115 580332007935 PhoU domain; Region: PhoU; pfam01895 580332007936 PhoU domain; Region: PhoU; pfam01895 580332007937 RPI_A: Ribose 5-phosphate isomerase type A (RPI_A) subfamily; RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate, the first step of the non-oxidative branch of the pentose phosphate pathway. This reaction leads to the...; Region: RPI_A; cd01398 580332007938 tetramer (dimer of dimers) interface [polypeptide binding]; other site 580332007939 active site 580332007940 dimer interface [polypeptide binding]; other site 580332007941 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 580332007942 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 580332007943 active site 580332007944 Int/Topo IB signature motif; other site 580332007945 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 580332007946 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 580332007947 DNA binding site [nucleotide binding] 580332007948 active site 580332007949 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 580332007950 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 580332007951 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 580332007952 RimM N-terminal domain; Region: RimM; pfam01782 580332007953 Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to produce...; Region: PRCH; cl09959 580332007954 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 580332007955 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 580332007956 signal recognition particle protein; Provisional; Region: PRK10867 580332007957 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 580332007958 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 580332007959 P loop; other site 580332007960 GTP binding site [chemical binding]; other site 580332007961 Signal peptide binding domain; Region: SRP_SPB; pfam02978 580332007962 beta-phosphoglucomutase family hydrolase; Region: PGMB-YQAB-SF; TIGR02009 580332007963 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 580332007964 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 580332007965 motif II; other site 580332007966 threonine dehydratase; Reviewed; Region: PRK09224 580332007967 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 580332007968 tetramer interface [polypeptide binding]; other site 580332007969 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332007970 catalytic residue [active] 580332007971 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 580332007972 putative Ile/Val binding site [chemical binding]; other site 580332007973 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 580332007974 putative Ile/Val binding site [chemical binding]; other site 580332007975 TfoX N-terminal domain; Region: TfoX_N; cl01167 580332007976 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 580332007977 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 580332007978 Thiamine pyrophosphate (TPP) family, E1 of E. coli PDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDC). PDC catalyzes the oxidative...; Region: TPP_E1_EcPDC_like; cd02017 580332007979 dimer interface [polypeptide binding]; other site 580332007980 TPP-binding site [chemical binding]; other site 580332007981 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 580332007982 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 580332007983 E3 interaction surface; other site 580332007984 lipoyl attachment site [posttranslational modification]; other site 580332007985 e3 binding domain; Region: E3_binding; pfam02817 580332007986 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 580332007987 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 580332007988 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 580332007989 active site 580332007990 (T/H)XGH motif; other site 580332007991 Oligomerisation domain; Region: Oligomerisation; cl00519 580332007992 Uncharacterized conserved protein [Function unknown]; Region: COG1576; cl00679 580332007993 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; pfam02590 580332007994 Maf-like protein; Region: Maf; pfam02545 580332007995 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 580332007996 active site 580332007997 dimer interface [polypeptide binding]; other site 580332007998 ribonuclease G; Provisional; Region: PRK11712 580332007999 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 580332008000 homodimer interface [polypeptide binding]; other site 580332008001 oligonucleotide binding site [chemical binding]; other site 580332008002 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 580332008003 IHF dimer interface [polypeptide binding]; other site 580332008004 IHF - DNA interface [nucleotide binding]; other site 580332008005 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 580332008006 hydrophobic ligand binding site; other site 580332008007 Uncharacterized ACR, YggU family COG1872; Region: DUF167; cl00811 580332008008 YGGT family; Region: YGGT; cl00508 580332008009 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 580332008010 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332008011 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 580332008012 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 580332008013 catalytic residue [active] 580332008014 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 580332008015 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 580332008016 Walker A motif; other site 580332008017 ATP binding site [chemical binding]; other site 580332008018 Walker B motif; other site 580332008019 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 580332008020 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332008021 Walker A motif; other site 580332008022 ATP binding site [chemical binding]; other site 580332008023 Walker B motif; other site 580332008024 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 580332008025 Protein of unknown function (DUF692); Region: DUF692; cl01263 580332008026 Predicted integral membrane protein (DUF2282); Region: DUF2282; cl02366 580332008027 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 580332008028 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 580332008029 TlpA-like family, DipZ-like subfamily; composed uncharacterized proteins containing a TlpA-like TRX