-- dump date 20140620_065635 -- 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; pfam04361 580332000048 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 580332000049 DNA protecting protein DprA; Region: dprA; TIGR00732 580332000050 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 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 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 580332000069 dimerization interface [polypeptide binding]; other site 580332000070 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 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; cd00130 580332000072 putative active site [active] 580332000073 heme pocket [chemical binding]; other site 580332000074 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 580332000075 dimer interface [polypeptide binding]; other site 580332000076 phosphorylation site [posttranslational modification] 580332000077 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 580332000078 ATP binding site [chemical binding]; other site 580332000079 Mg2+ binding site [ion binding]; other site 580332000080 G-X-G motif; other site 580332000081 Response regulator receiver domain; Region: Response_reg; pfam00072 580332000082 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 580332000083 active site 580332000084 phosphorylation site [posttranslational modification] 580332000085 intermolecular recognition site; other site 580332000086 dimerization interface [polypeptide binding]; other site 580332000087 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 580332000088 transketolase; Reviewed; Region: PRK12753 580332000089 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 580332000090 TPP-binding site [chemical binding]; other site 580332000091 dimer interface [polypeptide binding]; other site 580332000092 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 580332000093 PYR/PP interface [polypeptide binding]; other site 580332000094 dimer interface [polypeptide binding]; other site 580332000095 TPP binding site [chemical binding]; other site 580332000096 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 580332000097 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 580332000098 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 580332000099 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 580332000100 phosphoglycerate kinase; Provisional; Region: pgk; PRK00073 580332000101 Phosphoglycerate kinase; Region: PGK; pfam00162 580332000102 substrate binding site [chemical binding]; other site 580332000103 hinge regions; other site 580332000104 ADP binding site [chemical binding]; other site 580332000105 catalytic site [active] 580332000106 pyruvate kinase; Provisional; Region: PRK05826 580332000107 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl17342 580332000108 domain interfaces; other site 580332000109 active site 580332000110 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 580332000111 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 580332000112 intersubunit interface [polypeptide binding]; other site 580332000113 active site 580332000114 zinc binding site [ion binding]; other site 580332000115 Na+ binding site [ion binding]; other site 580332000116 Cytochrome c; Region: Cytochrom_C; cl11414 580332000117 EamA-like transporter family; Region: EamA; pfam00892 580332000118 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 580332000119 EamA-like transporter family; Region: EamA; pfam00892 580332000120 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 580332000121 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 580332000122 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 580332000123 putative dimerization interface [polypeptide binding]; other site 580332000124 ribulose bisphosphate carboxylase; Provisional; Region: PRK13475 580332000125 Ribulose bisphosphate carboxylase large chain, Form II; Region: RuBisCO_large_II; cd08211 580332000126 dimer interface [polypeptide binding]; other site 580332000127 active site 580332000128 catalytic residue [active] 580332000129 metal binding site [ion binding]; metal-binding site 580332000130 MoxR-like ATPases [General function prediction only]; Region: COG0714 580332000131 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 580332000132 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 580332000133 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 580332000134 metal ion-dependent adhesion site (MIDAS); other site 580332000135 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 580332000136 AMP binding site [chemical binding]; other site 580332000137 metal binding site [ion binding]; metal-binding site 580332000138 active site 580332000139 AIR carboxylase; Region: AIRC; pfam00731 580332000140 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 580332000141 ATP binding site [chemical binding]; other site 580332000142 active site 580332000143 substrate binding site [chemical binding]; other site 580332000144 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 580332000145 active site clefts [active] 580332000146 zinc binding site [ion binding]; other site 580332000147 dimer interface [polypeptide binding]; other site 580332000148 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 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; Reviewed; Region: ampG; PRK11902 580332000161 AmpG-like permease; Region: 2A0125; TIGR00901 580332000162 Methyltransferase domain; Region: Methyltransf_23; pfam13489 580332000163 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 580332000164 S-adenosylmethionine binding site [chemical binding]; other site 580332000165 homoserine O-acetyltransferase; Provisional; Region: metX; PRK00175 580332000166 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 580332000167 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 580332000168 dimer interface [polypeptide binding]; other site 580332000169 active site 580332000170 aspartate-rich active site metal binding site; other site 580332000171 allosteric magnesium binding site [ion binding]; other site 580332000172 Schiff base residues; other site 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 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 580332000196 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 580332000197 S-adenosylmethionine binding site [chemical binding]; other site 580332000198 4-hydroxythreonine-4-phosphate dehydrogenase; Region: pdxA; TIGR00557 580332000199 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 580332000200 SurA N-terminal domain; Region: SurA_N; pfam09312 580332000201 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 580332000202 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 580332000203 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 580332000204 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 580332000205 Organic solvent tolerance protein; Region: OstA_C; pfam04453 580332000206 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 580332000207 Phosphotransferase enzyme family; Region: APH; pfam01636 580332000208 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 580332000209 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 580332000210 Substrate binding site; other site 580332000211 metal-binding site 580332000212 Aminopeptidase P, N-terminal domain; Region: AMP_N; pfam05195 580332000213 proline aminopeptidase P II; Provisional; Region: PRK10879 580332000214 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 580332000215 active site 580332000216 2-polyprenyl-6-methoxyphenol 4-hydroxylase; Region: UbiH; TIGR01984 580332000217 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 580332000218 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 580332000219 cyclase homology domain; Region: CHD; cd07302 580332000220 nucleotidyl binding site; other site 580332000221 metal binding site [ion binding]; metal-binding site 580332000222 dimer interface [polypeptide binding]; other site 580332000223 FHA domain; Region: FHA; pfam00498 580332000224 phosphopeptide binding site; other site 580332000225 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 580332000226 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 580332000227 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 580332000228 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 580332000229 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 580332000230 Protein of unknown function, DUF486; Region: DUF486; cl01236 580332000231 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 580332000232 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 580332000233 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 580332000234 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 580332000235 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 580332000236 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 580332000237 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 580332000238 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 580332000239 excinuclease ABC, C subunit; Region: uvrC; TIGR00194 580332000240 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 580332000241 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 580332000242 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 580332000243 substrate binding pocket [chemical binding]; other site 580332000244 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 580332000245 B12 binding site [chemical binding]; other site 580332000246 cobalt ligand [ion binding]; other site 580332000247 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 580332000248 Hemerythrin; Region: Hemerythrin; cd12107 580332000249 Fe binding site [ion binding]; other site 580332000250 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 580332000251 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 580332000252 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 580332000253 Walker A motif; other site 580332000254 ATP binding site [chemical binding]; other site 580332000255 Walker B motif; other site 580332000256 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 580332000257 Membrane fusogenic activity; Region: BMFP; pfam04380 580332000258 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 580332000259 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 580332000260 Nitrogen regulatory protein P-II; Region: P-II; smart00938 580332000261 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 580332000262 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 580332000263 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 580332000264 putative active site [active] 580332000265 heme pocket [chemical binding]; other site 580332000266 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 580332000267 putative active site [active] 580332000268 heme pocket [chemical binding]; other site 580332000269 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332000270 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332000271 metal binding site [ion binding]; metal-binding site 580332000272 active site 580332000273 I-site; other site 580332000274 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 580332000275 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 580332000276 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332000277 dimer interface [polypeptide binding]; other site 580332000278 putative CheW interface [polypeptide binding]; other site 580332000279 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 580332000280 substrate binding site [chemical binding]; other site 580332000281 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 580332000282 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 580332000283 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 580332000284 putative active site [active] 580332000285 putative substrate binding site [chemical binding]; other site 580332000286 putative cosubstrate binding site; other site 580332000287 catalytic site [active] 580332000288 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 580332000289 Putative catalytic NodB homology domain of uncharacterized BH0857 protein from Bacillus halodurans and its bacterial homologs; Region: CE4_BH0857_like; cd10955 580332000290 NodB motif; other site 580332000291 putative active site [active] 580332000292 putative catalytic site [active] 580332000293 MltA-interacting protein MipA; Region: MipA; cl01504 580332000294 Iron-binding zinc finger CDGSH type; Region: zf-CDGSH; pfam09360 580332000295 Iron-binding zinc finger CDGSH type; Region: zf-CDGSH; pfam09360 580332000296 urea carboxylase-associated protein 1; Region: urea_degr_1; TIGR03424 580332000297 urea carboxylase-associated protein 2; Region: urea_degr_2; TIGR03425 580332000298 urea carboxylase-associated protein 1; Region: urea_degr_1; TIGR03424 580332000299 Domain of unknown function (DUF1989); Region: DUF1989; pfam09347 580332000300 urea carboxylase; Region: urea_carbox; TIGR02712 580332000301 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 580332000302 ATP-grasp domain; Region: ATP-grasp_4; cl17255 580332000303 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 580332000304 Allophanate hydrolase subunit 2; Region: AHS2; smart00797 580332000305 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; cl00896 580332000306 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 580332000307 carboxyltransferase (CT) interaction site; other site 580332000308 biotinylation site [posttranslational modification]; other site 580332000309 allophanate hydrolase; Provisional; Region: PRK08186 580332000310 Amidase; Region: Amidase; cl11426 580332000311 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 580332000312 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 580332000313 non-specific DNA binding site [nucleotide binding]; other site 580332000314 salt bridge; other site 580332000315 sequence-specific DNA binding site [nucleotide binding]; other site 580332000316 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 580332000317 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 580332000318 putative active site [active] 580332000319 putative NTP binding site [chemical binding]; other site 580332000320 putative nucleic acid binding site [nucleotide binding]; other site 580332000321 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 580332000322 putative active site [active] 580332000323 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 580332000324 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 580332000325 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 580332000326 ABC transporter periplasmic binding protein, urea carboxylase region; Region: ABC_peri_uca; TIGR03427 580332000327 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 580332000328 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 580332000329 dimer interface [polypeptide binding]; other site 580332000330 conserved gate region; other site 580332000331 putative PBP binding loops; other site 580332000332 ABC-ATPase subunit interface; other site 580332000333 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 580332000334 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 580332000335 Walker A/P-loop; other site 580332000336 ATP binding site [chemical binding]; other site 580332000337 Q-loop/lid; other site 580332000338 ABC transporter signature motif; other site 580332000339 Walker B; other site 580332000340 D-loop; other site 580332000341 H-loop/switch region; other site 580332000342 Creatinine amidohydrolase; Region: Creatininase; pfam02633 580332000343 glutamine synthetase, type III; Region: gln_synth_III; TIGR03105 580332000344 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 580332000345 Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Transcription]; Region: NikR; COG0864 580332000346 Uncharacterized protein family (UPF0156); Region: RHH_2; cl17383 580332000347 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 580332000348 glutamate racemase; Provisional; Region: PRK00865 580332000349 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 580332000350 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 580332000351 Walker A/P-loop; other site 580332000352 ATP binding site [chemical binding]; other site 580332000353 ABC transporter signature motif; other site 580332000354 Walker B; other site 580332000355 D-loop; other site 580332000356 H-loop/switch region; other site 580332000357 ABC transporter; Region: ABC_tran_2; pfam12848 580332000358 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 580332000359 Serine hydrolase; Region: Ser_hydrolase; pfam06821 580332000360 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 580332000361 glutamate--cysteine ligase, T. ferrooxidans family; Region: gshA_ferroox; TIGR02049 580332000362 Glutamate-cysteine ligase; Region: GshA; pfam08886 580332000363 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 580332000364 ApbE family; Region: ApbE; pfam02424 580332000365 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 580332000366 active pocket/dimerization site; other site 580332000367 active site 580332000368 phosphorylation site [posttranslational modification] 580332000369 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 580332000370 dimerization domain swap beta strand [polypeptide binding]; other site 580332000371 regulatory protein interface [polypeptide binding]; other site 580332000372 active site 580332000373 regulatory phosphorylation site [posttranslational modification]; other site 580332000374 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 580332000375 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 580332000376 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 580332000377 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 580332000378 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 580332000379 metal binding triad [ion binding]; metal-binding site 580332000380 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 580332000381 Transglycosylase; Region: Transgly; pfam00912 580332000382 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 580332000383 Cell division protein FtsA; Region: FtsA; cl17206 580332000384 Competence protein A; Region: Competence_A; pfam11104 580332000385 Cell division protein FtsA; Region: FtsA; pfam14450 580332000386 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 580332000387 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 580332000388 Pilus assembly protein, PilO; Region: PilO; pfam04350 580332000389 Tfp pilus assembly protein PilP [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilP; COG3168 580332000390 Pilus assembly protein, PilP; Region: PilP; pfam04351 580332000391 AMIN domain; Region: AMIN; pfam11741 580332000392 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 580332000393 Secretin and TonB N terminus short domain; Region: STN; smart00965 580332000394 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 580332000395 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 580332000396 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 580332000397 bifunctional shikimate kinase/3-dehydroquinate synthase; Provisional; Region: PRK14021 580332000398 ADP binding site [chemical binding]; other site 580332000399 magnesium binding site [ion binding]; other site 580332000400 putative shikimate binding site; other site 580332000401 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 580332000402 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 580332000403 active site 580332000404 dimer interface [polypeptide binding]; other site 580332000405 metal binding site [ion binding]; metal-binding site 580332000406 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 580332000407 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332000408 Zn2+ binding site [ion binding]; other site 580332000409 Mg2+ binding site [ion binding]; other site 580332000410 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 580332000411 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 580332000412 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 580332000413 active site 580332000414 dimer interface [polypeptide binding]; other site 580332000415 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 580332000416 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 580332000417 active site 580332000418 FMN binding site [chemical binding]; other site 580332000419 substrate binding site [chemical binding]; other site 580332000420 3Fe-4S cluster binding site [ion binding]; other site 580332000421 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 580332000422 domain interface; other site 580332000423 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 580332000424 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 580332000425 substrate binding site [chemical binding]; other site 580332000426 active site 580332000427 primosome assembly protein PriA; Validated; Region: PRK05580 580332000428 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 580332000429 ATP binding site [chemical binding]; other site 580332000430 putative Mg++ binding site [ion binding]; other site 580332000431 helicase superfamily c-terminal domain; Region: HELICc; smart00490 580332000432 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 580332000433 FAD binding domain; Region: FAD_binding_4; pfam01565 580332000434 Uncharacterized conserved protein [Function unknown]; Region: COG1432 580332000435 LabA_like proteins; Region: LabA_like; cd06167 580332000436 putative metal binding site [ion binding]; other site 580332000437 C-terminal domain of LabA_like proteins; Region: LabA_like_C; cd10146 580332000438 ferredoxin--NADP+ reductase; Provisional; Region: PLN03116 580332000439 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 580332000440 FAD binding pocket [chemical binding]; other site 580332000441 conserved FAD binding motif [chemical binding]; other site 580332000442 phosphate binding motif [ion binding]; other site 580332000443 beta-alpha-beta structure motif; other site 580332000444 NAD binding pocket [chemical binding]; other site 580332000445 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 580332000446 active site 580332000447 Domain of unknown function (DUF4337); Region: DUF4337; pfam14235 580332000448 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 580332000449 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 580332000450 active site 580332000451 catalytic tetrad [active] 580332000452 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 580332000453 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 580332000454 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 580332000455 active site 580332000456 HIGH motif; other site 580332000457 KMSK motif region; other site 580332000458 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 580332000459 tRNA binding surface [nucleotide binding]; other site 580332000460 anticodon binding site; other site 580332000461 Sporulation related domain; Region: SPOR; pfam05036 580332000462 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 580332000463 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 580332000464 catalytic residues [active] 580332000465 hinge region; other site 580332000466 alpha helical domain; other site 580332000467 short chain dehydrogenase; Provisional; Region: PRK07024 580332000468 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332000469 NAD(P) binding site [chemical binding]; other site 580332000470 active site 580332000471 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 580332000472 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 580332000473 [2Fe-2S] cluster binding site [ion binding]; other site 580332000474 cytochrome b; Provisional; Region: CYTB; MTH00119 580332000475 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 580332000476 Qi binding site; other site 580332000477 intrachain domain interface; other site 580332000478 interchain domain interface [polypeptide binding]; other site 580332000479 heme bH binding site [chemical binding]; other site 580332000480 heme bL binding site [chemical binding]; other site 580332000481 Qo binding site; other site 580332000482 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 580332000483 interchain domain interface [polypeptide binding]; other site 580332000484 intrachain domain interface; other site 580332000485 Qi binding site; other site 580332000486 Qo binding site; other site 580332000487 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 580332000488 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 580332000489 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 580332000490 GatB domain; Region: GatB_Yqey; smart00845 580332000491 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 580332000492 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 580332000493 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 580332000494 rod shape-determining protein MreB; Provisional; Region: PRK13927 580332000495 MreB and similar proteins; Region: MreB_like; cd10225 580332000496 nucleotide binding site [chemical binding]; other site 580332000497 Mg binding site [ion binding]; other site 580332000498 putative protofilament interaction site [polypeptide binding]; other site 580332000499 RodZ interaction site [polypeptide binding]; other site 580332000500 rod shape-determining protein MreC; Region: mreC; TIGR00219 580332000501 rod shape-determining protein MreC; Region: MreC; pfam04085 580332000502 rod shape-determining protein MreD; Region: shape_MreD; TIGR03426 580332000503 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 580332000504 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 580332000505 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 580332000506 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 580332000507 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 580332000508 rare lipoprotein A; Region: rlpA; TIGR00413 580332000509 Sporulation related domain; Region: SPOR; pfam05036 580332000510 Protein of unknown function (DUF1304); Region: DUF1304; pfam06993 580332000511 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 580332000512 active site residue [active] 580332000513 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 580332000514 active site residue [active] 580332000515 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 580332000516 Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase; Region: PUA; smart00359 580332000517 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 580332000518 putative RNA binding site [nucleotide binding]; other site 580332000519 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 580332000520 S-adenosylmethionine binding site [chemical binding]; other site 580332000521 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 580332000522 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 580332000523 active site 580332000524 DNA binding site [nucleotide binding] 580332000525 Int/Topo IB signature motif; other site 580332000526 Protein of unknown function, DUF484; Region: DUF484; cl17449 580332000527 GAF domain; Region: GAF_2; pfam13185 580332000528 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 580332000529 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 580332000530 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 580332000531 Predicted CoA-binding protein [General function prediction only]; Region: COG1832 580332000532 PDZ domain; Region: PDZ_2; pfam13180 580332000533 protein binding site [polypeptide binding]; other site 580332000534 Bacterial ABC transporter protein EcsB; Region: EcsB; cl11542 580332000535 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 580332000536 Histidine kinase; Region: HisKA_3; pfam07730 580332000537 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 580332000538 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 580332000539 active site 580332000540 phosphorylation site [posttranslational modification] 580332000541 intermolecular recognition site; other site 580332000542 dimerization interface [polypeptide binding]; other site 580332000543 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 580332000544 DNA binding residues [nucleotide binding] 580332000545 dimerization interface [polypeptide binding]; other site 580332000546 Nitrate and nitrite sensing; Region: NIT; pfam08376 580332000547 ANTAR domain; Region: ANTAR; pfam03861 580332000548 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 580332000549 NMT1-like family; Region: NMT1_2; pfam13379 580332000550 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 580332000551 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 580332000552 dimer interface [polypeptide binding]; other site 580332000553 conserved gate region; other site 580332000554 putative PBP binding loops; other site 580332000555 ABC-ATPase subunit interface; other site 580332000556 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 580332000557 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 580332000558 Walker A/P-loop; other site 580332000559 ATP binding site [chemical binding]; other site 580332000560 Q-loop/lid; other site 580332000561 ABC transporter signature motif; other site 580332000562 Walker B; other site 580332000563 D-loop; other site 580332000564 H-loop/switch region; other site 580332000565 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 580332000566 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 580332000567 Walker A/P-loop; other site 580332000568 ATP binding site [chemical binding]; other site 580332000569 Q-loop/lid; other site 580332000570 ABC transporter signature motif; other site 580332000571 Walker B; other site 580332000572 D-loop; other site 580332000573 H-loop/switch region; other site 580332000574 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 580332000575 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 580332000576 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 580332000577 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 580332000578 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 580332000579 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 580332000580 [2Fe-2S] cluster binding site [ion binding]; other site 580332000581 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 580332000582 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 580332000583 [4Fe-4S] binding site [ion binding]; other site 580332000584 molybdopterin cofactor binding site; other site 580332000585 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 580332000586 molybdopterin cofactor binding site; other site 580332000587 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 580332000588 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; pfam00690 580332000589 plasma-membrane proton-efflux P-type ATPase; Region: ATPase-IIIA_H; TIGR01647 580332000590 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 580332000591 Soluble P-type ATPase [General function prediction only]; Region: COG4087 580332000592 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 580332000593 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 580332000594 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 580332000595 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 580332000596 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 580332000597 N-acetyl-D-glucosamine binding site [chemical binding]; other site 580332000598 catalytic residue [active] 580332000599 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 580332000600 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 580332000601 active site 580332000602 NTP binding site [chemical binding]; other site 580332000603 metal binding triad [ion binding]; metal-binding site 580332000604 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 580332000605 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 580332000606 putative active site [active] 580332000607 Uncharacterized conserved protein [Function unknown]; Region: COG1565 580332000608 pteridine reductase; Provisional; Region: PRK09135 580332000609 pteridine reductase (PR), classical (c) SDRs; Region: PR_SDR_c; cd05357 580332000610 NADP binding site [chemical binding]; other site 580332000611 substrate binding pocket [chemical binding]; other site 580332000612 active site 580332000613 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 580332000614 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 580332000615 Ligand Binding Site [chemical binding]; other site 580332000616 Domain of unknown function (DUF386); Region: DUF386; cl01047 580332000617 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 580332000618 putative protease; Provisional; Region: PRK15452 580332000619 Peptidase family U32; Region: Peptidase_U32; pfam01136 580332000620 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 580332000621 FAD binding site [chemical binding]; other site 580332000622 Predicted membrane protein [Function unknown]; Region: COG1950 580332000623 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 580332000624 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 580332000625 homotetramer interface [polypeptide binding]; other site 580332000626 ligand binding site [chemical binding]; other site 580332000627 catalytic site [active] 580332000628 NAD binding site [chemical binding]; other site 580332000629 S-adenosylmethionine synthetase; Validated; Region: PRK05250 580332000630 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 580332000631 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 580332000632 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 580332000633 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 580332000634 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 580332000635 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 580332000636 putative acyl-acceptor binding pocket; other site 580332000637 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 580332000638 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 580332000639 putative acyl-acceptor binding pocket; other site 580332000640 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 580332000641 putative active site [active] 580332000642 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 580332000643 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 580332000644 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 4) [Cell envelope biogenesis, outer membrane]; Region: DacB; COG2027 580332000645 D-alanyl-D-alanine carboxypeptidase, serine-type, PBP4 family; Region: PBP4; TIGR00666 580332000646 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK06943 580332000647 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 580332000648 inhibitor-cofactor binding pocket; inhibition site 580332000649 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332000650 catalytic residue [active] 580332000651 Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]; Region: COG1090 580332000652 atypical (a) SDRs, subgroup 8; Region: SDR_a8; cd05242 580332000653 putative NAD(P) binding site [chemical binding]; other site 580332000654 putative active site [active] 580332000655 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 580332000656 oligomerisation interface [polypeptide binding]; other site 580332000657 mobile loop; other site 580332000658 roof hairpin; other site 580332000659 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 580332000660 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 580332000661 ring oligomerisation interface [polypeptide binding]; other site 580332000662 ATP/Mg binding site [chemical binding]; other site 580332000663 stacking interactions; other site 580332000664 hinge regions; other site 580332000665 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 580332000666 non-specific DNA binding site [nucleotide binding]; other site 580332000667 salt bridge; other site 580332000668 sequence-specific DNA binding site [nucleotide binding]; other site 580332000669 Predicted transcriptional regulator [Transcription]; Region: COG2932 580332000670 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 580332000671 Catalytic site [active] 580332000672 Winged helix-turn-helix DNA-binding; Region: HTH_35; cl17423 580332000673 putative transposase OrfB; Reviewed; Region: PHA02517 580332000674 Integrase core domain; Region: rve; pfam00665 580332000675 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 580332000676 AAA domain; Region: AAA_22; pfam13401 580332000677 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 580332000678 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 580332000679 putative active site [active] 580332000680 putative NTP binding site [chemical binding]; other site 580332000681 putative nucleic acid binding site [nucleotide binding]; other site 580332000682 Replication protein A C terminal; Region: RPA_C; pfam08784 580332000683 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 580332000684 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 580332000685 IHF - DNA interface [nucleotide binding]; other site 580332000686 IHF dimer interface [polypeptide binding]; other site 580332000687 Protein of unknown function (DUF1018); Region: DUF1018; cl01815 580332000688 Mor transcription activator family; Region: Mor; cl02360 580332000689 Protein of unknown function (DUF4063); Region: DUF4063; pfam13272 580332000690 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 580332000691 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 580332000692 N-acetyl-D-glucosamine binding site [chemical binding]; other site 580332000693 catalytic residue [active] 580332000694 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 580332000695 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1223 580332000696 Protein of unknown function (DUF1804); Region: DUF1804; pfam08822 580332000697 Phage-related terminase [General function prediction only]; Region: COG5362; cl02216 580332000698 Protein of unknown function (DUF935); Region: DUF935; pfam06074 580332000699 Mu-like prophage protein gp29 [Function unknown]; Region: COG4383 580332000700 Phage Mu protein F like protein; Region: Phage_Mu_F; pfam04233 580332000701 Phage virion morphogenesis family; Region: Phage_tail_S; cl02089 580332000702 Mu-like prophage I protein; Region: Mu-like_Pro; pfam10123 580332000703 Mu-like prophage major head subunit gpT; Region: Mu-like_gpT; cl01826 580332000704 Mu-like prophage major head subunit gpT; Region: Mu-like_gpT; cl01826 580332000705 hypothetical protein; Region: PHA01971 580332000706 Protein of unknown function (DUF1320); Region: DUF1320; pfam07030 580332000707 Domain of unknown function (DUF1834); Region: DUF1834; pfam08873 580332000708 Protein of unknown function (DUF2635); Region: DUF2635; pfam10948 580332000709 Mu-like prophage tail sheath protein gpL [General function prediction only]; Region: COG4386 580332000710 Phage tail sheath protein; Region: Phage_sheath_1; cl01389 580332000711 Phage tail sheath protein; Region: Phage_sheath_1; cl01389 580332000712 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 580332000713 Phage-related minor tail protein; Region: PhageMin_Tail; pfam10145 580332000714 Mu-like prophage DNA circulation protein [General function prediction only]; Region: COG4228 580332000715 DNA circulation protein N-terminus; Region: DNA_circ_N; pfam07157 580332000716 Mu-like prophage tail protein gpP [General function prediction only]; Region: COG4379 580332000717 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 580332000718 Bacteriophage Mu Gp45 protein; Region: Phage_Mu_Gp45; cl15410 580332000719 Phage protein GP46; Region: GP46; cl01814 580332000720 Uncharacterized homolog of phage Mu protein gp47 [Function unknown]; Region: XkdT; COG3299 580332000721 Uncharacterized protein conserved in bacteria (DUF2313); Region: DUF2313; pfam10076 580332000722 Domain of unknown function (DUF4376); Region: DUF4376; pfam14301 580332000723 Mu-like prophage protein Com; Region: Mu-like_Com; cl11540 580332000724 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 580332000725 CHASE2 domain; Region: CHASE2; pfam05226 580332000726 Predicted transmembrane sensor domain [Signal transduction mechanisms]; Region: COG4252 580332000727 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 580332000728 cyclase homology domain; Region: CHD; cd07302 580332000729 nucleotidyl binding site; other site 580332000730 metal binding site [ion binding]; metal-binding site 580332000731 dimer interface [polypeptide binding]; other site 580332000732 NHL repeat; Region: NHL; pfam01436 580332000733 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 580332000734 Interdomain contacts; other site 580332000735 Cytokine receptor motif; other site 580332000736 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 580332000737 TPR motif; other site 580332000738 TPR repeat; Region: TPR_11; pfam13414 580332000739 binding surface 580332000740 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 580332000741 binding surface 580332000742 TPR motif; other site 580332000743 Tetratricopeptide repeat; Region: TPR_6; pfam13174 580332000744 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 580332000745 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 580332000746 tRNA; other site 580332000747 putative tRNA binding site [nucleotide binding]; other site 580332000748 putative NADP binding site [chemical binding]; other site 580332000749 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 580332000750 peptide chain release factor 1; Validated; Region: prfA; PRK00591 580332000751 This domain is found in peptide chain release factors; Region: PCRF; smart00937 580332000752 RF-1 domain; Region: RF-1; pfam00472 580332000753 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 580332000754 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 580332000755 S-adenosylmethionine binding site [chemical binding]; other site 580332000756 argininosuccinate lyase; Provisional; Region: PRK00855 580332000757 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 580332000758 active sites [active] 580332000759 tetramer interface [polypeptide binding]; other site 580332000760 Histidine kinase; Region: His_kinase; pfam06580 580332000761 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 580332000762 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 580332000763 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 580332000764 active site 580332000765 phosphorylation site [posttranslational modification] 580332000766 intermolecular recognition site; other site 580332000767 dimerization interface [polypeptide binding]; other site 580332000768 LytTr DNA-binding domain; Region: LytTR; smart00850 580332000769 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 580332000770 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 580332000771 active site 580332000772 phosphorylation site [posttranslational modification] 580332000773 intermolecular recognition site; other site 580332000774 dimerization interface [polypeptide binding]; other site 580332000775 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 580332000776 DNA binding site [nucleotide binding] 580332000777 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 580332000778 HAMP domain; Region: HAMP; pfam00672 580332000779 dimerization interface [polypeptide binding]; other site 580332000780 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 580332000781 dimer interface [polypeptide binding]; other site 580332000782 phosphorylation site [posttranslational modification] 580332000783 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 580332000784 ATP binding site [chemical binding]; other site 580332000785 Mg2+ binding site [ion binding]; other site 580332000786 G-X-G motif; other site 580332000787 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 580332000788 phosphoenolpyruvate carboxylase; Reviewed; Region: PRK00009 580332000789 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 580332000790 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 580332000791 domain interfaces; other site 580332000792 active site 580332000793 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 580332000794 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 580332000795 active site 580332000796 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 580332000797 heme biosynthesis-associated TPR protein; Region: TPR_hemY_coli; TIGR00540 580332000798 HemY protein N-terminus; Region: HemY_N; pfam07219 580332000799 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 580332000800 binding surface 580332000801 TPR motif; other site 580332000802 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 580332000803 catalytic motif [active] 580332000804 Catalytic residue [active] 580332000805 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 580332000806 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 580332000807 catalytic loop [active] 580332000808 iron binding site [ion binding]; other site 580332000809 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 580332000810 FAD binding pocket [chemical binding]; other site 580332000811 FAD binding motif [chemical binding]; other site 580332000812 phosphate binding motif [ion binding]; other site 580332000813 beta-alpha-beta structure motif; other site 580332000814 NAD binding pocket [chemical binding]; other site 580332000815 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 580332000816 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 580332000817 putative NAD(P) binding site [chemical binding]; other site 580332000818 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 580332000819 HD domain; Region: HD_4; pfam13328 580332000820 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 580332000821 synthetase active site [active] 580332000822 NTP binding site [chemical binding]; other site 580332000823 metal binding site [ion binding]; metal-binding site 580332000824 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 580332000825 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 580332000826 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 580332000827 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 580332000828 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 580332000829 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 580332000830 glutamine binding [chemical binding]; other site 580332000831 catalytic triad [active] 580332000832 anthranilate synthase component I; Provisional; Region: PRK13565 580332000833 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 580332000834 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 580332000835 phosphoglycolate phosphatase; Provisional; Region: PRK13222 580332000836 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 580332000837 motif II; other site 580332000838 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 580332000839 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 580332000840 substrate binding site [chemical binding]; other site 580332000841 hexamer interface [polypeptide binding]; other site 580332000842 metal binding site [ion binding]; metal-binding site 580332000843 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 580332000844 dimer interface [polypeptide binding]; other site 580332000845 phosphorylation site [posttranslational modification] 580332000846 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 580332000847 ATP binding site [chemical binding]; other site 580332000848 Mg2+ binding site [ion binding]; other site 580332000849 G-X-G motif; other site 580332000850 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 580332000851 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 580332000852 active site 580332000853 ATP binding site [chemical binding]; other site 580332000854 substrate binding site [chemical binding]; other site 580332000855 activation loop (A-loop); other site 580332000856 Response regulator receiver domain; Region: Response_reg; pfam00072 580332000857 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 580332000858 active site 580332000859 phosphorylation site [posttranslational modification] 580332000860 intermolecular recognition site; other site 580332000861 dimerization interface [polypeptide binding]; other site 580332000862 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 580332000863 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 580332000864 active site 580332000865 phosphorylation site [posttranslational modification] 580332000866 intermolecular recognition site; other site 580332000867 dimerization interface [polypeptide binding]; other site 580332000868 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 580332000869 Membrane-bound lytic murein transglycosylase [Cell envelope biogenesis, outer membrane]; Region: MltA; COG2821 580332000870 MltA specific insert domain; Region: MltA; smart00925 580332000871 3D domain; Region: 3D; pfam06725 580332000872 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 580332000873 active site residue [active] 580332000874 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 580332000875 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 580332000876 ligand binding site [chemical binding]; other site 580332000877 flexible hinge region; other site 580332000878 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 580332000879 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 580332000880 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 580332000881 dimerization domain [polypeptide binding]; other site 580332000882 dimer interface [polypeptide binding]; other site 580332000883 catalytic residues [active] 580332000884 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608 580332000885 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 580332000886 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 580332000887 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 580332000888 FMN binding site [chemical binding]; other site 580332000889 active site 580332000890 catalytic residues [active] 580332000891 substrate binding site [chemical binding]; other site 580332000892 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 580332000893 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 580332000894 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 580332000895 purine monophosphate binding site [chemical binding]; other site 580332000896 dimer interface [polypeptide binding]; other site 580332000897 putative catalytic residues [active] 580332000898 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 580332000899 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 580332000900 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 580332000901 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 580332000902 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 580332000903 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 580332000904 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 580332000905 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 580332000906 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 580332000907 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 580332000908 S-adenosylmethionine binding site [chemical binding]; other site 580332000909 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 580332000910 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332000911 Zn2+ binding site [ion binding]; other site 580332000912 Mg2+ binding site [ion binding]; other site 580332000913 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 580332000914 S-adenosylmethionine binding site [chemical binding]; other site 580332000915 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 580332000916 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 580332000917 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 580332000918 dimerization interface [polypeptide binding]; other site 580332000919 Rubrerythrin, ferritin-like diiron-binding domain; Region: Rubrerythrin; cd01041 580332000920 Ferritin-like domain; Region: Ferritin; pfam00210 580332000921 binuclear metal center [ion binding]; other site 580332000922 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 580332000923 Cysteine-rich domain; Region: CCG; pfam02754 580332000924 Protein of unknown function (DUF3501); Region: DUF3501; pfam12007 580332000925 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 580332000926 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 580332000927 dimerization interface [polypeptide binding]; other site 580332000928 DPS ferroxidase diiron center [ion binding]; other site 580332000929 ion pore; other site 580332000930 NnrS protein; Region: NnrS; pfam05940 580332000931 4-hydroxybenzoate octaprenyltransferase; Reviewed; Region: ubiA; PRK12848 580332000932 UbiA prenyltransferase family; Region: UbiA; pfam01040 580332000933 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 580332000934 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 580332000935 generic binding surface II; other site 580332000936 ssDNA binding site; other site 580332000937 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 580332000938 ATP binding site [chemical binding]; other site 580332000939 putative Mg++ binding site [ion binding]; other site 580332000940 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 580332000941 nucleotide binding region [chemical binding]; other site 580332000942 ATP-binding site [chemical binding]; other site 580332000943 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 580332000944 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 580332000945 active site 580332000946 ATP binding site [chemical binding]; other site 580332000947 substrate binding site [chemical binding]; other site 580332000948 activation loop (A-loop); other site 580332000949 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 580332000950 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 580332000951 ligand binding site [chemical binding]; other site 580332000952 flexible hinge region; other site 580332000953 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 580332000954 homotrimer interaction site [polypeptide binding]; other site 580332000955 putative active site [active] 580332000956 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 580332000957 Catalytic domain of Protein Kinases; Region: PKc; cd00180 580332000958 active site 580332000959 ATP binding site [chemical binding]; other site 580332000960 substrate binding site [chemical binding]; other site 580332000961 activation loop (A-loop); other site 580332000962 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 580332000963 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 580332000964 ligand binding site [chemical binding]; other site 580332000965 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 580332000966 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 580332000967 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 580332000968 putative active site [active] 580332000969 GtrA-like protein; Region: GtrA; pfam04138 580332000970 Predicted membrane protein [Function unknown]; Region: COG2246 580332000971 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 580332000972 Predicted neuraminidase (sialidase) [Carbohydrate transport and metabolism]; Region: COG4692 580332000973 BNR repeat-like domain; Region: BNR_2; pfam13088 580332000974 metabolite-proton symporter; Region: 2A0106; TIGR00883 580332000975 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 580332000976 putative substrate translocation pore; other site 580332000977 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 580332000978 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 580332000979 substrate binding pocket [chemical binding]; other site 580332000980 chain length determination region; other site 580332000981 substrate-Mg2+ binding site; other site 580332000982 catalytic residues [active] 580332000983 aspartate-rich region 1; other site 580332000984 active site lid residues [active] 580332000985 aspartate-rich region 2; other site 580332000986 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 580332000987 dimerization interface [polypeptide binding]; other site 580332000988 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 580332000989 PAS domain; Region: PAS_9; pfam13426 580332000990 putative active site [active] 580332000991 heme pocket [chemical binding]; other site 580332000992 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332000993 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332000994 metal binding site [ion binding]; metal-binding site 580332000995 active site 580332000996 I-site; other site 580332000997 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 580332000998 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 580332000999 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 580332001000 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 580332001001 S-adenosylmethionine binding site [chemical binding]; other site 580332001002 lipoprotein NlpD; Provisional; Region: nlpD; PRK10871 580332001003 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 580332001004 Peptidase family M23; Region: Peptidase_M23; pfam01551 580332001005 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 580332001006 FeS/SAM binding site; other site 580332001007 Na(+)- and Cl(-)-dependent choline cotransporter CHT and related proteins; solute-binding domain; Region: SLC5sbd_CHT; cd11474 580332001008 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 580332001009 Na binding site [ion binding]; other site 580332001010 putative glycosylation site [posttranslational modification]; other site 580332001011 putative glycosylation site [posttranslational modification]; other site 580332001012 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 580332001013 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 580332001014 active site 580332001015 phosphorylation site [posttranslational modification] 580332001016 intermolecular recognition site; other site 580332001017 dimerization interface [polypeptide binding]; other site 580332001018 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 580332001019 DNA binding site [nucleotide binding] 580332001020 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 580332001021 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 580332001022 PAS domain; Region: PAS; smart00091 580332001023 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 580332001024 dimer interface [polypeptide binding]; other site 580332001025 phosphorylation site [posttranslational modification] 580332001026 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 580332001027 ATP binding site [chemical binding]; other site 580332001028 Mg2+ binding site [ion binding]; other site 580332001029 G-X-G motif; other site 580332001030 Protein of unknown function (DUF3683); Region: DUF3683; pfam12447 580332001031 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 580332001032 FAD binding domain; Region: FAD_binding_4; pfam01565 580332001033 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 580332001034 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 580332001035 Cysteine-rich domain; Region: CCG; pfam02754 580332001036 Domain of unknown function (DUF3400); Region: DUF3400; pfam11880 580332001037 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 580332001038 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 580332001039 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 580332001040 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 580332001041 putative ATP binding site [chemical binding]; other site 580332001042 putative substrate interface [chemical binding]; other site 580332001043 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 580332001044 active site 580332001045 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR6; cd08272 580332001046 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 580332001047 putative NAD(P) binding site [chemical binding]; other site 580332001048 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 580332001049 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 580332001050 Tetramer interface [polypeptide binding]; other site 580332001051 active site 580332001052 FMN-binding site [chemical binding]; other site 580332001053 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cl00195 580332001054 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 580332001055 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 580332001056 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 580332001057 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 580332001058 Putative Zn-dependent protease [General function prediction only]; Region: COG4784 580332001059 Peptidase family M48; Region: Peptidase_M48; pfam01435 580332001060 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00019 580332001061 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 580332001062 homooctamer interface [polypeptide binding]; other site 580332001063 active site 580332001064 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 580332001065 UGMP family protein; Validated; Region: PRK09604 580332001066 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 580332001067 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 580332001068 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 580332001069 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 580332001070 FeS/SAM binding site; other site 580332001071 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK09185 580332001072 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 580332001073 dimer interface [polypeptide binding]; other site 580332001074 active site 580332001075 Beta-ketoacyl synthase, N-terminal domain; Region: Ketoacyl-synt_2; pfam13723 580332001076 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 580332001077 active site 2 [active] 580332001078 active site 1 [active] 580332001079 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 580332001080 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332001081 NAD(P) binding site [chemical binding]; other site 580332001082 active site 580332001083 Phosphopantetheine attachment site; Region: PP-binding; cl09936 580332001084 Phosphopantetheine attachment site; Region: PP-binding; cl09936 580332001085 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK09185 580332001086 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 580332001087 active site 580332001088 benzoate 1,2-dioxygenase, large subunit; Region: benzo_1_2_benA; TIGR03229 580332001089 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK06816 580332001090 "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...; Region: init_cond_enzymes; cd00827 580332001091 dimer interface [polypeptide binding]; other site 580332001092 active site 580332001093 A predicted NlpC/p60-like peptidase; Region: BtrH; pfam14399 580332001094 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 580332001095 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 580332001096 S-adenosylmethionine binding site [chemical binding]; other site 580332001097 Predicted membrane protein [Function unknown]; Region: COG4648 580332001098 O-succinylbenzoic acid--CoA ligase; Provisional; Region: PRK07824 580332001099 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 580332001100 acyl-activating enzyme (AAE) consensus motif; other site 580332001101 AMP binding site [chemical binding]; other site 580332001102 active site 580332001103 CoA binding site [chemical binding]; other site 580332001104 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 580332001105 active site 2 [active] 580332001106 active site 1 [active] 580332001107 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 580332001108 putative acyl-acceptor binding pocket; other site 580332001109 Predicted exporter [General function prediction only]; Region: COG4258 580332001110 SmpA / OmlA family; Region: SmpA_OmlA; cl17115 580332001111 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 580332001112 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 580332001113 homotrimer interaction site [polypeptide binding]; other site 580332001114 putative active site [active] 580332001115 Outer membrane protein V [Cell envelope biogenesis, outer membrane]; Region: OmpV; COG3713 580332001116 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 580332001117 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 580332001118 putative acyl-acceptor binding pocket; other site 580332001119 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 580332001120 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 580332001121 Ligand binding site; other site 580332001122 Putative Catalytic site; other site 580332001123 DXD motif; other site 580332001124 Fe-S oxidoreductase [Energy production and conversion]; Region: COG1032 580332001125 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 580332001126 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 580332001127 FeS/SAM binding site; other site 580332001128 integron integrase; Region: integrase_gron; TIGR02249 580332001129 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 580332001130 Int/Topo IB signature motif; other site 580332001131 Protein of unknown function (DUF497); Region: DUF497; pfam04365 580332001132 Domain of unknown function (DUF4415); Region: DUF4415; pfam14384 580332001133 Putative addiction module component; Region: Unstab_antitox; cl09921 580332001134 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 580332001135 active site 580332001136 Anthranilate/para-aminobenzoate synthases component I [Amino acid transport and metabolism / Coenzyme metabolism]; Region: TrpE; COG0147 580332001137 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 580332001138 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 580332001139 Uncharacterized conserved protein [Function unknown]; Region: COG1656 580332001140 Protein of unknown function DUF82; Region: DUF82; pfam01927 580332001141 Protein of unknown function (DUF2905); Region: DUF2905; pfam11146 580332001142 carbonyl