domain. Some members show domain architectures similar to that of E. coli DipZ protein (also known as DsbD). The only eukaryotic members of the TlpA...; Region: TlpA_like_DipZ_like; cd03012 580332008030 catalytic residues [active] 580332008031 methionine sulfoxide reductase B; Provisional; Region: PRK00222; cl15841 580332008032 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229 580332008033 FecR protein; Region: FecR; pfam04773 580332008034 RNA polymerase sigma factor; Provisional; Region: PRK12536 580332008035 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 580332008036 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 580332008037 DNA binding residues [nucleotide binding] 580332008038 Protein of unknown function (DUF1109); Region: DUF1109; cl02071 580332008039 Helix-turn-helix domains; Region: HTH; cl00088 580332008040 hypothetical protein; Provisional; Region: PRK11295 580332008041 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 580332008042 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332008043 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 580332008044 NAD(P) binding site [chemical binding]; other site 580332008045 active site 580332008046 Acylphosphatase; Region: Acylphosphatase; cl00551 580332008047 Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]; Region: NfeD; COG1030 580332008048 Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Region: Clp_protease_NfeD_1; cd07020 580332008049 dimer interface [polypeptide binding]; other site 580332008050 active site residues [active] 580332008051 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 580332008052 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 580332008053 Transcription elongation factor Spt4; Region: Spt4; cl12033 580332008054 Cytochrome c; Region: Cytochrom_C; cl11414 580332008055 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 580332008056 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 580332008057 ATP binding site [chemical binding]; other site 580332008058 Mg2+ binding site [ion binding]; other site 580332008059 G-X-G motif; other site 580332008060 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 580332008061 anchoring element; other site 580332008062 dimer interface [polypeptide binding]; other site 580332008063 ATP binding site [chemical binding]; other site 580332008064 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 580332008065 active site 580332008066 metal binding site [ion binding]; metal-binding site 580332008067 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 580332008068 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 580332008069 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA...; Region: TOP4c; cd00187 580332008070 CAP-like domain; other site 580332008071 active site 580332008072 primary dimer interface [polypeptide binding]; other site 580332008073 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 580332008074 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 580332008075 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 580332008076 ATP binding site [chemical binding]; other site 580332008077 Mg2+ binding site [ion binding]; other site 580332008078 G-X-G motif; other site 580332008079 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 580332008080 Helix-turn-helix domains; Region: HTH; cl00088 580332008081 putative transposase OrfB; Reviewed; Region: PHA02517 580332008082 HTH-like domain; Region: HTH_21; pfam13276 580332008083 Integrase core domain; Region: rve; cl01316 580332008084 Integrase core domain; Region: rve_3; cl15866 580332008085 Phage derived protein Gp49-like (DUF891); Region: Gp49; cl01470 580332008086 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 580332008087 Protein of unknown function (DUF1398); Region: DUF1398; cl11576 580332008088 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 580332008089 S-adenosylmethionine binding site [chemical binding]; other site 580332008090 Uncharacterized protein conserved in bacteria (DUF2136); Region: DUF2136; cl01912 580332008091 Predicted transcription regulator containing HTH domain [Transcription]; Region: COG5499 580332008092 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 580332008093 hypothetical protein; Provisional; Region: PRK10396 580332008094 Uncharacterized protein family (UPF0149); Region: UPF0149; cl01173 580332008095 SEC-C motif; Region: SEC-C; pfam02810 580332008096 dUTPase; Region: dUTPase_2; pfam08761 580332008097 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 580332008098 S-adenosylmethionine binding site [chemical binding]; other site 580332008099 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 580332008100 ligand binding site [chemical binding]; other site 580332008101 flexible hinge region; other site 580332008102 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 580332008103 ligand binding site [chemical binding]; other site 580332008104 flexible hinge region; other site 580332008105 Protein of unknown function (DUF2934); Region: DUF2934; pfam11154 580332008106 Isochorismatase family; Region: Isochorismatase; pfam00857 580332008107 YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them; Region: YcaC_related; cd01012 580332008108 catalytic triad [active] 580332008109 dimer interface [polypeptide binding]; other site 580332008110 conserved cis-peptide bond; other site 580332008111 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 580332008112 substrate binding site [chemical binding]; other site 580332008113 PAS domain S-box; Region: sensory_box; TIGR00229 580332008114 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 580332008115 putative active site [active] 580332008116 heme pocket [chemical binding]; other site 580332008117 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332008118 metal binding site [ion binding]; metal-binding site 580332008119 active site 580332008120 I-site; other site 580332008121 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 580332008122 PAS fold; Region: PAS_4; pfam08448 580332008123 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332008124 metal binding site [ion binding]; metal-binding site 580332008125 active site 580332008126 I-site; other site 580332008127 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 