reductase sniffer-like, classical (c) SDRs; Region: carb_red_sniffer_like_SDR_c; cd05325 580332001143 C factor cell-cell signaling protein; Provisional; Region: PRK09009 580332001144 NADP binding site [chemical binding]; other site 580332001145 homodimer interface [polypeptide binding]; other site 580332001146 active site 580332001147 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 580332001148 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 580332001149 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 580332001150 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 580332001151 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 580332001152 putative active site [active] 580332001153 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 580332001154 Predicted 6-phosphogluconate dehydrogenase [Carbohydrate transport and metabolism]; Region: Gnd; COG1023 580332001155 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 580332001156 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 580332001157 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 580332001158 Glycoside hydrolase family 15, N-terminal domain; Region: GH15_N; cd07430 580332001159 Domain interface; other site 580332001160 glucan 1,4-alpha-glucosidase; Region: glucan_glucosid; TIGR01535 580332001161 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 580332001162 Predicted thioesterase [General function prediction only]; Region: COG5496 580332001163 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 580332001164 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332001165 Zn2+ binding site [ion binding]; other site 580332001166 Mg2+ binding site [ion binding]; other site 580332001167 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 580332001168 synthetase active site [active] 580332001169 NTP binding site [chemical binding]; other site 580332001170 metal binding site [ion binding]; metal-binding site 580332001171 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 580332001172 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 580332001173 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 580332001174 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 580332001175 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 580332001176 catalytic site [active] 580332001177 G-X2-G-X-G-K; other site 580332001178 hypothetical protein; Provisional; Region: PRK11820 580332001179 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 580332001180 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 580332001181 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 580332001182 active site 580332001183 ribonuclease PH; Reviewed; Region: rph; PRK00173 580332001184 Ribonuclease PH; Region: RNase_PH_bact; cd11362 580332001185 hexamer interface [polypeptide binding]; other site 580332001186 active site 580332001187 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 580332001188 active site 580332001189 dimerization interface [polypeptide binding]; other site 580332001190 coproporphyrinogen III oxidase; Provisional; Region: PRK08898 580332001191 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 580332001192 FeS/SAM binding site; other site 580332001193 HemN C-terminal domain; Region: HemN_C; pfam06969 580332001194 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 580332001195 S-adenosylmethionine binding site [chemical binding]; other site 580332001196 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 580332001197 ThiS interaction site; other site 580332001198 putative active site [active] 580332001199 tetramer interface [polypeptide binding]; other site 580332001200 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 580332001201 thiS-thiF/thiG interaction site; other site 580332001202 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 580332001203 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 580332001204 Low-spin heme binding site [chemical binding]; other site 580332001205 Putative water exit pathway; other site 580332001206 Binuclear center (active site) [active] 580332001207 Putative proton exit pathway; other site 580332001208 cbb3-type cytochrome c oxidase subunit II; Provisional; Region: PRK14487 580332001209 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 580332001210 Cbb3-type cytochrome oxidase component FixQ; Region: FixQ; pfam05545 580332001211 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 580332001212 Cytochrome c; Region: Cytochrom_C; pfam00034 580332001213 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 580332001214 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 580332001215 4Fe-4S binding domain; Region: Fer4_5; pfam12801 580332001216 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 580332001217 FixH; Region: FixH; pfam05751 580332001218 Predicted integral membrane protein linked to a cation pump [Inorganic ion transport and metabolism]; Region: COG5456 580332001219 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 580332001220 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 580332001221 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 580332001222 metal-binding site [ion binding] 580332001223 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 580332001224 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 580332001225 motif II; other site 580332001226 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; pfam03597 580332001227 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 580332001228 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 580332001229 ligand binding site [chemical binding]; other site 580332001230 flexible hinge region; other site 580332001231 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 580332001232 putative switch regulator; other site 580332001233 non-specific DNA interactions [nucleotide binding]; other site 580332001234 DNA binding site [nucleotide binding] 580332001235 sequence specific DNA binding site [nucleotide binding]; other site 580332001236 putative cAMP binding site [chemical binding]; other site 580332001237 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 580332001238 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 580332001239 FeS/SAM binding site; other site 580332001240 HemN C-terminal domain; Region: HemN_C; pfam06969 580332001241 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 580332001242 FMN binding site [chemical binding]; other site 580332001243 substrate binding site [chemical binding]; other site 580332001244 putative catalytic residue [active] 580332001245 AsmA family; Region: AsmA; pfam05170 580332001246 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 580332001247 A/G-specific adenine glycosylase; Region: mutY; TIGR01084 580332001248 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 580332001249 minor groove reading motif; other site 580332001250 helix-hairpin-helix signature motif; other site 580332001251 substrate binding pocket [chemical binding]; other site 580332001252 active site 580332001253 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 580332001254 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 580332001255 DNA binding and oxoG recognition site [nucleotide binding] 580332001256 aromatic acid decarboxylase; Validated; Region: PRK05920 580332001257 Flavoprotein; Region: Flavoprotein; pfam02441 580332001258 Heptaprenyl diphosphate synthase component I; Region: Hpre_diP_synt_I; pfam07456 580332001259 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 580332001260 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 580332001261 HPr kinase/phosphorylase; Provisional; Region: PRK05428 580332001262 HPr Serine kinase N terminus; Region: Hpr_kinase_N; pfam02603 580332001263 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 580332001264 Hpr binding site; other site 580332001265 active site 580332001266 homohexamer subunit interaction site [polypeptide binding]; other site 580332001267 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 580332001268 active site 580332001269 phosphorylation site [posttranslational modification] 580332001270 RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal...; Region: RaiA; cd00552 580332001271 30S subunit binding site; other site 580332001272 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 580332001273 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 580332001274 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 580332001275 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 580332001276 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 580332001277 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 580332001278 Walker A/P-loop; other site 580332001279 ATP binding site [chemical binding]; other site 580332001280 Q-loop/lid; other site 580332001281 ABC transporter signature motif; other site 580332001282 Walker B; other site 580332001283 D-loop; other site 580332001284 H-loop/switch region; other site 580332001285 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 580332001286 OstA-like protein; Region: OstA; pfam03968 580332001287 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 580332001288 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 580332001289 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 580332001290 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 580332001291 active site 580332001292 motif I; other site 580332001293 motif II; other site 580332001294 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 580332001295 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 580332001296 putative active site [active] 580332001297 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 580332001298 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 580332001299 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 580332001300 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 580332001301 TrkA-N domain; Region: TrkA_N; pfam02254 580332001302 TrkA-C domain; Region: TrkA_C; pfam02080 580332001303 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 580332001304 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 580332001305 ATP binding site [chemical binding]; other site 580332001306 Mg2+ binding site [ion binding]; other site 580332001307 G-X-G motif; other site 580332001308 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 580332001309 ATP binding site [chemical binding]; other site 580332001310 putative Mg++ binding site [ion binding]; other site 580332001311 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 580332001312 putative active site [active] 580332001313 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 580332001314 nucleotide binding region [chemical binding]; other site 580332001315 ATP-binding site [chemical binding]; other site 580332001316 Helicase associated domain (HA2); Region: HA2; pfam04408 580332001317 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 580332001318 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 580332001319 malate:quinone oxidoreductase; Validated; Region: PRK05257 580332001320 malate:quinone-oxidoreductase; Region: mal_quin_oxido; TIGR01320 580332001321 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 580332001322 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 580332001323 dimer interface [polypeptide binding]; other site 580332001324 active site 580332001325 acyl carrier protein; Provisional; Region: acpP; PRK00982 580332001326 Esterase/lipase [General function prediction only]; Region: COG1647 580332001327 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 580332001328 Malic enzyme, N-terminal domain; Region: malic; pfam00390 580332001329 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 580332001330 putative NAD(P) binding site [chemical binding]; other site 580332001331 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 580332001332 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 580332001333 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 580332001334 active site 580332001335 nucleophile elbow; other site 580332001336 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 580332001337 Biotin operon repressor [Transcription]; Region: BirA; COG1654 580332001338 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 580332001339 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 580332001340 Type III pantothenate kinase; Region: Pan_kinase; cl17198 580332001341 Sporulation related domain; Region: SPOR; pfam05036 580332001342 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 580332001343 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 580332001344 TRAM domain; Region: TRAM; pfam01938 580332001345 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 580332001346 PhoH-like protein; Region: PhoH; pfam02562 580332001347 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 580332001348 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 580332001349 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 580332001350 Transporter associated domain; Region: CorC_HlyC; smart01091 580332001351 lysophospholipid transporter LplT; Provisional; Region: PRK11195 580332001352 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 580332001353 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 580332001354 RNA binding surface [nucleotide binding]; other site 580332001355 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 580332001356 active site 580332001357 MarC family integral membrane protein; Region: MarC; cl00919 580332001358 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 580332001359 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 580332001360 ligand binding site [chemical binding]; other site 580332001361 flexible hinge region; other site 580332001362 apolipoprotein N-acyltransferase; Region: lnt; TIGR00546 580332001363 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 580332001364 putative active site [active] 580332001365 catalytic triad [active] 580332001366 putative dimer interface [polypeptide binding]; other site 580332001367 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 580332001368 GIY-YIG motif/motif A; other site 580332001369 putative active site [active] 580332001370 putative metal binding site [ion binding]; other site 580332001371 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 580332001372 dimer interface [polypeptide binding]; other site 580332001373 motif 1; other site 580332001374 active site 580332001375 motif 2; other site 580332001376 motif 3; other site 580332001377 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 580332001378 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 580332001379 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 580332001380 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 580332001381 active site 580332001382 motif I; other site 580332001383 motif II; other site 580332001384 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 580332001385 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 580332001386 putative acyl-acceptor binding pocket; other site 580332001387 Protein of unknown function DUF45; Region: DUF45; pfam01863 580332001388 iron donor protein CyaY; Region: FeS_CyaY; TIGR03421 580332001389 putative iron binding site [ion binding]; other site 580332001390 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...; Region: Frataxin; cl00238 580332001391 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 580332001392 catalytic motif [active] 580332001393 Catalytic residue [active] 580332001394 diaminopimelate decarboxylase; Region: lysA; TIGR01048 580332001395 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 580332001396 active site 580332001397 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 580332001398 substrate binding site [chemical binding]; other site 580332001399 catalytic residues [active] 580332001400 dimer interface [polypeptide binding]; other site 580332001401 HDOD domain; Region: HDOD; pfam08668 580332001402 CRISPR/Cas system-associated protein Cas3'' Region: Cas3''_I; cl17503 580332001403 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 580332001404 PAS fold; Region: PAS_3; pfam08447 580332001405 putative active site [active] 580332001406 heme pocket [chemical binding]; other site 580332001407 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332001408 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332001409 metal binding site [ion binding]; metal-binding site 580332001410 active site 580332001411 I-site; other site 580332001412 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 580332001413 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 580332001414 MgtE intracellular N domain; Region: MgtE_N; smart00924 580332001415 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 580332001416 Divalent cation transporter; Region: MgtE; pfam01769 580332001417 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 580332001418 Escherichia coli Mg2+ transporter CorA_like subgroup; Region: EcCorA-like_1; cd12835 580332001419 Cl binding site [ion binding]; other site 580332001420 oligomer interface [polypeptide binding]; other site 580332001421 Transglycosylase; Region: Transgly; cl17702 580332001422 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 580332001423 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 580332001424 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 580332001425 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 580332001426 shikimate binding site; other site 580332001427 NAD(P) binding site [chemical binding]; other site 580332001428 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 580332001429 dimerization interface [polypeptide binding]; other site 580332001430 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 580332001431 ATP binding site [chemical binding]; other site 580332001432 Mg2+ binding site [ion binding]; other site 580332001433 G-X-G motif; other site 580332001434 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 580332001435 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 580332001436 active site 580332001437 phosphorylation site [posttranslational modification] 580332001438 intermolecular recognition site; other site 580332001439 dimerization interface [polypeptide binding]; other site 580332001440 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 580332001441 DNA binding site [nucleotide binding] 580332001442 LTXXQ motif family protein; Region: LTXXQ; pfam07813 580332001443 Type II secretion system (T2SS), protein N; Region: T2SN; pfam01203 580332001444 Type II secretion system (T2SS), protein M; Region: T2SM; pfam04612 580332001445 Type II secretion system (T2SS), protein L; Region: T2SL; pfam05134 580332001446 type II secretion system protein L; Region: typeII_sec_gspL; TIGR01709 580332001447 GspL periplasmic domain; Region: GspL_C; cl14909 580332001448 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 580332001449 type II secretion system protein J; Region: gspJ; TIGR01711 580332001450 Type II secretion system (T2SS), protein J; Region: T2SJ; pfam11612 580332001451 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 580332001452 type II secretion system protein H; Region: typeII_sec_gspH; TIGR01708 580332001453 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 580332001454 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 580332001455 type II secretion system protein F; Region: GspF; TIGR02120 580332001456 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 580332001457 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 580332001458 type II secretion system protein E; Region: type_II_gspE; TIGR02533 580332001459 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 580332001460 Walker A motif; other site 580332001461 ATP binding site [chemical binding]; other site 580332001462 Walker B motif; other site 580332001463 type II secretion system protein D; Region: type_II_gspD; TIGR02517 580332001464 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 580332001465 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 580332001466 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 580332001467 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 580332001468 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 580332001469 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 580332001470 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 580332001471 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 580332001472 putative ligand binding site [chemical binding]; other site 580332001473 NHL repeat; Region: NHL; pfam01436 580332001474 NHL repeat; Region: NHL; pfam01436 580332001475 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 580332001476 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 580332001477 This domain is the catalytic domain of ribonuclease II; Region: RNB; smart00955 580332001478 RNB domain; Region: RNB; pfam00773 580332001479 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cd00051 580332001480 EF-hand domain pair; Region: EF_hand_5; pfam13499 580332001481 Ca2+ binding site [ion binding]; other site 580332001482 EF-hand domain pair; Region: EF_hand_5; pfam13499 580332001483 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; cl17302 580332001484 pseudo EF-hand loop; other site 580332001485 peptide binding pocket; other site 580332001486 Ca2+ binding site [ion binding]; other site 580332001487 Cytochrome c; Region: Cytochrom_C; cl11414 580332001488 hypothetical protein; Validated; Region: PRK00110 580332001489 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD...; Region: RuvC_resolvase; cd00529 580332001490 active site 580332001491 putative DNA-binding cleft [nucleotide binding]; other site 580332001492 dimer interface [polypeptide binding]; other site 580332001493 1,4-dihydroxy-2-naphthoate octaprenyltransferase [Coenzyme metabolism]; Region: MenA; cl17224 580332001494 UbiA prenyltransferase family; Region: UbiA; pfam01040 580332001495 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 580332001496 RuvA N terminal domain; Region: RuvA_N; pfam01330 580332001497 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 580332001498 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 580332001499 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 580332001500 Walker A motif; other site 580332001501 ATP binding site [chemical binding]; other site 580332001502 Walker B motif; other site 580332001503 arginine finger; other site 580332001504 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 580332001505 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 580332001506 active site 580332001507 TolQ protein; Region: tolQ; TIGR02796 580332001508 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 580332001509 TolR protein; Region: tolR; TIGR02801 580332001510 TonB C terminal; Region: TonB_2; pfam13103 580332001511 TolA protein; Region: tolA_full; TIGR02794 580332001512 translocation protein TolB; Provisional; Region: tolB; PRK02889 580332001513 TolB amino-terminal domain; Region: TolB_N; pfam04052 580332001514 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 580332001515 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 580332001516 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 580332001517 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 580332001518 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 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 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1729 580332001522 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, gammaproteobacterial type; Region: rSAM_QueE_gams; TIGR04349 580332001523 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 580332001524 FeS/SAM binding site; other site 580332001525 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 580332001526 Ligand Binding Site [chemical binding]; other site 580332001527 4Fe-4S binding domain; Region: Fer4_6; pfam12837 580332001528 Ferredoxin [Energy production and conversion]; Region: COG1146 580332001529 4Fe-4S binding domain; Region: Fer4; pfam00037 580332001530 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 580332001531 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 580332001532 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 580332001533 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 580332001534 CoA-ligase; Region: Ligase_CoA; pfam00549 580332001535 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 580332001536 CoA binding domain; Region: CoA_binding; smart00881 580332001537 CoA-ligase; Region: Ligase_CoA; pfam00549 580332001538 integral membrane protein, YjbE family; Region: R_switched_YjbE; TIGR03717 580332001539 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 580332001540 Ligand Binding Site [chemical binding]; other site 580332001541 Predicted transmembrane sensor domain [Signal transduction mechanisms]; Region: COG4252 580332001542 CHASE2 domain; Region: CHASE2; pfam05226 580332001543 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 580332001544 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 580332001545 active site 580332001546 ATP binding site [chemical binding]; other site 580332001547 substrate binding site [chemical binding]; other site 580332001548 activation loop (A-loop); other site 580332001549 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 580332001550 active site 580332001551 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 580332001552 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 580332001553 phosphopeptide binding site; other site 580332001554 CHASE2 domain; Region: CHASE2; pfam05226 580332001555 Adenylyl- / guanylyl cyclase, catalytic domain; Region: CYCc; smart00044 580332001556 cyclase homology domain; Region: CHD; cd07302 580332001557 nucleotidyl binding site; other site 580332001558 metal binding site [ion binding]; metal-binding site 580332001559 dimer interface [polypeptide binding]; other site 580332001560 Metal-dependent hydrolases of the beta-lactamase superfamily III [General function prediction only]; Region: ElaC; COG1234 580332001561 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 580332001562 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 580332001563 ligand binding site [chemical binding]; other site 580332001564 flexible hinge region; other site 580332001565 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 580332001566 active site residue [active] 580332001567 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 580332001568 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 580332001569 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 580332001570 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 580332001571 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 580332001572 Walker A motif; other site 580332001573 ATP binding site [chemical binding]; other site 580332001574 Walker B motif; other site 580332001575 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 580332001576 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 580332001577 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332001578 Zn2+ binding site [ion binding]; other site 580332001579 Mg2+ binding site [ion binding]; other site 580332001580 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332001581 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 580332001582 Pilin (bacterial filament); Region: Pilin; pfam00114 580332001583 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 580332001584 binding surface 580332001585 TPR repeat; Region: TPR_11; pfam13414 580332001586 TPR motif; other site 580332001587 transcriptional activator FlhD; Provisional; Region: PRK02909 580332001588 transcriptional activator FlhC; Provisional; Region: PRK12722 580332001589 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 580332001590 flagellar motor protein MotA; Validated; Region: PRK09110 580332001591 flagellar motor protein MotB; Validated; Region: motB; PRK09041 580332001592 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 580332001593 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 580332001594 ligand binding site [chemical binding]; other site 580332001595 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 580332001596 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 580332001597 dimerization interface [polypeptide binding]; other site 580332001598 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332001599 dimer interface [polypeptide binding]; other site 580332001600 putative CheW interface [polypeptide binding]; other site 580332001601 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 580332001602 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 580332001603 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 580332001604 dimerization interface [polypeptide binding]; other site 580332001605 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332001606 dimer interface [polypeptide binding]; other site 580332001607 putative CheW interface [polypeptide binding]; other site 580332001608 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 580332001609 PAS domain; Region: PAS_9; pfam13426 580332001610 putative active site [active] 580332001611 heme pocket [chemical binding]; other site 580332001612 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 580332001613 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332001614 dimer interface [polypeptide binding]; other site 580332001615 putative CheW interface [polypeptide binding]; other site 580332001616 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 580332001617 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 580332001618 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 580332001619 active site 580332001620 phosphorylation site [posttranslational modification] 580332001621 intermolecular recognition site; other site 580332001622 dimerization interface [polypeptide binding]; other site 580332001623 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 580332001624 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 580332001625 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 580332001626 active site 580332001627 phosphorylation site [posttranslational modification] 580332001628 intermolecular recognition site; other site 580332001629 dimerization interface [polypeptide binding]; other site 580332001630 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 580332001631 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 580332001632 active site 580332001633 phosphorylation site [posttranslational modification] 580332001634 intermolecular recognition site; other site 580332001635 dimerization interface [polypeptide binding]; other site 580332001636 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 580332001637 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 580332001638 putative binding surface; other site 580332001639 active site 580332001640 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 580332001641 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 580332001642 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 580332001643 ATP binding site [chemical binding]; other site 580332001644 Mg2+ binding site [ion binding]; other site 580332001645 G-X-G motif; other site 580332001646 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 580332001647 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332001648 dimer interface [polypeptide binding]; other site 580332001649 putative CheW interface [polypeptide binding]; other site 580332001650 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 580332001651 chemotaxis methyltransferase CheR; Provisional; Region: PRK10611 580332001652 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 580332001653 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 580332001654 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 580332001655 CheB methylesterase; Region: CheB_methylest; pfam01339 580332001656 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 580332001657 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 580332001658 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 580332001659 FHIPEP family; Region: FHIPEP; pfam00771 580332001660 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK06995 580332001661 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 580332001662 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 580332001663 This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains...; Region: CpaE_like; cd03111 580332001664 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 580332001665 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 580332001666 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 580332001667 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 580332001668 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 580332001669 DNA binding residues [nucleotide binding] 580332001670 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 580332001671 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 580332001672 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 580332001673 