580332008128 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 580332008129 putative active site [active] 580332008130 heme pocket [chemical binding]; other site 580332008131 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 580332008132 PAS domain; Region: PAS_9; pfam13426 580332008133 putative active site [active] 580332008134 heme pocket [chemical binding]; other site 580332008135 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332008136 metal binding site [ion binding]; metal-binding site 580332008137 active site 580332008138 I-site; other site 580332008139 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 580332008140 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 580332008141 THUMP domain; Region: THUMP; cl12076 580332008142 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332008143 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 580332008144 ABC-2 type transporter; Region: ABC2_membrane; cl11417 580332008145 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 580332008146 active site 580332008147 nodulation ABC transporter NodI; Provisional; Region: PRK13537 580332008148 The ABCA subfamily mediates the transport of a variety of lipid compounds. Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency; Region: ABC_subfamily_A; cd03263 580332008149 Walker A/P-loop; other site 580332008150 ATP binding site [chemical binding]; other site 580332008151 Q-loop/lid; other site 580332008152 ABC transporter signature motif; other site 580332008153 Walker B; other site 580332008154 D-loop; other site 580332008155 H-loop/switch region; other site 580332008156 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 580332008157 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 580332008158 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:...; Region: TRX_Fd_family; cd02980 580332008159 dimer interface [polypeptide binding]; other site 580332008160 [2Fe-2S] cluster binding site [ion binding]; other site 580332008161 VanZ like family; Region: VanZ; cl01971 580332008162 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 580332008163 octamerization interface [polypeptide binding]; other site 580332008164 diferric-oxygen binding site [ion binding]; other site 580332008165 Uncharacterized ACR, YggU family COG1872; Region: DUF167; cl00811 580332008166 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 580332008167 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 580332008168 RNA binding surface [nucleotide binding]; other site 580332008169 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family. This group is comprised of bacterial proteins assigned to the RsuA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA...; Region: PSSA_1; cd02555 580332008170 active site 580332008171 Uncharacterized conserved protein (DUF2132); Region: DUF2132; cl01894 580332008172 Response regulator receiver domain; Region: Response_reg; pfam00072 580332008173 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 580332008174 active site 580332008175 phosphorylation site [posttranslational modification] 580332008176 intermolecular recognition site; other site 580332008177 dimerization interface [polypeptide binding]; other site 580332008178 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 580332008179 PAS fold; Region: PAS_3; pfam08447 580332008180 putative active site [active] 580332008181 heme pocket [chemical binding]; other site 580332008182 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 580332008183 PAS domain; Region: PAS_9; pfam13426 580332008184 putative active site [active] 580332008185 heme pocket [chemical binding]; other site 580332008186 Response regulator receiver domain; Region: Response_reg; pfam00072 580332008187 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 580332008188 active site 580332008189 phosphorylation site [posttranslational modification] 580332008190 intermolecular recognition site; other site 580332008191 dimerization interface [polypeptide binding]; other site 580332008192 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 580332008193 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 580332008194 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 580332008195 putative active site [active] 580332008196 heme pocket [chemical binding]; other site 580332008197 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 580332008198 dimer interface [polypeptide binding]; other site 580332008199 phosphorylation site [posttranslational modification] 580332008200 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 580332008201 ATP binding site [chemical binding]; other site 580332008202 Mg2+ binding site [ion binding]; other site 580332008203 G-X-G motif; other site 580332008204 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 580332008205 heme-binding site [chemical binding]; other site 580332008206 DsrC like protein; Region: DsrC; cl01101 580332008207 DNA polymerase I; Provisional; Region: PRK05755 580332008208 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 580332008209 active site 580332008210 metal binding site 1 [ion binding]; metal-binding site 580332008211 putative 5' ssDNA interaction site; other site 580332008212 metal binding site 3; metal-binding site 580332008213 metal binding site 2 [ion binding]; metal-binding site 580332008214 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 580332008215 putative DNA binding site [nucleotide binding]; other site 580332008216 putative metal binding site [ion binding]; other site 580332008217 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases; Region: DNA_polA_I_Ecoli_like_exo; cd06139 580332008218 active site 580332008219 catalytic site [active] 580332008220 substrate binding site [chemical binding]; other site 580332008221 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 580332008222 active site 580332008223 DNA binding site [nucleotide binding] 580332008224 catalytic site [active] 580332008225 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 580332008226 Protein of unknown function (DUF2782); Region: DUF2782; pfam11191 580332008227 Homoserine Kinase, type II. Homoserine kinase is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and...; Region: HomoserineK_II; cd05153 580332008228 Phosphotransferase enzyme family; Region: APH; pfam01636 580332008229 putative active site [active] 580332008230 putative substrate binding site [chemical binding]; other site 580332008231 ATP binding site [chemical binding]; other site 580332008232 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 580332008233 active site residue [active] 580332008234 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 580332008235 MEKHLA domain; Region: MEKHLA; pfam08670 580332008236 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 580332008237 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332008238 Family description; Region: UvrD_C_2; cl15862 580332008239 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 580332008240 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332008241 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 580332008242 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 580332008243 HIGH motif; other site 580332008244 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 580332008245 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 580332008246 active site 580332008247 KMSKS motif; other site 580332008248 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 580332008249 tRNA binding surface [nucleotide binding]; other site 580332008250 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 580332008251 Lipopolysaccharide-assembly; Region: LptE; cl01125 580332008252 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 580332008253 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 580332008254 CutA1 divalent ion tolerance protein; Region: CutA1; cl00584 580332008255 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 580332008256 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 580332008257 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 580332008258 DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD...; Region: DsbDgamma; cd02953 580332008259 DsbD alpha interface [polypeptide binding]; other site 580332008260 catalytic residues [active] 580332008261 Domain of unknown function (DUF202); Region: DUF202; cl09954 580332008262 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 580332008263 trimer interface [polypeptide binding]; other site 580332008264 active site 580332008265 dimer interface [polypeptide binding]; other site 580332008266 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 580332008267 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 580332008268 carboxyltransferase (CT) interaction site; other site 580332008269 biotinylation site [posttranslational modification]; other site 580332008270 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 580332008271 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 580332008272 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 580332008273 ATP-grasp domain; Region: ATP-grasp_4; cl03087 580332008274 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 580332008275 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 580332008276 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 580332008277 S-adenosylmethionine binding site [chemical binding]; other site 580332008278 zinc-ribbon domain; Region: zinc_ribbon_5; cl11777 580332008279 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 580332008280 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 580332008281 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 580332008282 Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and...; Region: GCS_H; cd06848 580332008283 lipoyl attachment site [posttranslational modification]; other site 580332008284 glycine dehydrogenase; Provisional; Region: PRK05367 580332008285 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 580332008286 tetramer interface [polypeptide binding]; other site 580332008287 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332008288 catalytic residue [active] 580332008289 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 580332008290 tetramer interface [polypeptide binding]; other site 580332008291 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332008292 catalytic residue [active] 580332008293 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 580332008294 dimer interface [polypeptide binding]; other site 580332008295 catalytic triad [active] 580332008296 peroxidatic and resolving cysteines [active] 580332008297 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; cl02930 580332008298 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 580332008299 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 580332008300 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 580332008301 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 580332008302 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 580332008303 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 580332008304 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 580332008305 Ribokinase-like subgroup A. Found in bacteria and archaea, this subgroup is part of the ribokinase/pfkB superfamily. Its oligomerization state is unknown at this time; Region: ribokinase_group_A; cd01942 580332008306 substrate binding site [chemical binding]; other site 580332008307 ATP binding site [chemical binding]; other site 580332008308 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_10; cd07251 580332008309 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 580332008310 Phosphotransferase enzyme family; Region: APH; pfam01636 580332008311 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein; Region: CSP_CDS; cd04458 580332008312 DNA-binding site [nucleotide binding]; DNA binding site 580332008313 RNA-binding motif; other site 580332008314 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 580332008315 rRNA binding site [nucleotide binding]; other site 580332008316 predicted 30S ribosome binding site; other site 580332008317 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 580332008318 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 580332008319 active site 580332008320 metal binding site [ion binding]; metal-binding site 580332008321 MBOAT, membrane-bound O-acyltransferase family; Region: MBOAT; cl00738 580332008322 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 580332008323 