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 580332001674 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 580332001675 ligand binding site [chemical binding]; other site 580332001676 FlgN protein; Region: FlgN; pfam05130 580332001677 flagellar biosynthesis anti-sigma factor FlgM; Region: FlgM_jcvi; TIGR03824 580332001678 flagellar basal body P-ring biosynthesis protein FlgA; Reviewed; Region: flgA; PRK07018 580332001679 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 580332001680 Domains similar to fish antifreeze type III protein; Region: SAF; cl00555 580332001681 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 580332001682 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 580332001683 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 580332001684 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 580332001685 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 580332001686 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK06655 580332001687 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 580332001688 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 580332001689 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 580332001690 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 580332001691 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 580332001692 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 580332001693 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 580332001694 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 580332001695 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 580332001696 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 580332001697 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 580332001698 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 580332001699 Flagellar basal body L-ring protein [Cell motility and secretion]; Region: FlgH; COG2063 580332001700 Flagellar L-ring protein; Region: FlgH; pfam02107 580332001701 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 580332001702 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 580332001703 flagellar rod assembly protein/muramidase FlgJ; Validated; Region: flgJ; PRK05684 580332001704 Rod binding protein [Cell envelope biogenesis, outer membrane / Cell motility and secretion / Posttranslational modification, protein turnover, chaperones]; Region: COG3951 580332001705 Muramidase (flagellum-specific) [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlgJ; COG1705 580332001706 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 580332001707 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 580332001708 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 580332001709 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 580332001710 TPR repeat; Region: TPR_11; pfam13414 580332001711 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 580332001712 binding surface 580332001713 TPR motif; other site 580332001714 TPR repeat; Region: TPR_11; pfam13414 580332001715 TPR repeat; Region: TPR_11; pfam13414 580332001716 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 580332001717 binding surface 580332001718 TPR motif; other site 580332001719 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 580332001720 ABC-2 type transporter; Region: ABC2_membrane; cl17235 580332001721 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 580332001722 ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system; Region: PQQ_ABC_ATP; TIGR03864 580332001723 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 580332001724 Walker A/P-loop; other site 580332001725 ATP binding site [chemical binding]; other site 580332001726 Q-loop/lid; other site 580332001727 ABC transporter signature motif; other site 580332001728 Walker B; other site 580332001729 D-loop; other site 580332001730 H-loop/switch region; other site 580332001731 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4320 580332001732 Uncharacterized protein conserved in bacteria (DUF2252); Region: DUF2252; pfam10009 580332001733 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 580332001734 TPR motif; other site 580332001735 binding surface 580332001736 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 580332001737 binding surface 580332001738 TPR motif; other site 580332001739 Predicted methyltransferase (contains TPR repeat) [General function prediction only]; Region: COG4976 580332001740 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 580332001741 S-adenosylmethionine binding site [chemical binding]; other site 580332001742 SCP-2 sterol transfer family; Region: SCP2; cl01225 580332001743 putative protease; Provisional; Region: PRK15447 580332001744 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 580332001745 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 580332001746 Peptidase family U32; Region: Peptidase_U32; pfam01136 580332001747 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 580332001748 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 580332001749 active site 580332001750 phosphorylation site [posttranslational modification] 580332001751 intermolecular recognition site; other site 580332001752 dimerization interface [polypeptide binding]; other site 580332001753 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 580332001754 Response regulator receiver domain; Region: Response_reg; pfam00072 580332001755 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 580332001756 active site 580332001757 phosphorylation site [posttranslational modification] 580332001758 intermolecular recognition site; other site 580332001759 dimerization interface [polypeptide binding]; other site 580332001760 PAS fold; Region: PAS_4; pfam08448 580332001761 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 580332001762 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 580332001763 dimer interface [polypeptide binding]; other site 580332001764 phosphorylation site [posttranslational modification] 580332001765 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 580332001766 ATP binding site [chemical binding]; other site 580332001767 Mg2+ binding site [ion binding]; other site 580332001768 G-X-G motif; other site 580332001769 Response regulator receiver domain; Region: Response_reg; pfam00072 580332001770 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 580332001771 active site 580332001772 phosphorylation site [posttranslational modification] 580332001773 intermolecular recognition site; other site 580332001774 dimerization interface [polypeptide binding]; other site 580332001775 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 580332001776 putative binding surface; other site 580332001777 active site 580332001778 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 580332001779 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 580332001780 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 580332001781 Flagellar biosynthesis protein, FliO; Region: FliO; pfam04347 580332001782 flagellar motor switch protein; Validated; Region: fliN; PRK05698 580332001783 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 580332001784 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 580332001785 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 580332001786 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 580332001787 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 580332001788 flagellar export protein FliJ; Region: flagell_FliJ; TIGR02473 580332001789 flagellar biosynthesis chaperone; Validated; Region: fliJ; PRK05689 580332001790 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 580332001791 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 580332001792 Walker A motif/ATP binding site; other site 580332001793 Walker B motif; other site 580332001794 flagellar assembly protein H; Validated; Region: fliH; PRK05687 580332001795 Flagellar assembly protein FliH; Region: FliH; pfam02108 580332001796 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 580332001797 FliG C-terminal domain; Region: FliG_C; pfam01706 580332001798 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 580332001799 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; pfam01514 580332001800 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 580332001801 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK00253 580332001802 Uncharacterized protein conserved in bacteria (DUF2264); Region: DUF2264; cl01752 580332001803 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 580332001804 binding surface 580332001805 TPR motif; other site 580332001806 TPR repeat; Region: TPR_11; pfam13414 580332001807 TPR repeat; Region: TPR_11; pfam13414 580332001808 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 580332001809 binding surface 580332001810 TPR motif; other site 580332001811 TPR repeat; Region: TPR_11; pfam13414 580332001812 TPR repeat; Region: TPR_11; pfam13414 580332001813 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 580332001814 binding surface 580332001815 TPR motif; other site 580332001816 TPR repeat; Region: TPR_11; pfam13414 580332001817 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 580332001818 binding surface 580332001819 TPR repeat; Region: TPR_11; pfam13414 580332001820 TPR motif; other site 580332001821 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 580332001822 binding surface 580332001823 TPR motif; other site 580332001824 TPR repeat; Region: TPR_11; pfam13414 580332001825 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 580332001826 binding surface 580332001827 TPR motif; other site 580332001828 Predicted methyltransferase (contains TPR repeat) [General function prediction only]; Region: COG4976 580332001829 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 580332001830 S-adenosylmethionine binding site [chemical binding]; other site 580332001831 Methyltransferase domain; Region: Methyltransf_23; pfam13489 580332001832 Methyltransferase domain; Region: Methyltransf_11; pfam08241 580332001833 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 580332001834 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 580332001835 inhibitor-cofactor binding pocket; inhibition site 580332001836 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332001837 catalytic residue [active] 580332001838 WbqC-like protein family; Region: WbqC; pfam08889 580332001839 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 580332001840 S-adenosylmethionine binding site [chemical binding]; other site 580332001841 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 580332001842 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 580332001843 putative trimer interface [polypeptide binding]; other site 580332001844 putative CoA binding site [chemical binding]; other site 580332001845 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 580332001846 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 580332001847 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; cl17312 580332001848 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 580332001849 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 580332001850 active site 580332001851 Glycosyltransferase like family; Region: Glyco_tranf_2_5; pfam13712 580332001852 TPR repeat; Region: TPR_11; pfam13414 580332001853 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 580332001854 binding surface 580332001855 TPR motif; other site 580332001856 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 580332001857 binding surface 580332001858 TPR motif; other site 580332001859 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 580332001860 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 580332001861 binding surface 580332001862 TPR motif; other site 580332001863 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 580332001864 binding surface 580332001865 TPR motif; other site 580332001866 Flagellar regulator YcgR; Region: YcgR; pfam07317 580332001867 PilZ domain; Region: PilZ; pfam07238 580332001868 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 580332001869 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 580332001870 Flagellar protein FliT; Region: FliT; pfam05400 580332001871 flagellar protein FliS; Validated; Region: fliS; PRK05685 580332001872 flagellar capping protein; Reviewed; Region: fliD; PRK08032 580332001873 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 580332001874 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 580332001875 FlaG protein; Region: FlaG; pfam03646 580332001876 flagellin; Provisional; Region: PRK12802 580332001877 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 580332001878 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 580332001879 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332001880 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332001881 metal binding site [ion binding]; metal-binding site 580332001882 active site 580332001883 I-site; other site 580332001884 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 580332001885 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 580332001886 active site 580332001887 phosphorylation site [posttranslational modification] 580332001888 intermolecular recognition site; other site 580332001889 dimerization interface [polypeptide binding]; other site 580332001890 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 580332001891 DNA binding residues [nucleotide binding] 580332001892 dimerization interface [polypeptide binding]; other site 580332001893 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 580332001894 heme pocket [chemical binding]; other site 580332001895 putative active site [active] 580332001896 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 580332001897 Histidine kinase; Region: HisKA_3; pfam07730 580332001898 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 580332001899 ATP binding site [chemical binding]; other site 580332001900 Mg2+ binding site [ion binding]; other site 580332001901 G-X-G motif; other site 580332001902 histidinol-phosphate aminotransferase; Provisional; Region: PRK04870 580332001903 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 580332001904 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332001905 homodimer interface [polypeptide binding]; other site 580332001906 catalytic residue [active] 580332001907 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 580332001908 putative active site pocket [active] 580332001909 4-fold oligomerization interface [polypeptide binding]; other site 580332001910 metal binding residues [ion binding]; metal-binding site 580332001911 3-fold/trimer interface [polypeptide binding]; other site 580332001912 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 580332001913 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 580332001914 putative active site [active] 580332001915 oxyanion strand; other site 580332001916 catalytic triad [active] 580332001917 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 580332001918 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 580332001919 catalytic residues [active] 580332001920 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 580332001921 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 580332001922 substrate binding site [chemical binding]; other site 580332001923 glutamase interaction surface [polypeptide binding]; other site 580332001924 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 580332001925 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase (HisIE or PRATP-PH) and its homologs; Region: NTP-PPase_HisIE_like; cd11534 580332001926 metal binding site [ion binding]; metal-binding site 580332001927 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 580332001928 nucleotide binding site/active site [active] 580332001929 HIT family signature motif; other site 580332001930 catalytic residue [active] 580332001931 twin arginine translocase protein A; Provisional; Region: tatA; PRK02958 580332001932 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 580332001933 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 580332001934 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 580332001935 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 580332001936 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 580332001937 protein binding site [polypeptide binding]; other site 580332001938 Uncharacterized conserved protein [Function unknown]; Region: COG0327 580332001939 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 580332001940 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 580332001941 MgtC family; Region: MgtC; pfam02308 580332001942 Predicted transcriptional regulators [Transcription]; Region: COG1510 580332001943 MarR family; Region: MarR_2; pfam12802 580332001944 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cd08168 580332001945 heme-binding residues [chemical binding]; other site 580332001946 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 580332001947 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 580332001948 molybdopterin cofactor binding site; other site 580332001949 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 580332001950 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 580332001951 Polysulphide reductase [Energy production and conversion]; Region: COG5557; cl17901 580332001952 Polysulphide reductase, NrfD; Region: NrfD; pfam03916 580332001953 Protein of unknown function (DUF3341); Region: DUF3341; pfam11821 580332001954 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 580332001955 Polysulphide reductase [Energy production and conversion]; Region: COG5557; cl17901 580332001956 stringent starvation protein A; Provisional; Region: sspA; PRK09481 580332001957 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 580332001958 C-terminal domain interface [polypeptide binding]; other site 580332001959 putative GSH binding site (G-site) [chemical binding]; other site 580332001960 dimer interface [polypeptide binding]; other site 580332001961 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 580332001962 dimer interface [polypeptide binding]; other site 580332001963 N-terminal domain interface [polypeptide binding]; other site 580332001964 ClpXP protease specificity-enhancing factor; Provisional; Region: PRK11798 580332001965 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 580332001966 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 580332001967 Sigma-70, region 4; Region: Sigma70_r4; pfam04545 580332001968 DNA binding residues [nucleotide binding] 580332001969 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 580332001970 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 580332001971 dimer interface [polypeptide binding]; other site 580332001972 active site 580332001973 glycine-pyridoxal phosphate binding site [chemical binding]; other site 580332001974 folate binding site [chemical binding]; other site 580332001975 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 580332001976 ATP cone domain; Region: ATP-cone; pfam03477 580332001977 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 580332001978 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 580332001979 catalytic motif [active] 580332001980 Zn binding site [ion binding]; other site 580332001981 RibD C-terminal domain; Region: RibD_C; cl17279 580332001982 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 580332001983 Lumazine binding domain; Region: Lum_binding; pfam00677 580332001984 Lumazine binding domain; Region: Lum_binding; pfam00677 580332001985 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 580332001986 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 580332001987 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 580332001988 dimerization interface [polypeptide binding]; other site 580332001989 active site 580332001990 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 580332001991 homopentamer interface [polypeptide binding]; other site 580332001992 active site 580332001993 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 580332001994 putative RNA binding site [nucleotide binding]; other site 580332001995 thiamine monophosphate kinase; Provisional; Region: PRK05731 580332001996 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 580332001997 ATP binding site [chemical binding]; other site 580332001998 dimerization interface [polypeptide binding]; other site 580332001999 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 580332002000 tetramer interfaces [polypeptide binding]; other site 580332002001 binuclear metal-binding site [ion binding]; other site 580332002002 Staphylococcal nuclease homologues; Region: SNc; smart00318 580332002003 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cd00175 580332002004 Catalytic site; other site 580332002005 Excalibur calcium-binding domain; Region: Excalibur; pfam05901 580332002006 MarR family; Region: MarR_2; pfam12802 580332002007 Transcriptional regulators [Transcription]; Region: MarR; COG1846 580332002008 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 580332002009 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 580332002010 active site 580332002011 FMN binding site [chemical binding]; other site 580332002012 substrate binding site [chemical binding]; other site 580332002013 homotetramer interface [polypeptide binding]; other site 580332002014 catalytic residue [active] 580332002015 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 580332002016 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 580332002017 putative active site [active] 580332002018 heme pocket [chemical binding]; other site 580332002019 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 580332002020 putative active site [active] 580332002021 heme pocket [chemical binding]; other site 580332002022 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332002023 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332002024 metal binding site [ion binding]; metal-binding site 580332002025 active site 580332002026 I-site; other site 580332002027 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 580332002028 Protein of unknown function (DUF3820); Region: DUF3820; pfam12843 580332002029 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 580332002030 Domain of unknown function (DUF4156); Region: DUF4156; pfam13698 580332002031 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 580332002032 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 580332002033 ATP binding site [chemical binding]; other site 580332002034 Mg++ binding site [ion binding]; other site 580332002035 motif III; other site 580332002036 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 580332002037 nucleotide binding region [chemical binding]; other site 580332002038 ATP-binding site [chemical binding]; other site 580332002039 RNA recognition motif in Escherichia coli RNA helicase dbpA and similar proteins; Region: RRM_EcDbpA_like; cd12501 580332002040 putative RNA binding site [nucleotide binding]; other site 580332002041 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 580332002042 putative active site [active] 580332002043 putative metal binding site [ion binding]; other site 580332002044 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 580332002045 substrate binding site [chemical binding]; other site 580332002046 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 580332002047 SnoaL-like domain; Region: SnoaL_3; pfam13474 580332002048 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 580332002049 TPR motif; other site 580332002050 binding surface 580332002051 TPR repeat; Region: TPR_11; pfam13414 580332002052 TPR repeat; Region: TPR_11; pfam13414 580332002053 SnoaL-like domain; Region: SnoaL_3; pfam13474 580332002054 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 580332002055 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 580332002056 active site 580332002057 HIGH motif; other site 580332002058 nucleotide binding site [chemical binding]; other site 580332002059 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 580332002060 KMSKS motif; other site 580332002061 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 580332002062 Predicted membrane protein [Function unknown]; Region: COG3671 580332002063 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 580332002064 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 580332002065 active site 580332002066 HIGH motif; other site 580332002067 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 580332002068 KMSKS motif; other site 580332002069 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 580332002070 tRNA binding surface [nucleotide binding]; other site 580332002071 anticodon binding site; other site 580332002072 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4634 580332002073 Protein of unknown function (DUF433); Region: DUF433; pfam04255 580332002074 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 580332002075 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 580332002076 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 580332002077 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 580332002078 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 580332002079 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 580332002080 Walker A motif; other site 580332002081 ATP binding site [chemical binding]; other site 580332002082 Walker B motif; other site 580332002083 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 580332002084 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 580332002085 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 580332002086 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 580332002087 Walker A motif; other site 580332002088 ATP binding site [chemical binding]; other site 580332002089 Walker B motif; other site 580332002090 arginine finger; other site 580332002091 Sporulation related domain; Region: SPOR; pfam05036 580332002092 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 580332002093 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 580332002094 active site 580332002095 phosphorylation site [posttranslational modification] 580332002096 intermolecular recognition site; other site 580332002097 dimerization interface [polypeptide binding]; other site 580332002098 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 580332002099 Walker A motif; other site 580332002100 ATP binding site [chemical binding]; other site 580332002101 Walker B motif; other site 580332002102 arginine finger; other site 580332002103 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 580332002104 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 580332002105 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 580332002106 Walker A/P-loop; other site 580332002107 ATP binding site [chemical binding]; other site 580332002108 Q-loop/lid; other site 580332002109 ABC transporter signature motif; other site 580332002110 Walker B; other site 580332002111 D-loop; other site 580332002112 H-loop/switch region; other site 580332002113 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 580332002114 Permease; Region: Permease; cl00510 580332002115 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 580332002116 mce related protein; Region: MCE; pfam02470 580332002117 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 580332002118 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 580332002119 anti sigma factor interaction site; other site 580332002120 regulatory phosphorylation site [posttranslational modification]; other site 580332002121 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 580332002122 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 580332002123 hinge; other site 580332002124 active site 580332002125 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 580332002126 ATP phosphoribosyltransferase catalytic subunit; Reviewed; Region: hisG; PRK01686 580332002127 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 580332002128 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 580332002129 NAD binding site [chemical binding]; other site 580332002130 dimerization interface [polypeptide binding]; other site 580332002131 product binding site; other site 580332002132 substrate binding site [chemical binding]; other site 580332002133 zinc binding site [ion binding]; other site 580332002134 catalytic residues [active] 580332002135 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 580332002136 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 580332002137 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 580332002138 EamA-like transporter family; Region: EamA; cl17759 580332002139 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 580332002140 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 580332002141 [2Fe-2S] cluster binding site [ion binding]; other site 580332002142 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 580332002143 alpha subunit interface [polypeptide binding]; other site 580332002144 active site 580332002145 substrate binding site [chemical binding]; other site 580332002146 Fe binding site [ion binding]; other site 580332002147 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 580332002148 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 580332002149 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 580332002150 substrate binding pocket [chemical binding]; other site 580332002151 chain length determination region; other site 580332002152 substrate-Mg2+ binding site; other site 580332002153 catalytic residues [active] 580332002154 aspartate-rich region 1; other site 580332002155 active site lid residues [active] 580332002156 aspartate-rich region 2; other site 580332002157 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 580332002158 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 580332002159 TPP-binding site; other site 580332002160 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 580332002161 PYR/PP interface [polypeptide binding]; other site 580332002162 dimer interface [polypeptide binding]; other site 580332002163 TPP binding site [chemical binding]; other site 580332002164 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 580332002165 putative GTP cyclohydrolase; Provisional; Region: PRK13674 580332002166 heat shock protein 90; Provisional; Region: PRK05218 580332002167 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 580332002168 ATP binding site [chemical binding]; other site 580332002169 Mg2+ binding site [ion binding]; other site 580332002170 G-X-G motif; other site 580332002171 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 580332002172 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 580332002173 catalytic triad [active] 580332002174 Ferredoxin [Energy production and conversion]; Region: COG1146 580332002175 4Fe-4S binding domain; Region: Fer4; cl02805 580332002176 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 580332002177 double-strand break repair protein AddB, alphaproteobacterial type; Region: addB_alphas; TIGR02786 580332002178 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 580332002179 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 580332002180 Part of AAA domain; Region: AAA_19; pfam13245 580332002181 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 580332002182 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 580332002183 putative heme binding pocket [chemical binding]; other site 580332002184 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 580332002185 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 580332002186 Coenzyme A binding pocket [chemical binding]; other site 580332002187 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 580332002188 CoenzymeA binding site [chemical binding]; other site 580332002189 subunit interaction site [polypeptide binding]; other site 580332002190 PHB binding site; other site 580332002191 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 580332002192 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 580332002193 IHF dimer interface [polypeptide binding]; other site 580332002194 IHF - DNA interface [nucleotide binding]; other site 580332002195 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 580332002196 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 580332002197 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 580332002198 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 580332002199 Walker A/P-loop; other site 580332002200 ATP binding site [chemical binding]; other site 580332002201 Q-loop/lid; other site 580332002202 ABC transporter signature motif; other site 580332002203 Walker B; other site 580332002204 D-loop; other site 580332002205 H-loop/switch region; other site 580332002206 lipoate-protein ligase B; Provisional; Region: PRK14342 580332002207 Protein of unknown function (DUF493); Region: DUF493; cl01102 580332002208 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 580332002209 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 580332002210 homodimer interface [polypeptide binding]; other site 580332002211 