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 580332008324 active site 580332008325 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 580332008326 O-Antigen ligase; Region: Wzy_C; cl04850 580332008327 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 580332008328 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 580332008329 Methyltransferase domain; Region: Methyltransf_31; pfam13847 580332008330 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 580332008331 S-adenosylmethionine binding site [chemical binding]; other site 580332008332 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 580332008333 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 580332008334 active site 580332008335 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 580332008336 putative metal binding site; other site 580332008337 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 580332008338 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 580332008339 NAD(P) binding site [chemical binding]; other site 580332008340 homodimer interface [polypeptide binding]; other site 580332008341 substrate binding site [chemical binding]; other site 580332008342 active site 580332008343 The members of this subfamily catalyze the formation of a phosphodiester bond between a membrane-associated undecaprenyl-phosphate (Und-P) molecule and N-acetylhexosamine 1-phosphate, which is usually donated by a soluble UDP-N-acetylhexosamine precursor; Region: GT_WbpL_WbcO_like; cd06854 580332008344 Mg++ binding site [ion binding]; other site 580332008345 putative catalytic motif [active] 580332008346 putative substrate binding site [chemical binding]; other site 580332008347 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 580332008348 UDP-glucose 4 epimerase, subgroup 4, extended (e) SDRs; Region: UDP_G4E_4_SDR_e; cd05232 580332008349 putative NAD(P) binding site [chemical binding]; other site 580332008350 active site 580332008351 putative substrate binding site [chemical binding]; other site 580332008352 OpgC protein; Region: OpgC_C; cl00792 580332008353 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332008354 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 580332008355 active site 580332008356 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 580332008357 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 580332008358 active site 580332008359 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 580332008360 active site 580332008361 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332008362 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 580332008363 NAD(P) binding site [chemical binding]; other site 580332008364 active site 580332008365 Glycosyl transferase family 11; Region: Glyco_transf_11; pfam01531 580332008366 Glycosyltransferase family 10 (fucosyltransferase); Region: Glyco_transf_10; pfam00852 580332008367 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 580332008368 active site 580332008369 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 580332008370 MatE; Region: MatE; cl10513 580332008371 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332008372 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 580332008373 Putative Acyltransferase (AT), Left-handed parallel beta-Helix (LbH) domain; This group is composed of mostly uncharacterized proteins containing an N-terminal helical subdomain followed by a LbH domain. The alignment contains 6 turns, each containing...; Region: LbH_AT_putative; cd03360 580332008374 putative trimer interface [polypeptide binding]; other site 580332008375 putative CoA binding site [chemical binding]; other site 580332008376 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 580332008377 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 580332008378 inhibitor-cofactor binding pocket; inhibition site 580332008379 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332008380 catalytic residue [active] 580332008381 Putative zinc binding domain; Region: Methyltransf_13; pfam08421 580332008382 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332008383 C-methyltransferase C-terminal domain; Region: Methyltransf_14; pfam08484 580332008384 Cupin domain; Region: Cupin_2; cl09118 580332008385 CDP-glucose 4,6-dehydratase; Region: CDP_4_6_dhtase; TIGR02622 580332008386 CDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: CDP_GD_SDR_e; cd05252 580332008387 NAD binding site [chemical binding]; other site 580332008388 homotetramer interface [polypeptide binding]; other site 580332008389 homodimer interface [polypeptide binding]; other site 580332008390 substrate binding site [chemical binding]; other site 580332008391 active site 580332008392 G1P_cytidylyltransferase catalyzes the production of CDP-D-Glucose; Region: G1P_cytidylyltransferase; cd02524 580332008393 substrate binding site; other site 580332008394 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 580332008395 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 580332008396 inhibitor-cofactor binding pocket; inhibition site 580332008397 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332008398 catalytic residue [active] 580332008399 GDP-fucose synthetase, extended (e) SDRs; Region: GDP_FS_SDR_e; cd05239 580332008400 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 580332008401 NADP binding site [chemical binding]; other site 580332008402 active site 580332008403 putative substrate binding site [chemical binding]; other site 580332008404 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 580332008405 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 580332008406 NADP-binding site; other site 580332008407 homotetramer interface [polypeptide binding]; other site 580332008408 substrate binding site [chemical binding]; other site 580332008409 homodimer interface [polypeptide binding]; other site 580332008410 active site 580332008411 mannose-1-phosphate guanyltransferase; Provisional; Region: cpsB; PRK15460 580332008412 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 580332008413 active site 580332008414 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 580332008415 Cupin domain; Region: Cupin_2; cl09118 580332008416 Helix-turn-helix domains; Region: HTH; cl00088 580332008417 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 580332008418 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 580332008419 putative active site [active] 580332008420 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 580332008421 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 580332008422 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 580332008423 dTDP-glucose 4,6 dehydratase; Provisional; Region: PRK10084 580332008424 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 580332008425 NAD binding site [chemical binding]; other site 580332008426 substrate binding site [chemical binding]; other site 580332008427 homodimer interface [polypeptide binding]; other site 580332008428 active site 580332008429 S23 ribosomal protein; Region: Ribosomal_S23p; cl05287 580332008430 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 580332008431 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 580332008432 substrate binding site; other site 580332008433 tetramer interface; other site 580332008434 Cupin domain; Region: Cupin_2; cl09118 580332008435 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 580332008436 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 580332008437 NADP binding site [chemical binding]; other site 580332008438 active site 580332008439 putative substrate binding site [chemical binding]; other site 580332008440 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 580332008441 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 580332008442 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 580332008443 S-adenosylmethionine binding site [chemical binding]; other site 580332008444 ThiC-associated domain; Region: ThiC-associated; pfam13667 580332008445 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 580332008446 ThiC family; Region: ThiC; cl08031 580332008447 Predicted restriction endonuclease [Defense mechanisms]; Region: COG3440 580332008448 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 580332008449 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 580332008450 Bacitracin resistance protein BacA; Region: BacA; cl00858 580332008451 Member of the Rhodanese Homology Domain superfamily, subgroup 1. This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins; Region: RHOD_1; cd01522 580332008452 active site residue [active] 580332008453 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 580332008454 Cation efflux family; Region: Cation_efflux; cl00316 580332008455 glutamine synthetase; Provisional; Region: glnA; PRK09469 580332008456 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 580332008457 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 580332008458 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 580332008459 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 580332008460 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 580332008461 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 580332008462 dimer interface [polypeptide binding]; other site 580332008463 phosphorylation site [posttranslational modification] 580332008464 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 580332008465 ATP binding site [chemical binding]; other site 580332008466 Mg2+ binding site [ion binding]; other site 580332008467 G-X-G motif; other site 580332008468 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 580332008469 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 580332008470 active site 580332008471 phosphorylation site [posttranslational modification] 580332008472 intermolecular recognition site; other site 580332008473 dimerization interface [polypeptide binding]; other site 580332008474 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 580332008475 Walker A motif; other site 580332008476 ATP binding site [chemical binding]; other site 580332008477 Walker B motif; other site 580332008478 arginine finger; other site 580332008479 Helix-turn-helix domains; Region: HTH; cl00088 580332008480 Phosphoesterase family; Region: Phosphoesterase; cl15450 580332008481 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 580332008482 putative catalytic site [active] 580332008483 putative phosphate binding site [ion binding]; other site 580332008484 active site 580332008485 metal binding site A [ion binding]; metal-binding site 580332008486 DNA binding site [nucleotide binding] 580332008487 putative AP binding site [nucleotide binding]; other site 580332008488 putative metal binding site B [ion binding]; other site 580332008489 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 580332008490 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 580332008491 catalytic residues [active] 580332008492 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 580332008493 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 580332008494 active site 580332008495 Zn binding site [ion binding]; other site 580332008496 dihydroorotase; Provisional; Region: PRK07627 580332008497 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 580332008498 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 580332008499 active site 580332008500 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 580332008501 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 580332008502 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332008503 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cl00243 580332008504 Uncharacterized ACR, COG1678; Region: DUF179; cl00731 580332008505 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 580332008506 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 580332008507 putative binding surface; other site 580332008508 active site 580332008509 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 580332008510 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 580332008511 ATP binding site [chemical binding]; other site 580332008512 Mg2+ binding site [ion binding]; other site 580332008513 G-X-G motif; other site 580332008514 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 580332008515 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 580332008516 Response regulator receiver domain; Region: Response_reg; pfam00072 580332008517 active site 580332008518 phosphorylation site [posttranslational modification] 580332008519 intermolecular recognition site; other site 580332008520 