substrate-cofactor binding pocket; other site 580332002212 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332002213 catalytic residue [active] 580332002214 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 580332002215 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 580332002216 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; smart00936 580332002217 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 580332002218 5-bromo-4-chloroindolyl phosphate hydrolysis protein; Region: Halogen_Hydrol; cl02059 580332002219 HDOD domain; Region: HDOD; pfam08668 580332002220 CRISPR/Cas system-associated protein Cas10; Region: Cas10_III; cd09680 580332002221 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 580332002222 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 580332002223 active site 580332002224 phosphorylation site [posttranslational modification] 580332002225 intermolecular recognition site; other site 580332002226 dimerization interface [polypeptide binding]; other site 580332002227 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 580332002228 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 580332002229 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 580332002230 dimer interface [polypeptide binding]; other site 580332002231 phosphorylation site [posttranslational modification] 580332002232 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 580332002233 ATP binding site [chemical binding]; other site 580332002234 G-X-G motif; other site 580332002235 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 580332002236 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 580332002237 N-terminal plug; other site 580332002238 ligand-binding site [chemical binding]; other site 580332002239 Protein of unknown function (DUF461); Region: DUF461; pfam04314 580332002240 Protein of unknown function (DUF461); Region: DUF461; pfam04314 580332002241 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 580332002242 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 580332002243 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 580332002244 feedback inhibition sensing region; other site 580332002245 homohexameric interface [polypeptide binding]; other site 580332002246 carbamate kinase; Reviewed; Region: PRK12686 580332002247 nucleotide binding site [chemical binding]; other site 580332002248 N-acetyl-L-glutamate binding site [chemical binding]; other site 580332002249 pyrimidine 5'-nucleotidase; Region: Pyr-5-nucltdase; TIGR01993 580332002250 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 580332002251 motif II; other site 580332002252 division inhibitor protein; Provisional; Region: slmA; PRK09480 580332002253 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 580332002254 3-deoxy-7-phosphoheptulonate synthase; Reviewed; Region: PRK08673 580332002255 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; cl17225 580332002256 2-isopropylmalate synthase; Validated; Region: PRK00915 580332002257 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 580332002258 active site 580332002259 catalytic residues [active] 580332002260 metal binding site [ion binding]; metal-binding site 580332002261 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 580332002262 Pyridoxamine 5'-phosphate oxidase; Region: Pyrid_oxidase_2; pfam13883 580332002263 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 580332002264 Uncharacterized protein family, UPF0114; Region: UPF0114; pfam03350 580332002265 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 580332002266 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 580332002267 catalytic residues [active] 580332002268 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 580332002269 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 580332002270 N-acetyl-D-glucosamine binding site [chemical binding]; other site 580332002271 catalytic residue [active] 580332002272 prolyl-tRNA synthetase; Provisional; Region: PRK09194 580332002273 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ProRS_core_prok; cd00779 580332002274 dimer interface [polypeptide binding]; other site 580332002275 motif 1; other site 580332002276 active site 580332002277 motif 2; other site 580332002278 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 580332002279 putative deacylase active site [active] 580332002280 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 580332002281 active site 580332002282 motif 3; other site 580332002283 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 580332002284 anticodon binding site; other site 580332002285 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 580332002286 putative active site [active] 580332002287 Ap4A binding site [chemical binding]; other site 580332002288 nudix motif; other site 580332002289 putative metal binding site [ion binding]; other site 580332002290 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 580332002291 PEGA domain; Region: PEGA; pfam08308 580332002292 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 580332002293 trimer interface [polypeptide binding]; other site 580332002294 active site 580332002295 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 580332002296 Flavoprotein; Region: Flavoprotein; pfam02441 580332002297 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 580332002298 hypothetical protein; Reviewed; Region: PRK00024 580332002299 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 580332002300 MPN+ (JAMM) motif; other site 580332002301 Zinc-binding site [ion binding]; other site 580332002302 elongation factor Tu; Reviewed; Region: PRK00049 580332002303 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 580332002304 G1 box; other site 580332002305 GEF interaction site [polypeptide binding]; other site 580332002306 GTP/Mg2+ binding site [chemical binding]; other site 580332002307 Switch I region; other site 580332002308 G2 box; other site 580332002309 G3 box; other site 580332002310 Switch II region; other site 580332002311 G4 box; other site 580332002312 G5 box; other site 580332002313 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 580332002314 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 580332002315 Antibiotic Binding Site [chemical binding]; other site 580332002316 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK05740 580332002317 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 580332002318 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 580332002319 putative homodimer interface [polypeptide binding]; other site 580332002320 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 580332002321 heterodimer interface [polypeptide binding]; other site 580332002322 homodimer interface [polypeptide binding]; other site 580332002323 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 580332002324 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 580332002325 23S rRNA interface [nucleotide binding]; other site 580332002326 L7/L12 interface [polypeptide binding]; other site 580332002327 putative thiostrepton binding site; other site 580332002328 L25 interface [polypeptide binding]; other site 580332002329 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 580332002330 mRNA/rRNA interface [nucleotide binding]; other site 580332002331 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 580332002332 23S rRNA interface [nucleotide binding]; other site 580332002333 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 580332002334 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 580332002335 core dimer interface [polypeptide binding]; other site 580332002336 L10 interface [polypeptide binding]; other site 580332002337 L11 interface [polypeptide binding]; other site 580332002338 putative EF-Tu interaction site [polypeptide binding]; other site 580332002339 putative EF-G interaction site [polypeptide binding]; other site 580332002340 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 580332002341 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl17585 580332002342 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 580332002343 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 580332002344 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 580332002345 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 580332002346 RPB3 interaction site [polypeptide binding]; other site 580332002347 RPB1 interaction site [polypeptide binding]; other site 580332002348 RPB11 interaction site [polypeptide binding]; other site 580332002349 RPB10 interaction site [polypeptide binding]; other site 580332002350 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 580332002351 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 580332002352 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 580332002353 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 580332002354 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 580332002355 RNA polymerase Rpb1, domain 5; Region: RNA_pol_Rpb1_5; pfam04998 580332002356 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 580332002357 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 580332002358 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 580332002359 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 580332002360 DNA binding site [nucleotide binding] 580332002361 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 580332002362 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 580332002363 S17 interaction site [polypeptide binding]; other site 580332002364 S8 interaction site; other site 580332002365 16S rRNA interaction site [nucleotide binding]; other site 580332002366 streptomycin interaction site [chemical binding]; other site 580332002367 23S rRNA interaction site [nucleotide binding]; other site 580332002368 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 580332002369 30S ribosomal protein S7; Validated; Region: PRK05302 580332002370 elongation factor G; Reviewed; Region: PRK00007 580332002371 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 580332002372 G1 box; other site 580332002373 putative GEF interaction site [polypeptide binding]; other site 580332002374 GTP/Mg2+ binding site [chemical binding]; other site 580332002375 Switch I region; other site 580332002376 G2 box; other site 580332002377 G3 box; other site 580332002378 Switch II region; other site 580332002379 G4 box; other site 580332002380 G5 box; other site 580332002381 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 580332002382 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 580332002383 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 580332002384 elongation factor Tu; Reviewed; Region: PRK00049 580332002385 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 580332002386 G1 box; other site 580332002387 GEF interaction site [polypeptide binding]; other site 580332002388 GTP/Mg2+ binding site [chemical binding]; other site 580332002389 Switch I region; other site 580332002390 G2 box; other site 580332002391 G3 box; other site 580332002392 Switch II region; other site 580332002393 G4 box; other site 580332002394 G5 box; other site 580332002395 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 580332002396 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 580332002397 Antibiotic Binding Site [chemical binding]; other site 580332002398 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 580332002399 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 580332002400 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 580332002401 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 580332002402 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 580332002403 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 580332002404 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 580332002405 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 580332002406 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 580332002407 putative translocon binding site; other site 580332002408 protein-rRNA interface [nucleotide binding]; other site 580332002409 ribosomal protein S3, bacterial type; Region: rpsC_bact; TIGR01009 580332002410 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 580332002411 G-X-X-G motif; other site 580332002412 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 580332002413 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 580332002414 23S rRNA interface [nucleotide binding]; other site 580332002415 5S rRNA interface [nucleotide binding]; other site 580332002416 putative antibiotic binding site [chemical binding]; other site 580332002417 L25 interface [polypeptide binding]; other site 580332002418 L27 interface [polypeptide binding]; other site 580332002419 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 580332002420 23S rRNA interface [nucleotide binding]; other site 580332002421 putative translocon interaction site; other site 580332002422 signal recognition particle (SRP54) interaction site; other site 580332002423 L23 interface [polypeptide binding]; other site 580332002424 trigger factor interaction site; other site 580332002425 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 580332002426 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 580332002427 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 580332002428 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 580332002429 RNA binding site [nucleotide binding]; other site 580332002430 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 580332002431 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 580332002432 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 580332002433 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 580332002434 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 580332002435 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 580332002436 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 580332002437 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 580332002438 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 580332002439 5S rRNA interface [nucleotide binding]; other site 580332002440 23S rRNA interface [nucleotide binding]; other site 580332002441 L5 interface [polypeptide binding]; other site 580332002442 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 580332002443 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 580332002444 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 580332002445 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 580332002446 23S rRNA binding site [nucleotide binding]; other site 580332002447 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 580332002448 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 580332002449 SecY translocase; Region: SecY; pfam00344 580332002450 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 580332002451 rRNA binding site [nucleotide binding]; other site 580332002452 predicted 30S ribosome binding site; other site 580332002453 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 580332002454 30S ribosomal protein S13; Region: bact_S13; TIGR03631 580332002455 30S ribosomal protein S11; Validated; Region: PRK05309 580332002456 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 580332002457 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 580332002458 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 580332002459 RNA binding surface [nucleotide binding]; other site 580332002460 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 580332002461 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 580332002462 alphaNTD homodimer interface [polypeptide binding]; other site 580332002463 alphaNTD - beta interaction site [polypeptide binding]; other site 580332002464 alphaNTD - beta' interaction site [polypeptide binding]; other site 580332002465 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 580332002466 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 580332002467 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 580332002468 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 580332002469 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 580332002470 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 580332002471 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 580332002472 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 580332002473 Major Facilitator Superfamily; Region: MFS_1; pfam07690 580332002474 putative substrate translocation pore; other site 580332002475 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 580332002476 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 580332002477 dimer interface [polypeptide binding]; other site 580332002478 ssDNA binding site [nucleotide binding]; other site 580332002479 tetramer (dimer of dimers) interface [polypeptide binding]; other site 580332002480 PAS fold; Region: PAS_4; pfam08448 580332002481 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 580332002482 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 580332002483 Walker A motif; other site 580332002484 ATP binding site [chemical binding]; other site 580332002485 Walker B motif; other site 580332002486 arginine finger; other site 580332002487 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 580332002488 4Fe-4S dicluster domain; Region: Fer4_9; pfam13187 580332002489 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 580332002490 Iron-sulfur cluster assembly accessory protein; Region: TIGR00049 580332002491 Fe-S cluster assembly protein NifU; Region: NifU_proper; TIGR02000 580332002492 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 580332002493 trimerization site [polypeptide binding]; other site 580332002494 active site 580332002495 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 580332002496 NifU-like domain; Region: NifU; pfam01106 580332002497 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 580332002498 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 580332002499 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 580332002500 catalytic residue [active] 580332002501 homocitrate synthase NifV; Region: nifV_homocitr; TIGR02660 580332002502 Streptomyces rubellomurinus FrbC and related proteins, catalytic TIM barrel domain; Region: DRE_TIM_NifV; cd07939 580332002503 active site 580332002504 catalytic residues [active] 580332002505 metal binding site [ion binding]; metal-binding site 580332002506 serine O-acetyltransferase; Region: cysE; TIGR01172 580332002507 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 580332002508 trimer interface [polypeptide binding]; other site 580332002509 active site 580332002510 substrate binding site [chemical binding]; other site 580332002511 CoA binding site [chemical binding]; other site 580332002512 Nitrogen fixation protein NifW; Region: NifW; pfam03206 580332002513 NifZ domain; Region: NifZ; pfam04319 580332002514 nitrogen fixation protein NifM; Region: nifM_nitrog; TIGR02933 580332002515 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 580332002516 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 580332002517 HicB family; Region: HicB; pfam05534 580332002518 YcfA-like protein; Region: YcfA; cl00752 580332002519 DctM-like transporters; Region: DctM; pfam06808 580332002520 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 580332002521 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 580332002522 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 580332002523 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 580332002524 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 580332002525 Cysteine-rich domain; Region: CCG; pfam02754 580332002526 Cysteine-rich domain; Region: CCG; pfam02754 580332002527 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 580332002528 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 580332002529 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 580332002530 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 580332002531 Domain of unknown function (DUF3390); Region: DUF3390; pfam11870 580332002532 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 580332002533 homodimer interface [polypeptide binding]; other site 580332002534 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332002535 catalytic residue [active] 580332002536 glycolate oxidase iron-sulfur subunit; Provisional; Region: glcF; PRK11274 580332002537 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 580332002538 Cysteine-rich domain; Region: CCG; pfam02754 580332002539 Cysteine-rich domain; Region: CCG; pfam02754 580332002540 glycolate oxidase FAD binding subunit; Provisional; Region: glcE; PRK11282 580332002541 FAD binding domain; Region: FAD_binding_4; pfam01565 580332002542 glycolate oxidase subunit GlcD; Provisional; Region: PRK11230 580332002543 FAD binding domain; Region: FAD_binding_4; pfam01565 580332002544 Pirin-related protein [General function prediction only]; Region: COG1741 580332002545 Pirin; Region: Pirin; pfam02678 580332002546 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 580332002547 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 580332002548 active site 580332002549 DNA binding site [nucleotide binding] 580332002550 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 580332002551 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 580332002552 Catalytic site [active] 580332002553 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; cl00614 580332002554 NifQ; Region: NifQ; pfam04891 580332002555 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 580332002556 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 580332002557 catalytic loop [active] 580332002558 iron binding site [ion binding]; other site 580332002559 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 580332002560 ArsC family; Region: ArsC; pfam03960 580332002561 putative catalytic residues [active] 580332002562 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 580332002563 nitrogenase cofactor biosynthesis protein NifB; Region: nifB; TIGR01290 580332002564 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 580332002565 FeS/SAM binding site; other site 580332002566 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 580332002567 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 580332002568 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 580332002569 Oxygen tolerance; Region: BatD; pfam13584 580332002570 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 580332002571 metal ion-dependent adhesion site (MIDAS); other site 580332002572 Domain of unknown function (DUF4381); Region: DUF4381; pfam14316 580332002573 Protein of unknown function DUF58; Region: DUF58; pfam01882 580332002574 MoxR-like ATPases [General function prediction only]; Region: COG0714 580332002575 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 580332002576 Walker A motif; other site 580332002577 ATP binding site [chemical binding]; other site 580332002578 Walker B motif; other site 580332002579 arginine finger; other site 580332002580 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 580332002581 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 580332002582 Walker A/P-loop; other site 580332002583 ATP binding site [chemical binding]; other site 580332002584 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 580332002585 Q-loop/lid; other site 580332002586 AAA domain; Region: AAA_21; pfam13304 580332002587 ABC transporter signature motif; other site 580332002588 Walker B; other site 580332002589 D-loop; other site 580332002590 H-loop/switch region; other site 580332002591 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 580332002592 Protein of unknown function (DUF3620); Region: DUF3620; pfam12281 580332002593 Nitrogen fixation protein of unknown function; Region: Nif11; pfam07862 580332002594 Nif-specific regulatory protein; Region: nifA; TIGR01817 580332002595 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 580332002596 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 580332002597 Walker A motif; other site 580332002598 ATP binding site [chemical binding]; other site 580332002599 Walker B motif; other site 580332002600 arginine finger; other site 580332002601 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 580332002602 nitrogen fixation negative regulator NifL; Region: nifL_nitrog; TIGR02938 580332002603 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 580332002604 putative active site [active] 580332002605 heme pocket [chemical binding]; other site 580332002606 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 580332002607 ATP binding site [chemical binding]; other site 580332002608 Mg2+ binding site [ion binding]; other site 580332002609 G-X-G motif; other site 580332002610 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 580332002611 electron transport complex protein RnfB; Provisional; Region: PRK05113 580332002612 Putative Fe-S cluster; Region: FeS; cl17515 580332002613 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 580332002614 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 580332002615 SLBB domain; Region: SLBB; pfam10531 580332002616 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 580332002617 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; pfam03116 580332002618 electron transport complex, RnfABCDGE type, G subunit; Region: rnfG; TIGR01947 580332002619 electron transport complex RsxE subunit; Provisional; Region: PRK12405 580332002620 RnfH family Ubiquitin; Region: Ub-RnfH; pfam03658 580332002621 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 580332002622 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 580332002623 Ferredoxin [Energy production and conversion]; Region: COG1146 580332002624 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 580332002625 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 580332002626 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 580332002627 chaperone protein DnaJ; Provisional; Region: PRK14280 580332002628 octaheme c-type cytochrome, tetrathionate reductase family; Region: octaheme_Shew; TIGR04315 580332002629 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 580332002630 Hemerythrin; Region: Hemerythrin; cd12107 580332002631 Fe binding site [ion binding]; other site 580332002632 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 580332002633 HSP70 interaction site [polypeptide binding]; other site 580332002634 Hemerythrin; Region: Hemerythrin; cd12107 580332002635 Fe binding site [ion binding]; other site 580332002636 Malonate/sodium symporter MadM subunit; Region: MadM; cl04274 580332002637 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 580332002638 PAS fold; Region: PAS_4; pfam08448 580332002639 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 580332002640 putative active site [active] 580332002641 heme pocket [chemical binding]; other site 580332002642 PAS domain S-box; Region: sensory_box; TIGR00229 580332002643 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 580332002644 putative active site [active] 580332002645 heme pocket [chemical binding]; other site 580332002646 PAS domain S-box; Region: sensory_box; TIGR00229 580332002647 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 580332002648 putative active site [active] 580332002649 heme pocket [chemical binding]; other site 580332002650 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 580332002651 PAS domain; Region: PAS_9; pfam13426 580332002652 putative active site [active] 580332002653 heme pocket [chemical binding]; other site 580332002654 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332002655 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332002656 metal binding site [ion binding]; metal-binding site 580332002657 active site 580332002658 I-site; other site 580332002659 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 580332002660 Dinitrogenase reductase ADP-ribosyltransferase (DRAT); Region: DRAT; pfam07357 580332002661 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 580332002662 nitrogenase iron protein; Region: nifH; TIGR01287 580332002663 Nucleotide-binding sites [chemical binding]; other site 580332002664 Walker A motif; other site 580332002665 Switch I region of nucleotide binding site; other site 580332002666 Fe4S4 binding sites [ion binding]; other site 580332002667 Switch II region of nucleotide binding site; other site 580332002668 Nitrogenase molybdenum-iron protein, alpha and beta chains [Energy production and conversion]; Region: NifD; COG2710 580332002669 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 580332002670 MoFe protein alpha/beta subunit interactions; other site 580332002671 Alpha subunit P cluster binding residues; other site 580332002672 FeMoco binding residues [chemical binding]; other site 580332002673 MoFe protein alpha subunit/Fe protein contacts; other site 580332002674 MoFe protein dimer/ dimer interactions; other site 580332002675 nitrogenase molybdenum-iron protein beta chain; Region: nifK; TIGR01286 580332002676 Domain of unknown function (DUF3364); Region: DUF3364; pfam11844 580332002677 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 580332002678 MoFe protein beta/alpha subunit interactions; other site 580332002679 Beta subunit P cluster binding residues; other site 580332002680 MoFe protein beta subunit/Fe protein contacts; other site 580332002681 MoFe protein dimer/ dimer interactions; other site 580332002682 NifT/FixU protein; Region: NifT; pfam06988 580332002683 glycine radical enzyme activase, YjjW family; Region: activase_YjjW; TIGR04041 580332002684 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 580332002685 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332002686 Zn2+ binding site [ion binding]; other site 580332002687 Mg2+ binding site [ion binding]; other site 580332002688 Predicted O-methyltransferase [General function prediction only]; Region: COG4122 580332002689 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 580332002690 S-adenosylmethionine binding site [chemical binding]; other site 580332002691 Protein of unknown function (DUF1311); Region: DUF1311; pfam07007 580332002692 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 580332002693 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 580332002694 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; cl17549 580332002695 DNA-binding transcriptional regulator ModE; Provisional; Region: PRK10676 580332002696 molybdenum-pterin binding domain; Region: Mop; TIGR00638 580332002697 molybdenum-pterin binding domain; Region: Mop; TIGR00638 580332002698 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 580332002699 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 580332002700 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 580332002701 putative PBP binding loops; other site 580332002702 dimer interface [polypeptide binding]; other site 580332002703 ABC-ATPase subunit interface; other site 580332002704 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 580332002705 molybdenum ABC transporter, ATP-binding protein; Region: modC_ABC; TIGR02142 580332002706 Walker A/P-loop; other site 580332002707 ATP binding site [chemical binding]; other site 580332002708 Q-loop/lid; other site 580332002709 ABC transporter signature motif; other site 580332002710 Walker B; other site 580332002711 D-loop; other site 580332002712 H-loop/switch region; other site 580332002713 TOBE domain; Region: TOBE; cl01440 580332002714 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 580332002715 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 580332002716 Coenzyme A binding pocket [chemical binding]; other site 580332002717 LRV protein FeS4 cluster; Region: LRV_FeS; pfam05484 580332002718 nitrogenase molybdenum-cofactor biosynthesis protein NifE; Provisional; Region: PRK14478 580332002719 nitrogenase molybdenum-iron cofactor biosynthesis protein NifE; Region: nifE; TIGR01283 580332002720 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 580332002721 Nitrogenase component 1 type Oxidoreductase; Region: Oxidored_nitro; pfam00148 580332002722 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 580332002723 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; pfam04246 580332002724 probable nitrogen fixation protein; Region: TIGR02935 580332002725 Rop-like; Region: Rop-like; pfam05082 580332002726 ferredoxin III, nif-specific; Region: fdxN_nitrog; TIGR02936 580332002727 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 580332002728 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 580332002729 dimer interface [polypeptide binding]; other site 580332002730 [2Fe-2S] cluster binding site [ion binding]; other site 580332002731 NifZ domain; Region: NifZ; pfam04319 580332002732 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 580332002733 NADPH bind site [chemical binding]; other site 580332002734 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 580332002735 putative FMN binding site [chemical binding]; other site 580332002736 NADPH bind site [chemical binding]; other site 580332002737 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 580332002738 