dimerization interface [polypeptide binding]; other site 580332008521 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 580332008522 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 580332008523 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332008524 dimer interface [polypeptide binding]; other site 580332008525 putative CheW interface [polypeptide binding]; other site 580332008526 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 580332008527 Response regulator receiver domain; Region: Response_reg; pfam00072 580332008528 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 580332008529 active site 580332008530 phosphorylation site [posttranslational modification] 580332008531 intermolecular recognition site; other site 580332008532 dimerization interface [polypeptide binding]; other site 580332008533 Response regulator receiver domain; Region: Response_reg; pfam00072 580332008534 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 580332008535 active site 580332008536 phosphorylation site [posttranslational modification] 580332008537 intermolecular recognition site; other site 580332008538 dimerization interface [polypeptide binding]; other site 580332008539 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 580332008540 Cation transport protein; Region: TrkH; cl10514 580332008541 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 580332008542 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332008543 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 580332008544 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332008545 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 580332008546 Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic...; Region: PRX_like1; cd02969 580332008547 putative catalytic residue [active] 580332008548 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385; cl00611 580332008549 RNA methyltransferase; Region: Methyltrans_RNA; pfam04452 580332008550 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 580332008551 ligand binding site [chemical binding]; other site 580332008552 FecR protein; Region: FecR; pfam04773 580332008553 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 580332008554 active site 1 [active] 580332008555 dimer interface [polypeptide binding]; other site 580332008556 hexamer interface [polypeptide binding]; other site 580332008557 active site 2 [active] 580332008558 N-acetylglutamate synthase; Validated; Region: PRK05279 580332008559 AAK_NAGS-ABP: N-acetylglutamate (NAG) kinase-like domain of the NAG Synthase (NAGS) of the arginine-biosynthesis pathway (ABP) found in gamma- and beta-proteobacteria and higher plant chloroplasts. Domain architecture of these NAGS consisted of an...; Region: AAK_NAGS-ABP; cd04237 580332008560 putative feedback inhibition sensing region; other site 580332008561 putative nucleotide binding site [chemical binding]; other site 580332008562 putative substrate binding site [chemical binding]; other site 580332008563 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 580332008564 Coenzyme A binding pocket [chemical binding]; other site 580332008565 Bacterial Fe(2+) trafficking; Region: Iron_traffic; cl01104 580332008566 polyphosphate kinase; Provisional; Region: PRK05443 580332008567 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 580332008568 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 580332008569 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 580332008570 putative domain interface [polypeptide binding]; other site 580332008571 putative active site [active] 580332008572 catalytic site [active] 580332008573 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 580332008574 putative domain interface [polypeptide binding]; other site 580332008575 putative active site [active] 580332008576 catalytic site [active] 580332008577 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cd07040 580332008578 catalytic core [active] 580332008579 polyphosphate:AMP phosphotransferase; Region: poly_P_AMP_trns; TIGR03708 580332008580 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 580332008581 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332008582 active site 580332008583 Protein of unknown function (DUF2288); Region: DUF2288; cl02399 580332008584 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 580332008585 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 580332008586 trimer interface [polypeptide binding]; other site 580332008587 putative metal binding site [ion binding]; other site 580332008588 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 580332008589 Ribbon-helix-helix protein, copG family; Region: RHH_1; cl15783 580332008590 Dihydroorotase (DHOase) catalyzes the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in the pyrimidine biosynthesis. In contrast to the large polyfunctional CAD proteins of higher organisms, this group of DHOases is...; Region: DHOase; cd01294 580332008591 active site 580332008592 substrate binding pocket [chemical binding]; other site 580332008593 dimer interface [polypeptide binding]; other site 580332008594 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 580332008595 Predicted methyltransferases [General function prediction only]; Region: COG0313 580332008596 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 580332008597 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 580332008598 putative ligand binding site [chemical binding]; other site 580332008599 Restriction endonuclease; Region: Mrr_cat; cl00516 580332008600 Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of...; Region: SIS_GmhA; cd05006 580332008601 dimer interface [polypeptide binding]; other site 580332008602 active site 580332008603 BON domain; Region: BON; cl02771 580332008604 BON domain; Region: BON; cl02771 580332008605 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 580332008606 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 580332008607 active site 580332008608 nucleotide binding site [chemical binding]; other site 580332008609 HIGH motif; other site 580332008610 KMSKS motif; other site 580332008611 Protein of unknown function (DUF971); Region: DUF971; cl01414 580332008612 ubiE/COQ5 methyltransferase family; Region: Ubie_methyltran; pfam01209 580332008613 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 580332008614 S-adenosylmethionine binding site [chemical binding]; other site 580332008615 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332008616 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 580332008617 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 580332008618 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 580332008619 PhnA protein; Region: PhnA; pfam03831 580332008620 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 580332008621 active site 580332008622 Tim44-like domain; Region: Tim44; cl09208 580332008623 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 580332008624 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 580332008625 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 580332008626 active site 580332008627 ATP binding site [chemical binding]; other site 580332008628 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 580332008629 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 580332008630 P-loop; other site 580332008631 Magnesium ion binding site [ion binding]; other site 580332008632 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 580332008633 Magnesium ion binding site [ion binding]; other site 580332008634 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 580332008635 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 580332008636 glutaminase active site [active] 580332008637 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 580332008638 dimer interface [polypeptide binding]; other site 580332008639 active site 580332008640 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 580332008641 dimer interface [polypeptide binding]; other site 580332008642 active site 580332008643 UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase; Region: glmU; TIGR01173 580332008644 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 580332008645 Substrate binding site; other site 580332008646 Mg++ binding site; other site 580332008647 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 580332008648 active site 580332008649 substrate binding site [chemical binding]; other site 580332008650 CoA binding site [chemical binding]; other site 580332008651 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 580332008652 ATP synthase, Delta/Epsilon chain, long alpha-helix domain; Region: ATP-synt_DE; pfam00401 580332008653 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 580332008654 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 580332008655 F1 ATP synthase beta subunit, nucleotide-binding domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a...; Region: F1-ATPase_beta; cd01133 580332008656 alpha subunit interaction interface [polypeptide binding]; other site 580332008657 Walker A motif; other site 580332008658 ATP binding site [chemical binding]; other site 580332008659 Walker B motif; other site 580332008660 inhibitor binding site; inhibition site 580332008661 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 580332008662 ATP synthase; Region: ATP-synt; cl00365 580332008663 F0F1 ATP synthase subunit gamma; Provisional; Region: PRK13422 580332008664 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 580332008665 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 580332008666 F1 ATP synthase alpha, central domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to...; Region: F1_ATPase_alpha; cd01132 580332008667 beta subunit interaction interface [polypeptide binding]; other site 580332008668 Walker A motif; other site 580332008669 ATP binding site [chemical binding]; other site 580332008670 Walker B motif; other site 580332008671 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 580332008672 Plant ATP synthase F0; Region: YMF19; cl07975 580332008673 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 580332008674 Plant ATP synthase F0; Region: YMF19; cl07975 580332008675 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 580332008676 ATP synthase subunit C; Region: ATP-synt_C; cl00466 580332008677 ATP synthase A chain; Region: ATP-synt_A; cl00413 580332008678 ATP synthase I chain; Region: ATP_synt_I; cl09170 580332008679 ParB-like partition proteins; Region: parB_part; TIGR00180 580332008680 ParB-like nuclease domain; Region: ParBc; cl02129 580332008681 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 580332008682 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 580332008683 P-loop; other site 580332008684 Magnesium ion binding site [ion binding]; other site 580332008685 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 580332008686 Magnesium ion binding site [ion binding]; other site 580332008687 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 580332008688 S-adenosylmethionine binding site [chemical binding]; other site 580332008689 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 580332008690 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332008691 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332008692 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 580332008693 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 580332008694 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 580332008695 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 580332008696 G4 box; other site 580332008697 GTP/Mg2+ binding site [chemical binding]; other site 580332008698 G5 box; other site 580332008699 trmE is a tRNA modification GTPase; Region: trmE; cd04164 580332008700 G1 box; other site 580332008701 G1 box; other site 580332008702 GTP/Mg2+ binding site [chemical binding]; other site 580332008703 Switch I region; other site 580332008704 Switch I region; other site 580332008705 G2 box; other site 580332008706 G2 box; other site 580332008707 Switch II region; other site 580332008708 G3 box; other site 580332008709 G4 box; other site 580332008710 G5 box; other site 580332008711 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 580332008712 membrane protein insertase; Provisional; Region: PRK01318 580332008713 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 580332008714 Haemolytic domain; Region: Haemolytic; cl00506 580332008715 Ribonuclease P; Region: Ribonuclease_P; cl00457 580332008716 Ribosomal protein L34; Region: Ribosomal_L34; cl00370