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 580332002739 Domain of unknown function (DUF389); Region: DUF389; pfam04087 580332002740 Na+/H+ antiporter, bacterial form; Region: a_cpa1; TIGR00831 580332002741 peptidoglycan-associated outer membrane lipoprotein; Provisional; Region: PRK10802 580332002742 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 580332002743 ligand binding site [chemical binding]; other site 580332002744 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 580332002745 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 580332002746 putative ion selectivity filter; other site 580332002747 putative pore gating glutamate residue; other site 580332002748 putative H+/Cl- coupling transport residue; other site 580332002749 pyruvate phosphate dikinase; Provisional; Region: PRK09279 580332002750 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 580332002751 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 580332002752 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 580332002753 flavodoxin FldA; Validated; Region: PRK09267 580332002754 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 580332002755 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 580332002756 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 580332002757 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 580332002758 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 580332002759 biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Region: BVR-B_like_SDR_a; cd05244 580332002760 NADH(P)-binding; Region: NAD_binding_10; pfam13460 580332002761 NAD binding site [chemical binding]; other site 580332002762 substrate binding site [chemical binding]; other site 580332002763 putative active site [active] 580332002764 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 580332002765 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 580332002766 Domain of unknown function (DUF1956); Region: DUF1956; pfam09209 580332002767 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 580332002768 HlyD family secretion protein; Region: HlyD_3; pfam13437 580332002769 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 580332002770 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 580332002771 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 580332002772 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 580332002773 dimerization interface [polypeptide binding]; other site 580332002774 PAS fold; Region: PAS_3; pfam08447 580332002775 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 580332002776 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332002777 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332002778 metal binding site [ion binding]; metal-binding site 580332002779 active site 580332002780 I-site; other site 580332002781 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 580332002782 Domain of unknown function (DUF4154); Region: DUF4154; pfam13689 580332002783 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 580332002784 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 580332002785 16S rRNA methyltransferase B; Provisional; Region: PRK14901 580332002786 NOL1/NOP2/sun family putative RNA methylase; Region: nop2p; TIGR00446 580332002787 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 580332002788 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 580332002789 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 580332002790 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 580332002791 active site 580332002792 substrate binding site [chemical binding]; other site 580332002793 cosubstrate binding site; other site 580332002794 catalytic site [active] 580332002795 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 580332002796 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 580332002797 dimerization interface [polypeptide binding]; other site 580332002798 putative ATP binding site [chemical binding]; other site 580332002799 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 580332002800 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 580332002801 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 580332002802 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 580332002803 poly(A) polymerase; Region: pcnB; TIGR01942 580332002804 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 580332002805 active site 580332002806 NTP binding site [chemical binding]; other site 580332002807 metal binding triad [ion binding]; metal-binding site 580332002808 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 580332002809 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 580332002810 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 580332002811 catalytic center binding site [active] 580332002812 ATP binding site [chemical binding]; other site 580332002813 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 580332002814 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 580332002815 Substrate-binding site [chemical binding]; other site 580332002816 Substrate specificity [chemical binding]; other site 580332002817 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 580332002818 oligomerization interface [polypeptide binding]; other site 580332002819 active site 580332002820 metal binding site [ion binding]; metal-binding site 580332002821 pantoate--beta-alanine ligase; Region: panC; TIGR00018 580332002822 Pantoate-beta-alanine ligase; Region: PanC; cd00560 580332002823 active site 580332002824 ATP-binding site [chemical binding]; other site 580332002825 pantoate-binding site; other site 580332002826 HXXH motif; other site 580332002827 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 580332002828 tetramerization interface [polypeptide binding]; other site 580332002829 active site 580332002830 adenylosuccinate lyase; Provisional; Region: PRK09285 580332002831 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 580332002832 tetramer interface [polypeptide binding]; other site 580332002833 active site 580332002834 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 580332002835 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 580332002836 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 580332002837 nudix motif; other site 580332002838 Queuosine biosynthesis protein; Region: Queuosine_synth; pfam02547 580332002839 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 580332002840 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 580332002841 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 580332002842 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 580332002843 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 580332002844 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 580332002845 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 580332002846 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 580332002847 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 580332002848 Protein export membrane protein; Region: SecD_SecF; pfam02355 580332002849 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 580332002850 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 580332002851 Glutamyl- and glutaminyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]; Region: GlnS; COG0008 580332002852 glutamyl-queuosine tRNA(Asp) synthetase; Region: queuosine_YadB; TIGR03838 580332002853 active site 580332002854 HIGH motif; other site 580332002855 nucleotide binding site [chemical binding]; other site 580332002856 active site 580332002857 KMSKS motif; other site 580332002858 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 580332002859 Clp amino terminal domain; Region: Clp_N; pfam02861 580332002860 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 580332002861 Walker A motif; other site 580332002862 ATP binding site [chemical binding]; other site 580332002863 Walker B motif; other site 580332002864 arginine finger; other site 580332002865 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 580332002866 Walker A motif; other site 580332002867 ATP binding site [chemical binding]; other site 580332002868 Walker B motif; other site 580332002869 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 580332002870 Uncharacterized conserved protein [Function unknown]; Region: COG2127 580332002871 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 580332002872 DNA-binding site [nucleotide binding]; DNA binding site 580332002873 RNA-binding motif; other site 580332002874 Monomeric isocitrate dehydrogenase [Energy production and conversion]; Region: Icd; COG2838 580332002875 Monomeric isocitrate dehydrogenase; Region: IDH; cl15383 580332002876 Pseudouridine synthase, Escherichia coli RluE; Region: PseudoU_synth_RluE; cd02566 580332002877 pseudouridine synthase; Region: TIGR00093 580332002878 probable active site [active] 580332002879 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 580332002880 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 580332002881 active site 580332002882 homodimer interface [polypeptide binding]; other site 580332002883 putative regulatory protein, FmdB family; Region: CxxC_CxxC_SSSS; TIGR02605 580332002884 Uncharacterized conserved protein [Function unknown]; Region: COG2928 580332002885 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 580332002886 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 580332002887 dimer interface [polypeptide binding]; other site 580332002888 anticodon binding site; other site 580332002889 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 580332002890 homodimer interface [polypeptide binding]; other site 580332002891 motif 1; other site 580332002892 active site 580332002893 motif 2; other site 580332002894 GAD domain; Region: GAD; pfam02938 580332002895 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 580332002896 motif 3; other site 580332002897 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 580332002898 active site 580332002899 barstar interaction site; other site 580332002900 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 580332002901 putative RNAase interaction site [polypeptide binding]; other site 580332002902 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 580332002903 nudix motif; other site 580332002904 quinolinate synthetase; Provisional; Region: PRK09375 580332002905 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 580332002906 putative catalytic site [active] 580332002907 putative metal binding site [ion binding]; other site 580332002908 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 580332002909 PLD-like domain; Region: PLDc_2; pfam13091 580332002910 putative active site [active] 580332002911 catalytic site [active] 580332002912 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 580332002913 PLD-like domain; Region: PLDc_2; pfam13091 580332002914 putative active site [active] 580332002915 catalytic site [active] 580332002916 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 580332002917 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 580332002918 homodimer interface [polypeptide binding]; other site 580332002919 active site pocket [active] 580332002920 glucokinase, proteobacterial type; Region: glk; TIGR00749 580332002921 Glucokinase; Region: Glucokinase; pfam02685 580332002922 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 580332002923 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 580332002924 ATP-binding cassette domain of iron-sulfur clusters transporter, subfamily C; Region: ABCC_ATM1_transporter; cd03253 580332002925 Walker A/P-loop; other site 580332002926 ATP binding site [chemical binding]; other site 580332002927 Q-loop/lid; other site 580332002928 ABC transporter signature motif; other site 580332002929 Walker B; other site 580332002930 D-loop; other site 580332002931 H-loop/switch region; other site 580332002932 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 580332002933 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 580332002934 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 580332002935 aminoethylphosphonate catabolism associated LysR family transcriptional regulator; Region: phn_lysR; TIGR03339 580332002936 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 580332002937 putative dimerization interface [polypeptide binding]; other site 580332002938 ribulose bisophosphate carboxylase; Reviewed; Region: rbcL; PRK04208 580332002939 Ribulose bisphosphate carboxylase large chain; Region: RuBisCO_large; cl08232 580332002940 dimer interface [polypeptide binding]; other site 580332002941 catalytic residue [active] 580332002942 metal binding site [ion binding]; metal-binding site 580332002943 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 580332002944 multimerization interface [polypeptide binding]; other site 580332002945 MoxR-like ATPases [General function prediction only]; Region: COG0714 580332002946 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 580332002947 Walker A motif; other site 580332002948 ATP binding site [chemical binding]; other site 580332002949 Walker B motif; other site 580332002950 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 580332002951 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 580332002952 metal ion-dependent adhesion site (MIDAS); other site 580332002953 AIR carboxylase; Region: AIRC; pfam00731 580332002954 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 580332002955 intersubunit interface [polypeptide binding]; other site 580332002956 active site 580332002957 zinc binding site [ion binding]; other site 580332002958 Na+ binding site [ion binding]; other site 580332002959 Stress responsive A/B Barrel Domain; Region: Dabb; smart00886 580332002960 Predicted membrane protein [Function unknown]; Region: COG2510 580332002961 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 580332002962 putative DNA binding site [nucleotide binding]; other site 580332002963 dimerization interface [polypeptide binding]; other site 580332002964 putative Zn2+ binding site [ion binding]; other site 580332002965 Low molecular weight phosphatase family; Region: LMWPc; cd00115 580332002966 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 580332002967 active site 580332002968 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 580332002969 arsenical-resistance protein; Region: acr3; TIGR00832 580332002970 RNA polymerase sigma factor, SigZ family; Region: SigZ; TIGR02959 580332002971 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 580332002972 Predicted permeases [General function prediction only]; Region: COG0701 580332002973 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 580332002974 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 580332002975 catalytic residues [active] 580332002976 OsmC-like protein; Region: OsmC; pfam02566 580332002977 Glutaredoxin-like domain (DUF836); Region: DUF836; pfam05768 580332002978 gamma-glutamyl kinase; Provisional; Region: PRK05429 580332002979 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 580332002980 nucleotide binding site [chemical binding]; other site 580332002981 homotetrameric interface [polypeptide binding]; other site 580332002982 putative phosphate binding site [ion binding]; other site 580332002983 putative allosteric binding site; other site 580332002984 PUA domain; Region: PUA; pfam01472 580332002985 GTPase CgtA; Reviewed; Region: obgE; PRK12299 580332002986 GTP1/OBG; Region: GTP1_OBG; pfam01018 580332002987 Obg GTPase; Region: Obg; cd01898 580332002988 G1 box; other site 580332002989 GTP/Mg2+ binding site [chemical binding]; other site 580332002990 Switch I region; other site 580332002991 G2 box; other site 580332002992 G3 box; other site 580332002993 Switch II region; other site 580332002994 G4 box; other site 580332002995 G5 box; other site 580332002996 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 580332002997 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 580332002998 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 580332002999 transcription termination factor Rho; Provisional; Region: rho; PRK09376 580332003000 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 580332003001 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 580332003002 RNA binding site [nucleotide binding]; other site 580332003003 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 580332003004 multimer interface [polypeptide binding]; other site 580332003005 Walker A motif; other site 580332003006 ATP binding site [chemical binding]; other site 580332003007 Walker B motif; other site 580332003008 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 580332003009 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 580332003010 catalytic residues [active] 580332003011 sensor protein QseC; Provisional; Region: PRK10337 580332003012 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 580332003013 dimer interface [polypeptide binding]; other site 580332003014 phosphorylation site [posttranslational modification] 580332003015 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 580332003016 ATP binding site [chemical binding]; other site 580332003017 G-X-G motif; other site 580332003018 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 580332003019 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 580332003020 active site 580332003021 phosphorylation site [posttranslational modification] 580332003022 intermolecular recognition site; other site 580332003023 dimerization interface [polypeptide binding]; other site 580332003024 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 580332003025 DNA binding site [nucleotide binding] 580332003026 Dihaem cytochrome c; Region: DHC; pfam09626 580332003027 Domain of unknown function (DUF1924); Region: DUF1924; pfam09086 580332003028 Methyltransferase domain; Region: Methyltransf_18; pfam12847 580332003029 DJ-1 family protein; Region: not_thiJ; TIGR01383 580332003030 Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1; Region: GATase1_DJ-1; cd03135 580332003031 conserved cys residue [active] 580332003032 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 580332003033 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 580332003034 active site 580332003035 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 580332003036 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 580332003037 Protein of unknown function (DUF1255); Region: DUF1255; pfam06865 580332003038 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 580332003039 ADP-ribose binding site [chemical binding]; other site 580332003040 argininosuccinate synthase; Provisional; Region: PRK13820 580332003041 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 580332003042 ANP binding site [chemical binding]; other site 580332003043 Substrate Binding Site II [chemical binding]; other site 580332003044 Substrate Binding Site I [chemical binding]; other site 580332003045 ornithine carbamoyltransferase; Provisional; Region: PRK00779 580332003046 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 580332003047 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 580332003048 acetylornithine aminotransferase; Provisional; Region: PRK02627 580332003049 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 580332003050 inhibitor-cofactor binding pocket; inhibition site 580332003051 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332003052 catalytic residue [active] 580332003053 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 580332003054 Protein of unknown function (DUF3579); Region: DUF3579; pfam12112 580332003055 Protein of unknown function (DUF3579); Region: DUF3579; pfam12112 580332003056 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 580332003057 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 580332003058 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 580332003059 PAS domain S-box; Region: sensory_box; TIGR00229 580332003060 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 580332003061 putative active site [active] 580332003062 heme pocket [chemical binding]; other site 580332003063 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332003064 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332003065 metal binding site [ion binding]; metal-binding site 580332003066 active site 580332003067 I-site; other site 580332003068 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12684 580332003069 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 580332003070 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 580332003071 substrate binding site [chemical binding]; other site 580332003072 dimerization interface [polypeptide binding]; other site 580332003073 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 580332003074 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 580332003075 Nitrite and sulphite reductase 4Fe-4S domain; Region: NIR_SIR; pfam01077 580332003076 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 580332003077 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 580332003078 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 580332003079 Active Sites [active] 580332003080 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 580332003081 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 580332003082 Active Sites [active] 580332003083 GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]; Region: CysN; COG2895 580332003084 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 580332003085 CysD dimerization site [polypeptide binding]; other site 580332003086 G1 box; other site 580332003087 putative GEF interaction site [polypeptide binding]; other site 580332003088 GTP/Mg2+ binding site [chemical binding]; other site 580332003089 Switch I region; other site 580332003090 G2 box; other site 580332003091 G3 box; other site 580332003092 Switch II region; other site 580332003093 G4 box; other site 580332003094 G5 box; other site 580332003095 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 580332003096 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 580332003097 CobD/CbiB family protein; Provisional; Region: PRK07630 580332003098 4-alpha-glucanotransferase; Provisional; Region: PRK14508 580332003099 alpha-L-glutamate ligases, RimK family; Region: rimK_fam; TIGR00768 580332003100 GTPase RsgA; Reviewed; Region: PRK00098 580332003101 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 580332003102 RNA binding site [nucleotide binding]; other site 580332003103 homodimer interface [polypeptide binding]; other site 580332003104 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 580332003105 GTPase/Zn-binding domain interface [polypeptide binding]; other site 580332003106 GTP/Mg2+ binding site [chemical binding]; other site 580332003107 G4 box; other site 580332003108 G5 box; other site 580332003109 G1 box; other site 580332003110 Switch I region; other site 580332003111 G2 box; other site 580332003112 G3 box; other site 580332003113 Switch II region; other site 580332003114 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 580332003115 aromatic arch; other site 580332003116 DCoH dimer interaction site [polypeptide binding]; other site 580332003117 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 580332003118 DCoH tetramer interaction site [polypeptide binding]; other site 580332003119 substrate binding site [chemical binding]; other site 580332003120 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 580332003121 Peptidase family M48; Region: Peptidase_M48; pfam01435 580332003122 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 580332003123 catalytic site [active] 580332003124 putative active site [active] 580332003125 putative substrate binding site [chemical binding]; other site 580332003126 dimer interface [polypeptide binding]; other site 580332003127 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 580332003128 dimerization interface [polypeptide binding]; other site 580332003129 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 580332003130 PAS domain; Region: PAS_9; pfam13426 580332003131 putative active site [active] 580332003132 heme pocket [chemical binding]; other site 580332003133 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332003134 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332003135 metal binding site [ion binding]; metal-binding site 580332003136 active site 580332003137 I-site; other site 580332003138 Flagellar regulator YcgR; Region: YcgR; pfam07317 580332003139 PilZ domain; Region: PilZ; pfam07238 580332003140 ferrochelatase; Reviewed; Region: hemH; PRK00035 580332003141 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 580332003142 C-terminal domain interface [polypeptide binding]; other site 580332003143 active site 580332003144 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 580332003145 active site 580332003146 N-terminal domain interface [polypeptide binding]; other site 580332003147 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 580332003148 Winged helix-turn-helix transcription repressor, HrcA DNA-binding; Region: HrcA_DNA-bdg; pfam03444 580332003149 NAD(+)/NADH kinase family protein; Provisional; Region: ppnK; PRK02155 580332003150 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 580332003151 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 580332003152 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 580332003153 Walker A/P-loop; other site 580332003154 ATP binding site [chemical binding]; other site 580332003155 Q-loop/lid; other site 580332003156 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 580332003157 ABC transporter signature motif; other site 580332003158 Walker B; other site 580332003159 D-loop; other site 580332003160 H-loop/switch region; other site 580332003161 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 580332003162 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 580332003163 dihydrodipicolinate reductase; Provisional; Region: PRK00048 580332003164 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 580332003165 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 580332003166 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 580332003167 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 580332003168 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 580332003169 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332003170 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332003171 metal binding site [ion binding]; metal-binding site 580332003172 active site 580332003173 I-site; other site 580332003174 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 580332003175 Predicted membrane protein [Function unknown]; Region: COG1971 580332003176 Domain of unknown function DUF; Region: DUF204; pfam02659 580332003177 Domain of unknown function DUF; Region: DUF204; pfam02659 580332003178 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 580332003179 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 580332003180 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 580332003181 catalytic site [active] 580332003182 subunit interface [polypeptide binding]; other site 580332003183 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 580332003184 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 580332003185 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 580332003186 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 580332003187 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 580332003188 ATP-grasp domain; Region: ATP-grasp_4; cl17255 580332003189 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 580332003190 IMP binding site; other site 580332003191 dimer interface [polypeptide binding]; other site 580332003192 interdomain contacts; other site 580332003193 partial ornithine binding site; other site 580332003194 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 580332003195 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 580332003196 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 580332003197 Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; Region: CRS1_YhbY; smart01103 580332003198 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 580332003199 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 580332003200 S-adenosylmethionine binding site [chemical binding]; other site 580332003201 ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]; Region: HflB; COG0465 580332003202 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 580332003203 Walker A motif; other site 580332003204 ATP binding site [chemical binding]; other site 580332003205 Walker B motif; other site 580332003206 arginine finger; other site 580332003207 Peptidase family M41; Region: Peptidase_M41; pfam01434 580332003208 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 580332003209 dihydropteroate synthase; Region: DHPS; TIGR01496 580332003210 substrate binding pocket [chemical binding]; other site 580332003211 dimer interface [polypeptide binding]; other site 580332003212 inhibitor binding site; inhibition site 580332003213 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 580332003214 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 580332003215 active site 580332003216 substrate binding site [chemical binding]; other site 580332003217 metal binding site [ion binding]; metal-binding site 580332003218 phosphate transporter ATP-binding protein; Provisional; Region: pstB; PRK10744 580332003219 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 580332003220 Walker A/P-loop; other site 580332003221 ATP binding site [chemical binding]; other site 580332003222 Q-loop/lid; other site 580332003223 ABC transporter signature motif; other site 580332003224 Walker B; other site 580332003225 D-loop; other site 580332003226 H-loop/switch region; other site 580332003227 phosphate transporter permease subunit PtsA; Provisional; Region: pstA; PRK11268 580332003228 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 580332003229 dimer interface [polypeptide binding]; other site 580332003230 conserved gate region; other site 580332003231 putative PBP binding loops; other site 580332003232 ABC-ATPase subunit interface; other site 580332003233 phosphate transporter permease subunit PstC; Provisional; Region: pstC; PRK11275 580332003234 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 580332003235 dimer interface [polypeptide binding]; other site 580332003236 conserved gate region; other site 580332003237 putative PBP binding loops; other site 580332003238 ABC-ATPase subunit interface; other site 580332003239 PBP superfamily domain; Region: PBP_like_2; cl17296 580332003240 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 580332003241 substrate binding site [chemical binding]; other site 580332003242 dimer interface [polypeptide binding]; other site 580332003243 catalytic triad [active] 580332003244 Preprotein translocase SecG subunit; Region: SecG; pfam03840 580332003245 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 580332003246 NADH dehydrogenase subunit B; Validated; Region: PRK06411 580332003247 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 580332003248 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 580332003249 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 580332003250 NADH dehydrogenase subunit D; Validated; Region: PRK06075 580332003251 NADH dehydrogenase subunit E; Validated; Region: PRK07539 580332003252 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 580332003253 putative dimer interface [polypeptide binding]; other site 580332003254 [2Fe-2S] cluster binding site [ion binding]; other site 580332003255 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 580332003256 SLBB domain; Region: SLBB; pfam10531 580332003257 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 580332003258 NADH dehydrogenase subunit G; Validated; Region: PRK09129 580332003259 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 580332003260 catalytic loop [active] 580332003261 iron binding site [ion binding]; other site 580332003262 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 580332003263 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 580332003264 Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum-...; Region: MopB_CT; cl09929 580332003265 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 580332003266 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 580332003267 4Fe-4S binding domain; Region: Fer4; pfam00037 580332003268 4Fe-4S binding domain; Region: Fer4; pfam00037 580332003269 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 580332003270 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 580332003271 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 580332003272 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 580332003273 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 580332003274 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 580332003275 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 580332003276 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 580332003277 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 580332003278 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 580332003279 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 580332003280 dimer interface [polypeptide binding]; other site 580332003281 ADP-ribose binding site [chemical binding]; other site 580332003282 active site 580332003283 nudix motif; other site 580332003284 metal binding site [ion binding]; metal-binding site 580332003285 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 580332003286 TniQ; Region: TniQ; pfam06527 580332003287 Protein of unknown function (DUF429); Region: DUF429; pfam04250 580332003288 GIY-YIG nuclease domain superfamily; Region: GIY-YIG_SF; cd00719 580332003289 GIY-YIG motif/motif A; other site 580332003290 active site 580332003291 catalytic site [active] 580332003292 metal binding site [ion binding]; metal-binding site 580332003293 Domain of unknown function (DUF4357); Region: DUF4357; pfam14267 580332003294 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 580332003295 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 580332003296 S-adenosylmethionine binding site [chemical binding]; other site 580332003297 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 580332003298 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 580332003299 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 580332003300 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: HsdR; COG4096 580332003301 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 580332003302 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 580332003303 putative Mg++ binding site [ion binding]; other site 580332003304 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 580332003305 DNA-binding interface [nucleotide binding]; DNA binding site 580332003306 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 580332003307 sequence-specific DNA binding site [nucleotide binding]; other site 580332003308 salt bridge; other site 580332003309 AAA domain; Region: AAA_22; pfam13401 580332003310 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 580332003311 ski2-like helicase; Provisional; Region: PRK00254 580332003312 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 580332003313 ATP binding site [chemical binding]; other site 580332003314 putative Mg++ binding site [ion binding]; other site 580332003315 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 580332003316 nucleotide binding region [chemical binding]; other site 580332003317 ATP-binding site [chemical binding]; other site 580332003318 UDP-glucose 4-epimerase C-term subunit; Region: Epimerase_Csub; pfam13950 580332003319 FRG domain; Region: FRG; cl07460 580332003320 Mannitol repressor; Region: MtlR; cl11450 580332003321 RibD C-terminal domain; Region: RibD_C; cl17279 580332003322 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 580332003323 Protein of unknown function (DUF1444); Region: DUF1444; cl02011 580332003324 TPR repeat; Region: TPR_11; pfam13414 580332003325 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 580332003326 binding surface 580332003327 TPR motif; other site 580332003328 Protein of unknown function (DUF1260); Region: DUF1260; pfam06877 580332003329 Domain of unknown function (DUF4272); Region: DUF4272; pfam14094 580332003330 Predicted protein tyrosine phosphatase [General function prediction only]; Region: COG4551 580332003331 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 580332003332 active site 580332003333 Family of unknown function (DUF695); Region: DUF695; pfam05117 580332003334 Protein of unknown function (DUF1260); Region: DUF1260; pfam06877 580332003335 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 580332003336 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 580332003337 ligand binding site [chemical binding]; other site 580332003338 flexible hinge region; other site 580332003339 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 580332003340 non-specific DNA interactions [nucleotide binding]; other site 580332003341 DNA binding site [nucleotide binding] 580332003342 sequence specific DNA binding site [nucleotide binding]; other site 580332003343 putative cAMP binding site [chemical binding]; other site 580332003344 Hemerythrin-like domain; Region: Hr-like; cd12108 580332003345 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 580332003346 CPxP motif; other site 580332003347 Cytochrome c; Region: Cytochrom_C; pfam00034 580332003348 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 580332003349 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 580332003350 Low-spin heme binding site [chemical binding]; other site 580332003351 D-pathway; other site 580332003352 Putative water exit pathway; other site 580332003353 Binuclear center (active site) [active] 580332003354 K-pathway; other site 580332003355 Putative proton exit pathway; other site 580332003356 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 580332003357 Subunit I/III interface [polypeptide binding]; other site 580332003358 Prokaryotic Cytochrome C oxidase subunit IV; Region: COX4_pro; pfam03626 580332003359 MoxR-like ATPases [General function prediction only]; Region: COG0714 580332003360 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 580332003361 Walker A motif; other site 580332003362 ATP binding site [chemical binding]; other site 580332003363 Walker B motif; other site 580332003364 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 580332003365 ferredoxin-type protein, NapH/MauN family; Region: napH_; TIGR02163 580332003366 4Fe-4S binding domain; Region: Fer4_5; pfam12801 580332003367 Nitric oxide reductase activation protein [Inorganic ion transport and metabolism]; Region: NorD; COG4548 580332003368 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 580332003369 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 580332003370 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 580332003371 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 580332003372 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 580332003373 N-terminal plug; other site 580332003374 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 580332003375 ligand-binding site [chemical binding]; other site 580332003376 DsrC like protein; Region: DsrC; pfam04358 580332003377 NnrS protein; Region: NnrS; pfam05940 580332003378 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 580332003379 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 580332003380 HlyD family secretion protein; Region: HlyD_3; pfam13437 580332003381 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 580332003382 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 580332003383 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 580332003384 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 580332003385 Walker A/P-loop; other site 580332003386 ATP binding site [chemical binding]; other site 580332003387 Q-loop/lid; other site 580332003388 ABC transporter signature motif; other site 580332003389 Walker B; other site 580332003390 D-loop; other site 580332003391 H-loop/switch region; other site 580332003392 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 580332003393 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 580332003394 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; cl00257 580332003395 Domain of unknown function (DUF1840); Region: DUF1840; pfam08895 580332003396 thiopurine S-methyltransferase; Reviewed; Region: PRK13255 580332003397 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 580332003398 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 580332003399 Cyd operon protein YbgE (Cyd_oper_YbgE); Region: Cyd_oper_YbgE; cl11451 580332003400 Membrane bound YbgT-like protein; Region: YbgT_YccB; pfam08173 580332003401 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 580332003402 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 580332003403 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 580332003404 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 580332003405 PAS fold; Region: PAS_4; pfam08448 580332003406 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 580332003407 putative active site [active] 580332003408 heme pocket [chemical binding]; other site 580332003409 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 580332003410 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 580332003411 Walker A motif; other site 580332003412 ATP binding site [chemical binding]; other site 580332003413 Walker B motif; other site 580332003414 arginine finger; other site 580332003415 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 580332003416 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 580332003417 Methyltransferase domain; Region: Methyltransf_31; pfam13847 580332003418 S-adenosylmethionine binding site [chemical binding]; other site 580332003419 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; pfam06167 580332003420 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 580332003421 IHF - DNA interface [nucleotide binding]; other site 580332003422 IHF dimer interface [polypeptide binding]; other site 580332003423 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 580332003424 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 580332003425 dimer interface [polypeptide binding]; other site 580332003426 phosphorylation site [posttranslational modification] 580332003427 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 580332003428 ATP binding site [chemical binding]; other site 580332003429 Mg2+ binding site [ion binding]; other site 580332003430 G-X-G motif; other site 580332003431 Response regulator receiver domain; Region: Response_reg; pfam00072 580332003432 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 580332003433 active site 580332003434 phosphorylation site [posttranslational modification] 580332003435 intermolecular recognition site; other site 580332003436 dimerization interface [polypeptide binding]; other site 580332003437 Response regulator receiver domain; Region: Response_reg; pfam00072 580332003438 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 580332003439 active site 580332003440 phosphorylation site [posttranslational modification] 580332003441 intermolecular recognition site; other site 580332003442 dimerization interface [polypeptide binding]; other site 580332003443 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 580332003444 putative binding surface; other site 580332003445 active site 580332003446 PBP superfamily domain; Region: PBP_like_2; cl17296 580332003447 Response regulator receiver domain; Region: Response_reg; pfam00072 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 active site 580332003450 phosphorylation site [posttranslational modification] 580332003451 intermolecular recognition site; other site 580332003452 dimerization interface [polypeptide binding]; other site 580332003453 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 580332003454 Ankyrin repeats (many copies); Region: Ank_5; pfam13857 580332003455 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 580332003456 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_7; cd03862 580332003457 putative active site [active] 580332003458 Zn binding site [ion binding]; other site 580332003459 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 580332003460 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 580332003461 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 580332003462 dimerization interface [polypeptide binding]; other site 580332003463 substrate binding pocket [chemical binding]; other site 580332003464 EamA-like transporter family; Region: EamA; pfam00892 580332003465 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 580332003466 EamA-like transporter family; Region: EamA; pfam00892 580332003467 Biofilm formation and stress response factor; Region: BsmA; pfam10014 580332003468 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 580332003469 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 580332003470 dimer interface [polypeptide binding]; other site 580332003471 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332003472 catalytic residue [active] 580332003473 cysteine synthase B; Region: cysM; TIGR01138 580332003474 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 580332003475 dimer interface [polypeptide binding]; other site 580332003476 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332003477 catalytic residue [active] 580332003478 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 580332003479 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 580332003480 catalytic residues [active] 580332003481 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 580332003482 MG2 domain; Region: A2M_N; pfam01835 580332003483 Alpha-2-macroglobulin family; Region: A2M; pfam00207 580332003484 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 580332003485 surface patch; other site 580332003486 thioester region; other site 580332003487 specificity defining residues; other site 580332003488 penicillin-binding protein 1C; Region: PBP_1c; TIGR02073 580332003489 Transglycosylase; Region: Transgly; pfam00912 580332003490 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 580332003491 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 580332003492 AMIN domain; Region: AMIN; pfam11741 580332003493 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 580332003494 active site 580332003495 metal binding site [ion binding]; metal-binding site 580332003496 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 580332003497 epoxyqueuosine reductase; Region: TIGR00276 580332003498 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 580332003499 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 580332003500 PAS domain; Region: PAS_9; pfam13426 580332003501 putative active site [active] 580332003502 heme pocket [chemical binding]; other site 580332003503 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332003504 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332003505 metal binding site [ion binding]; metal-binding site 580332003506 active site 580332003507 I-site; other site 580332003508 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 580332003509 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 580332003510 GAF domain; Region: GAF; pfam01590 580332003511 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 580332003512 PAS domain; Region: PAS_9; pfam13426 580332003513 putative active site [active] 580332003514 heme pocket [chemical binding]; other site 580332003515 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332003516 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332003517 metal binding site [ion binding]; metal-binding site 580332003518 active site 580332003519 I-site; other site 580332003520 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 580332003521 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 580332003522 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 580332003523 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 580332003524 PAS domain; Region: PAS_9; pfam13426 580332003525 putative active site [active] 580332003526 heme pocket [chemical binding]; other site 580332003527 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 580332003528 cupin fold metalloprotein, WbuC family; Region: cupin_WbuC; TIGR04366 580332003529 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 580332003530 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 580332003531 acyl-activating enzyme (AAE) consensus motif; other site 580332003532 AMP binding site [chemical binding]; other site 580332003533 active site 580332003534 CoA binding site [chemical binding]; other site 580332003535 2-methylcitrate dehydratase; Provisional; Region: prpD; PRK09425 580332003536 2-methylcitrate dehydratase; Region: prpD; TIGR02330 580332003537 methylcitrate synthase; Provisional; Region: PRK12351 580332003538 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 580332003539 oxalacetate binding site [chemical binding]; other site 580332003540 citrylCoA binding site [chemical binding]; other site 580332003541 coenzyme A binding site [chemical binding]; other site 580332003542 catalytic triad [active] 580332003543 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 580332003544 tetramer interface [polypeptide binding]; other site 580332003545 active site 580332003546 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 580332003547 Mg2+/Mn2+ binding site [ion binding]; other site 580332003548 Transcriptional regulators [Transcription]; Region: GntR; COG1802 580332003549 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 580332003550 DNA-binding site [nucleotide binding]; DNA binding site 580332003551 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 580332003552 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 580332003553 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 580332003554 Walker A/P-loop; other site 580332003555 ATP binding site [chemical binding]; other site 580332003556 Q-loop/lid; other site 580332003557 ABC transporter signature motif; other site 580332003558 Walker B; other site 580332003559 D-loop; other site 580332003560 H-loop/switch region; other site 580332003561 TOBE domain; Region: TOBE_2; pfam08402 580332003562 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 580332003563 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 580332003564 dimer interface [polypeptide binding]; other site 580332003565 conserved gate region; other site 580332003566 putative PBP binding loops; other site 580332003567 ABC-ATPase subunit interface; other site 580332003568 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 580332003569 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 580332003570 dimer interface [polypeptide binding]; other site 580332003571 conserved gate region; other site 580332003572 ABC-ATPase subunit interface; other site 580332003573 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 580332003574 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 580332003575 AAA domain; Region: AAA_32; pfam13654 580332003576 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 580332003577 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 580332003578 S-adenosylmethionine binding site [chemical binding]; other site 580332003579 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; smart00831 580332003580 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 580332003581 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 580332003582 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 580332003583 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 580332003584 motif II; other site 580332003585 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 580332003586 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 580332003587 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 580332003588 ATP binding site [chemical binding]; other site 580332003589 Mg2+ binding site [ion binding]; other site 580332003590 G-X-G motif; other site 580332003591 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 580332003592 Response regulator receiver domain; Region: Response_reg; pfam00072 580332003593 active site 580332003594 phosphorylation site [posttranslational modification] 580332003595 intermolecular recognition site; other site 580332003596 dimerization interface [polypeptide binding]; other site 580332003597 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 580332003598 binding surface 580332003599 TPR motif; other site 580332003600 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 580332003601 TPR motif; other site 580332003602 binding surface 580332003603 transaldolase-like protein; Provisional; Region: PTZ00411 580332003604 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 580332003605 active site 580332003606 dimer interface [polypeptide binding]; other site 580332003607 catalytic residue [active] 580332003608 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 580332003609 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 580332003610 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 580332003611 ABC transporter; Region: ABC_tran_2; pfam12848 580332003612 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 580332003613 Protein of unknown function (DUF1566); Region: DUF1566; pfam07603 580332003614 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 580332003615 Sel1-like repeats; Region: SEL1; smart00671 580332003616 Sel1-like repeats; Region: SEL1; smart00671 580332003617 Sel1-like repeats; Region: SEL1; smart00671 580332003618 Sel1-like repeats; Region: SEL1; smart00671 580332003619 Sel1-like repeats; Region: SEL1; smart00671 580332003620 Sel1-like repeats; Region: SEL1; smart00671 580332003621 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 580332003622 active site residue [active] 580332003623 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 580332003624 active site residue [active] 580332003625 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 580332003626 Plasmid stabilisation system protein; Region: Plasmid_stabil; pfam05016 580332003627 Phospholipid methyltransferase; Region: PEMT; cl17370 580332003628 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 580332003629 apolar tunnel; other site 580332003630 heme binding site [chemical binding]; other site 580332003631 dimerization interface [polypeptide binding]; other site 580332003632 GTPase RsgA; Reviewed; Region: PRK01889 580332003633 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 580332003634 RNA binding site [nucleotide binding]; other site 580332003635 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 580332003636 GTPase/Zn-binding domain interface [polypeptide binding]; other site 580332003637 GTP/Mg2+ binding site [chemical binding]; other site 580332003638 G4 box; other site 580332003639 G5 box; other site 580332003640 G1 box; other site 580332003641 Switch I region; other site 580332003642 G2 box; other site 580332003643 G3 box; other site 580332003644 Switch II region; other site 580332003645 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 580332003646 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 580332003647 ligand binding site [chemical binding]; other site 580332003648 flexible hinge region; other site 580332003649 taurine ABC transporter, periplasmic binding protein; Region: taurine_ABC_bnd; TIGR01729 580332003650 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 580332003651 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 580332003652 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 580332003653 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 580332003654 Walker A/P-loop; other site 580332003655 ATP binding site [chemical binding]; other site 580332003656 Q-loop/lid; other site 580332003657 ABC transporter signature motif; other site 580332003658 Walker B; other site 580332003659 D-loop; other site 580332003660 H-loop/switch region; other site 580332003661 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 580332003662 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 580332003663 Coenzyme A binding pocket [chemical binding]; other site 580332003664 penicillin-binding protein 1B; Region: PBP_1b; TIGR02071 580332003665 Transglycosylase; Region: Transgly; pfam00912 580332003666 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 580332003667 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 580332003668 binding surface 580332003669 Tetratricopeptide repeat; Region: TPR_16; pfam13432 580332003670 TPR motif; other site 580332003671 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 580332003672 Pilin (bacterial filament); Region: Pilin; pfam00114 580332003673 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 580332003674 Ligand Binding Site [chemical binding]; other site 580332003675 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332003676 Zn2+ binding site [ion binding]; other site 580332003677 Mg2+ binding site [ion binding]; other site 580332003678 Etoposide-induced protein 2.4 (EI24); Region: EI24; pfam07264 580332003679 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 580332003680 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 580332003681 metal binding site [ion binding]; metal-binding site 580332003682 dimer interface [polypeptide binding]; other site 580332003683 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332003684 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332003685 metal binding site [ion binding]; metal-binding site 580332003686 active site 580332003687 I-site; other site 580332003688 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 580332003689 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332003690 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332003691 metal binding site [ion binding]; metal-binding site 580332003692 active site 580332003693 I-site; other site 580332003694 RecX family; Region: RecX; cl00936 580332003695 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332003696 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332003697 metal binding site [ion binding]; metal-binding site 580332003698 active site 580332003699 I-site; other site 580332003700 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 580332003701 Mechanosensitive ion channel; Region: MS_channel; pfam00924 580332003702 TraB family; Region: TraB; pfam01963 580332003703 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 580332003704 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 580332003705 ligand binding site [chemical binding]; other site 580332003706 flexible hinge region; other site 580332003707 BolA-like protein; Region: BolA; pfam01722 580332003708 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 580332003709 putative GSH binding site [chemical binding]; other site 580332003710 catalytic residues [active] 580332003711 YaeQ protein; Region: YaeQ; pfam07152 580332003712 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 580332003713 putative substrate translocation pore; other site 580332003714 Major Facilitator Superfamily; Region: MFS_1; pfam07690 580332003715 DsrC like protein; Region: DsrC; cl01101 580332003716 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 580332003717 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 580332003718 active site 580332003719 uracil binding [chemical binding]; other site 580332003720 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 580332003721 putative FMN binding site [chemical binding]; other site 580332003722 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 580332003723 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 580332003724 putative substrate translocation pore; other site 580332003725 asparagine synthase family amidotransferase; Region: trio_amidotrans; TIGR03104 580332003726 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 580332003727 active site 580332003728 dimer interface [polypeptide binding]; other site 580332003729 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 580332003730 Ligand Binding Site [chemical binding]; other site 580332003731 Molecular Tunnel; other site 580332003732 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 580332003733 EamA-like transporter family; Region: EamA; pfam00892 580332003734 EamA-like transporter family; Region: EamA; pfam00892 580332003735 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 580332003736 dimerization interface [polypeptide binding]; other site 580332003737 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332003738 dimer interface [polypeptide binding]; other site 580332003739 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 580332003740 putative CheW interface [polypeptide binding]; other site 580332003741 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 580332003742 Uncharacterized conserved protein [Function unknown]; Region: COG4121 580332003743 Methyltransferase domain; Region: Methyltransf_32; pfam13679 580332003744 Methyltransferase domain; Region: Methyltransf_31; pfam13847 580332003745 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 580332003746 apolar tunnel; other site 580332003747 heme binding site [chemical binding]; other site 580332003748 dimerization interface [polypeptide binding]; other site 580332003749 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 580332003750 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 580332003751 GTP/Mg2+ binding site [chemical binding]; other site 580332003752 G4 box; other site 580332003753 G5 box; other site 580332003754 G1 box; other site 580332003755 Switch I region; other site 580332003756 G2 box; other site 580332003757 G3 box; other site 580332003758 Switch II region; other site 580332003759 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 580332003760 Fumarase C-terminus; Region: Fumerase_C; pfam05683 580332003761 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14969 580332003762 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 580332003763 Walker A motif; other site 580332003764 ATP binding site [chemical binding]; other site 580332003765 Walker B motif; other site 580332003766 arginine finger; other site 580332003767 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 580332003768 hypothetical protein; Validated; Region: PRK00153 580332003769 recombination protein RecR; Reviewed; Region: recR; PRK00076 580332003770 RecR protein; Region: RecR; pfam02132 580332003771 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 580332003772 putative active site [active] 580332003773 putative metal-binding site [ion binding]; other site 580332003774 tetramer interface [polypeptide binding]; other site 580332003775 23S rRNA pseudouridylate synthase B; Provisional; Region: PRK10700 580332003776 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 580332003777 RNA binding surface [nucleotide binding]; other site 580332003778 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 580332003779 active site 580332003780 cyclase homology domain; Region: CHD; cd07302 580332003781 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 580332003782 nucleotidyl binding site; other site 580332003783 metal binding site [ion binding]; metal-binding site 580332003784 dimer interface [polypeptide binding]; other site 580332003785 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 580332003786 binding surface 580332003787 TPR motif; other site 580332003788 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 580332003789 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 580332003790 active site 580332003791 ATP binding site [chemical binding]; other site 580332003792 substrate binding site [chemical binding]; other site 580332003793 activation loop (A-loop); other site 580332003794 L-aspartate oxidase; Provisional; Region: PRK09077 580332003795 L-aspartate oxidase; Provisional; Region: PRK06175 580332003796 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 580332003797 RNA polymerase sigma factor RpoE; Region: RpoE_Sigma70; TIGR02939 580332003798 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 580332003799 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 580332003800 DNA binding residues [nucleotide binding] 580332003801 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 580332003802 Negative regulator of sigma E activity [Signal transduction mechanisms]; Region: RseB; COG3026 580332003803 anti-sigma E factor; Provisional; Region: rseB; PRK09455 580332003804 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; pfam04246 580332003805 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 580332003806 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 580332003807 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 580332003808 protein binding site [polypeptide binding]; other site 580332003809 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 580332003810 protein binding site [polypeptide binding]; other site 580332003811 GTP-binding protein LepA; Provisional; Region: PRK05433 580332003812 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 580332003813 G1 box; other site 580332003814 putative GEF interaction site [polypeptide binding]; other site 580332003815 GTP/Mg2+ binding site [chemical binding]; other site 580332003816 Switch I region; other site 580332003817 G2 box; other site 580332003818 G3 box; other site 580332003819 Switch II region; other site 580332003820 G4 box; other site 580332003821 G5 box; other site 580332003822 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 580332003823 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 580332003824 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 580332003825 signal peptidase I; Provisional; Region: PRK10861 580332003826 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 580332003827 Catalytic site [active] 580332003828 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 580332003829 ribonuclease III; Reviewed; Region: rnc; PRK00102 580332003830 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 580332003831 dimerization interface [polypeptide binding]; other site 580332003832 active site 580332003833 metal binding site [ion binding]; metal-binding site 580332003834 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 580332003835 dsRNA binding site [nucleotide binding]; other site 580332003836 GTPase Era; Reviewed; Region: era; PRK00089 580332003837 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 580332003838 G1 box; other site 580332003839 GTP/Mg2+ binding site [chemical binding]; other site 580332003840 Switch I region; other site 580332003841 G2 box; other site 580332003842 Switch II region; other site 580332003843 G3 box; other site 580332003844 G4 box; other site 580332003845 G5 box; other site 580332003846 KH domain; Region: KH_2; pfam07650 580332003847 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 580332003848 Recombination protein O N terminal; Region: RecO_N; pfam11967 580332003849 Recombination protein O C terminal; Region: RecO_C; pfam02565 580332003850 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in...; Region: PNPsynthase; cd00003 580332003851 active site 580332003852 hydrophilic channel; other site 580332003853 dimerization interface [polypeptide binding]; other site 580332003854 catalytic residues [active] 580332003855 active site lid [active] 580332003856 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 580332003857 beta-hexosaminidase; Provisional; Region: PRK05337 580332003858 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 580332003859 enoyl-CoA hydratase; Validated; Region: PRK08788 580332003860 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 580332003861 substrate binding site [chemical binding]; other site 580332003862 oxyanion hole (OAH) forming residues; other site 580332003863 trimer interface [polypeptide binding]; other site 580332003864 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 580332003865 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 580332003866 dimer interface [polypeptide binding]; other site 580332003867 phosphorylation site [posttranslational modification] 580332003868 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 580332003869 ATP binding site [chemical binding]; other site 580332003870 Mg2+ binding site [ion binding]; other site 580332003871 G-X-G motif; other site 580332003872 Response regulator receiver domain; Region: Response_reg; pfam00072 580332003873 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 580332003874 active site 580332003875 phosphorylation site [posttranslational modification] 580332003876 intermolecular recognition site; other site 580332003877 dimerization interface [polypeptide binding]; other site 580332003878 FOG: HPt domain [Signal transduction mechanisms]; Region: ArcB; COG2198 580332003879 putative binding surface; other site 580332003880 active site 580332003881 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 580332003882 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 580332003883 active site 580332003884 phosphorylation site [posttranslational modification] 580332003885 intermolecular recognition site; other site 580332003886 dimerization interface [polypeptide binding]; other site 580332003887 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332003888 Zn2+ binding site [ion binding]; other site 580332003889 Mg2+ binding site [ion binding]; other site 580332003890 ZipA, C-terminal domain (FtsZ-binding); Region: ZipA_C; smart00771 580332003891 FtsZ protein binding site [polypeptide binding]; other site 580332003892 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 580332003893 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 580332003894 nucleotide binding pocket [chemical binding]; other site 580332003895 K-X-D-G motif; other site 580332003896 catalytic site [active] 580332003897 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 580332003898 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 580332003899 Helix-hairpin-helix motif; Region: HHH; pfam00633 580332003900 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 580332003901 Dimer interface [polypeptide binding]; other site 580332003902 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 580332003903 active site 580332003904 tetramer interface; other site 580332003905 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 580332003906 active site 580332003907 5'-methylthioadenosine phosphorylase; Validated; Region: PRK09136 580332003908 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 580332003909 active site 580332003910 catalytic residues [active] 580332003911 metal binding site [ion binding]; metal-binding site 580332003912 Ion channel; Region: Ion_trans_2; pfam07885 580332003913 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 580332003914 TrkA-N domain; Region: TrkA_N; pfam02254 580332003915 TrkA-C domain; Region: TrkA_C; pfam02080 580332003916 Response regulator receiver domain; Region: Response_reg; pfam00072 580332003917 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 580332003918 active site 580332003919 phosphorylation site [posttranslational modification] 580332003920 intermolecular recognition site; other site 580332003921 dimerization interface [polypeptide binding]; other site 580332003922 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332003923 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332003924 metal binding site [ion binding]; metal-binding site 580332003925 active site 580332003926 I-site; other site 580332003927 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 580332003928 Response regulator receiver domain; Region: Response_reg; pfam00072 580332003929 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 580332003930 active site 580332003931 phosphorylation site [posttranslational modification] 580332003932 intermolecular recognition site; other site 580332003933 dimerization interface [polypeptide binding]; other site 580332003934 HDOD domain; Region: HDOD; pfam08668 580332003935 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332003936 Zn2+ binding site [ion binding]; other site 580332003937 Mg2+ binding site [ion binding]; other site 580332003938 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 580332003939 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 580332003940 active site 580332003941 phosphorylation site [posttranslational modification] 580332003942 intermolecular recognition site; other site 580332003943 dimerization interface [polypeptide binding]; other site 580332003944 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332003945 Zn2+ binding site [ion binding]; other site 580332003946 Mg2+ binding site [ion binding]; other site 580332003947 Hemerythrin; Region: Hemerythrin; cd12107 580332003948 Fe binding site [ion binding]; other site 580332003949 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 580332003950 ATP binding site [chemical binding]; other site 580332003951 Mg2+ binding site [ion binding]; other site 580332003952 G-X-G motif; other site 580332003953 HPP family; Region: HPP; pfam04982 580332003954 FOG: CBS domain [General function prediction only]; Region: COG0517 580332003955 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cd02205 580332003956 aconitate hydratase; Validated; Region: PRK09277 580332003957 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 580332003958 substrate binding site [chemical binding]; other site 580332003959 ligand binding site [chemical binding]; other site 580332003960 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 580332003961 substrate binding site [chemical binding]; other site 580332003962 CHASE domain; Region: CHASE; pfam03924 580332003963 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 580332003964 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332003965 Zn2+ binding site [ion binding]; other site 580332003966 Mg2+ binding site [ion binding]; other site 580332003967 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 580332003968 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 580332003969 putative substrate translocation pore; other site 580332003970 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 580332003971 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 580332003972 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 580332003973 HlyD family secretion protein; Region: HlyD_3; pfam13437 580332003974 Winged helix DNA-binding domain; Region: HTH_27; pfam13463 580332003975 tRNA 2-selenouridine synthase; Provisional; Region: PRK11784 580332003976 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 580332003977 active site residue [active] 580332003978 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 580332003979 Walker A/P-loop; other site 580332003980 ATP binding site [chemical binding]; other site 580332003981 selenophosphate synthetase; Provisional; Region: PRK00943 580332003982 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 580332003983 dimerization interface [polypeptide binding]; other site 580332003984 putative ATP binding site [chemical binding]; other site 580332003985 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 580332003986 Ankyrin repeat; Region: Ank; pfam00023 580332003987 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 580332003988 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 580332003989 Ankyrin repeats (many copies); Region: Ank_5; pfam13857 580332003990 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332003991 Zn2+ binding site [ion binding]; other site 580332003992 Mg2+ binding site [ion binding]; other site 580332003993 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 580332003994 heme-binding site [chemical binding]; other site 580332003995 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332003996 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332003997 metal binding site [ion binding]; metal-binding site 580332003998 active site 580332003999 I-site; other site 580332004000 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 580332004001 CRISPR/Cas system-associated DinG family helicase Csf4; Region: Csf4_U; cl17460 580332004002 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 580332004003 Protein of unknown function (DUF2721); Region: DUF2721; pfam11026 580332004004 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 580332004005 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; pfam02639 580332004006 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 580332004007 Major Facilitator Superfamily; Region: MFS_1; pfam07690 580332004008 putative substrate translocation pore; other site 580332004009 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 580332004010 Domain of unknown function (DUF1924); Region: DUF1924; pfam09086 580332004011 Dihaem cytochrome c; Region: DHC; pfam09626 580332004012 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 580332004013 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 580332004014 dimerization interface [polypeptide binding]; other site 580332004015 domain crossover interface; other site 580332004016 redox-dependent activation switch; other site 580332004017 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 580332004018 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 580332004019 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 580332004020 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 580332004021 putative active site [active] 580332004022 heme pocket [chemical binding]; other site 580332004023 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 580332004024 putative active site [active] 580332004025 heme pocket [chemical binding]; other site 580332004026 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 580332004027 PAS fold; Region: PAS_4; pfam08448 580332004028 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 580332004029 putative active site [active] 580332004030 heme pocket [chemical binding]; other site 580332004031 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 580332004032 dimer interface [polypeptide binding]; other site 580332004033 phosphorylation site [posttranslational modification] 580332004034 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 580332004035 ATP binding site [chemical binding]; other site 580332004036 Mg2+ binding site [ion binding]; other site 580332004037 G-X-G motif; other site 580332004038 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 580332004039 dimer interface [polypeptide binding]; other site 580332004040 phosphorylation site [posttranslational modification] 580332004041 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 580332004042 ATP binding site [chemical binding]; other site 580332004043 Mg2+ binding site [ion binding]; other site 580332004044 G-X-G motif; other site 580332004045 Response regulator receiver domain; Region: Response_reg; pfam00072 580332004046 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 580332004047 active site 580332004048 phosphorylation site [posttranslational modification] 580332004049 intermolecular recognition site; other site 580332004050 dimerization interface [polypeptide binding]; other site 580332004051 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 580332004052 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 580332004053 active site 580332004054 phosphorylation site [posttranslational modification] 580332004055 intermolecular recognition site; other site 580332004056 dimerization interface [polypeptide binding]; other site 580332004057 PAS domain S-box; Region: sensory_box; TIGR00229 580332004058 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 580332004059 putative active site [active] 580332004060 heme pocket [chemical binding]; other site 580332004061 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332004062 Zn2+ binding site [ion binding]; other site 580332004063 Mg2+ binding site [ion binding]; other site 580332004064 DNA repair protein RadA; Provisional; Region: PRK11823 580332004065 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 580332004066 Walker A motif/ATP binding site; other site 580332004067 ATP binding site [chemical binding]; other site 580332004068 Walker B motif; other site 580332004069 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 580332004070 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 580332004071 Protein of unknown function, DUF599; Region: DUF599; cl01575 580332004072 Uncharacterized membrane-anchored protein conserved in bacteria [Function unknown]; Region: COG4705 580332004073 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 580332004074 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 580332004075 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 580332004076 2-haloalkanoic acid dehalogenase, type II; Region: HAD_type_II; TIGR01428 580332004077 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 580332004078 motif II; other site 580332004079 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 580332004080 EamA-like transporter family; Region: EamA; pfam00892 580332004081 EamA-like transporter family; Region: EamA; pfam00892 580332004082 ATPase, P-type (transporting), HAD superfamily, subfamily IC; Region: ATPase_P-type; TIGR01494 580332004083 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 580332004084 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 580332004085 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 580332004086 motif II; other site 580332004087 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 580332004088 Cytochrome c; Region: Cytochrom_C; cl11414 580332004089 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 580332004090 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 580332004091 dimer interface [polypeptide binding]; other site 580332004092 active site 580332004093 metal binding site [ion binding]; metal-binding site 580332004094 glutathione binding site [chemical binding]; other site 580332004095 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 580332004096 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 580332004097 active site 580332004098 catalytic tetrad [active] 580332004099 Putative thioesterase (yiiD_Cterm); Region: YiiD_Cterm; pfam09500 580332004100 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14189 580332004101 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 580332004102 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 580332004103 homodimer interface [polypeptide binding]; other site 580332004104 NADP binding site [chemical binding]; other site 580332004105 substrate binding site [chemical binding]; other site 580332004106 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 580332004107 dimer interface [polypeptide binding]; other site 580332004108 substrate binding site [chemical binding]; other site 580332004109 metal binding sites [ion binding]; metal-binding site 580332004110 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 580332004111 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 580332004112 FMN binding site [chemical binding]; other site 580332004113 active site 580332004114 substrate binding site [chemical binding]; other site 580332004115 catalytic residue [active] 580332004116 Uncharacterized conserved protein [Function unknown]; Region: COG2353 580332004117 YceI-like domain; Region: YceI; smart00867 580332004118 Pirin-related protein [General function prediction only]; Region: COG1741 580332004119 Pirin; Region: Pirin; pfam02678 580332004120 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 580332004121 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 580332004122 Transcriptional regulator [Transcription]; Region: LysR; COG0583 580332004123 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 580332004124 putative effector binding pocket; other site 580332004125 dimerization interface [polypeptide binding]; other site 580332004126 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 580332004127 TPR motif; other site 580332004128 TPR repeat; Region: TPR_11; pfam13414 580332004129 binding surface 580332004130 Uncharacterized conserved protein [Function unknown]; Region: COG1262 580332004131 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 580332004132 Cytochrome c; Region: Cytochrom_C; cl11414 580332004133 H(+) -translocating inorganic pyrophosphatase; Region: PLN02255; cl11452 580332004134 membrane-bound proton-translocating pyrophosphatase; Validated; Region: hppA; PRK00733 580332004135 6-phosphofructokinase; Provisional; Region: PRK14072 580332004136 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 580332004137 active site 580332004138 ADP/pyrophosphate binding site [chemical binding]; other site 580332004139 dimerization interface [polypeptide binding]; other site 580332004140 allosteric effector site; other site 580332004141 fructose-1,6-bisphosphate binding site; other site 580332004142 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 580332004143 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 580332004144 Domain of unknown function (DUF336); Region: DUF336; cl01249 580332004145 adenylate kinase; Reviewed; Region: adk; PRK00279 580332004146 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 580332004147 AMP-binding site [chemical binding]; other site 580332004148 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 580332004149 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 580332004150 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 580332004151 Ligand binding site; other site 580332004152 oligomer interface; other site 580332004153 Uncharacterized conserved protein [Function unknown]; Region: COG2835 580332004154 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 580332004155 tetraacyldisaccharide 4'-kinase; Region: lpxK; TIGR00682 580332004156 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 580332004157 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 580332004158 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 580332004159 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 580332004160 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 580332004161 generic binding surface II; other site 580332004162 generic binding surface I; other site 580332004163 ParA/MinD ATPase like; Region: ParA; pfam10609 580332004164 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 580332004165 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 580332004166 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnE; Provisional; Region: PRK15051 580332004167 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 580332004168 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 580332004169 inhibitor-cofactor binding pocket; inhibition site 580332004170 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332004171 catalytic residue [active] 580332004172 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332004173 dimer interface [polypeptide binding]; other site 580332004174 putative CheW interface [polypeptide binding]; other site 580332004175 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 580332004176 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 580332004177 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 580332004178 Ligand binding site; other site 580332004179 Putative Catalytic site; other site 580332004180 DXD motif; other site 580332004181 putative formyltransferase; Provisional; Region: PRK06988 580332004182 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 580332004183 active site 580332004184 substrate binding site [chemical binding]; other site 580332004185 cosubstrate binding site; other site 580332004186 catalytic site [active] 580332004187 Carboxy-terminal domain of Formyltransferase and similar domains; Region: FMT_C_like; cl14785 580332004188 NAD-dependent epimerase/dehydratase family protein; Provisional; Region: PRK11908 580332004189 Arna decarboxylase_like, extended (e) SDRs; Region: Arna_like_SDR_e; cd05257 580332004190 NAD binding site [chemical binding]; other site 580332004191 substrate binding site [chemical binding]; other site 580332004192 active site 580332004193 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD; Provisional; Region: PRK15394 580332004194 Catalytic domain of Escherichia coli 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD and other bacterial homologs; Region: CE4_ArnD; cd10939 580332004195 putative active site [active] 580332004196 putative catalytic site [active] 580332004197 putative Zn binding site [ion binding]; other site 580332004198 HDOD domain; Region: HDOD; pfam08668 580332004199 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 580332004200 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 580332004201 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 580332004202 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 580332004203 Domain of unknown function DUF302; Region: DUF302; pfam03625 580332004204 Macro domain, Appr-1"-pase_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly...; Region: Macro_Appr_pase_like; cd02908 580332004205 putative ADP-ribose binding site [chemical binding]; other site 580332004206 putative active site [active] 580332004207 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 580332004208 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 580332004209 metabolite-proton symporter; Region: 2A0106; TIGR00883 580332004210 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 580332004211 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 580332004212 ATP binding site [chemical binding]; other site 580332004213 Mg2+ binding site [ion binding]; other site 580332004214 G-X-G motif; other site 580332004215 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 580332004216 ATP binding site [chemical binding]; other site 580332004217 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 580332004218 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 580332004219 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 580332004220 N-terminal plug; other site 580332004221 ligand-binding site [chemical binding]; other site 580332004222 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 580332004223 4Fe-4S binding domain; Region: Fer4_5; pfam12801 580332004224 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 580332004225 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 580332004226 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 580332004227 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 580332004228 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 580332004229 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 580332004230 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 580332004231 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 580332004232 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 580332004233 ligand binding site [chemical binding]; other site 580332004234 homodimer interface [polypeptide binding]; other site 580332004235 NAD(P) binding site [chemical binding]; other site 580332004236 trimer interface B [polypeptide binding]; other site 580332004237 trimer interface A [polypeptide binding]; other site 580332004238 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 580332004239 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 580332004240 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 580332004241 MASE1; Region: MASE1; pfam05231 580332004242 PAS fold; Region: PAS_3; pfam08447 580332004243 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 580332004244 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 580332004245 PAS domain; Region: PAS_9; pfam13426 580332004246 putative active site [active] 580332004247 heme pocket [chemical binding]; other site 580332004248 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332004249 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332004250 metal binding site [ion binding]; metal-binding site 580332004251 active site 580332004252 I-site; other site 580332004253 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 580332004254 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 580332004255 DNA internalization-related competence protein ComEC/Rec2; Region: ComEC_Rec2; TIGR00361 580332004256 Competence protein; Region: Competence; pfam03772 580332004257 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 580332004258 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; pfam09835 580332004259 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 580332004260 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 580332004261 Walker A/P-loop; other site 580332004262 ATP binding site [chemical binding]; other site 580332004263 Q-loop/lid; other site 580332004264 ABC transporter signature motif; other site 580332004265 Walker B; other site 580332004266 D-loop; other site 580332004267 H-loop/switch region; other site 580332004268 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 580332004269 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 580332004270 FtsX-like permease family; Region: FtsX; pfam02687 580332004271 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4255 580332004272 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 580332004273 Mechanosensitive ion channel; Region: MS_channel; pfam00924 580332004274 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 580332004275 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 580332004276 ligand binding site [chemical binding]; other site 580332004277 flexible hinge region; other site 580332004278 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 580332004279 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 580332004280 tRNA(Ile)-lysidine synthetase; Provisional; Region: tilS; PRK10660 580332004281 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 580332004282 Ligand Binding Site [chemical binding]; other site 580332004283 TilS substrate binding domain; Region: TilS; pfam09179 580332004284 TilS substrate C-terminal domain; Region: TilS_C; pfam11734 580332004285 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 580332004286 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 580332004287 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 580332004288 DctM-like transporters; Region: DctM; pfam06808 580332004289 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 580332004290 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 580332004291 active site 580332004292 multimer interface [polypeptide binding]; other site 580332004293 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 580332004294 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 580332004295 FeS/SAM binding site; other site 580332004296 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 580332004297 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 580332004298 binding surface 580332004299 TPR motif; other site 580332004300 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 580332004301 binding surface 580332004302 TPR motif; other site 580332004303 Helix-turn-helix domain; Region: HTH_25; pfam13413 580332004304 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 580332004305 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 580332004306 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 580332004307 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 580332004308 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 580332004309 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 580332004310 dimer interface [polypeptide binding]; other site 580332004311 motif 1; other site 580332004312 active site 580332004313 motif 2; other site 580332004314 motif 3; other site 580332004315 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 580332004316 anticodon binding site; other site 580332004317 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 580332004318 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 580332004319 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 580332004320 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 580332004321 Trp docking motif [polypeptide binding]; other site 580332004322 active site 580332004323 GTP-binding protein Der; Reviewed; Region: PRK00093 580332004324 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 580332004325 G1 box; other site 580332004326 GTP/Mg2+ binding site [chemical binding]; other site 580332004327 Switch I region; other site 580332004328 G2 box; other site 580332004329 Switch II region; other site 580332004330 G3 box; other site 580332004331 G4 box; other site 580332004332 G5 box; other site 580332004333 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 580332004334 G1 box; other site 580332004335 GTP/Mg2+ binding site [chemical binding]; other site 580332004336 Switch I region; other site 580332004337 G2 box; other site 580332004338 G3 box; other site 580332004339 Switch II region; other site 580332004340 G4 box; other site 580332004341 G5 box; other site 580332004342 bacterial Hfq-like; Region: Hfq; cd01716 580332004343 hexamer interface [polypeptide binding]; other site 580332004344 Sm1 motif; other site 580332004345 RNA binding site [nucleotide binding]; other site 580332004346 Sm2 motif; other site 580332004347 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 580332004348 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 580332004349 HflX GTPase family; Region: HflX; cd01878 580332004350 G1 box; other site 580332004351 GTP/Mg2+ binding site [chemical binding]; other site 580332004352 Switch I region; other site 580332004353 G2 box; other site 580332004354 G3 box; other site 580332004355 Switch II region; other site 580332004356 G4 box; other site 580332004357 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 580332004358 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 580332004359 HflK protein; Region: hflK; TIGR01933 580332004360 HflC protein; Region: hflC; TIGR01932 580332004361 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 580332004362 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; pfam09838 580332004363 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: PRK12421 580332004364 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 580332004365 dimer interface [polypeptide binding]; other site 580332004366 motif 1; other site 580332004367 active site 580332004368 motif 2; other site 580332004369 motif 3; other site 580332004370 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 580332004371 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 580332004372 GDP-binding site [chemical binding]; other site 580332004373 ACT binding site; other site 580332004374 IMP binding site; other site 580332004375 ribonuclease R; Region: RNase_R; TIGR02063 580332004376 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 580332004377 RNB domain; Region: RNB; pfam00773 580332004378 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase...; Region: S1_RNase_R; cd04471 580332004379 RNA binding site [nucleotide binding]; other site 580332004380 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 580332004381 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 580332004382 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 580332004383 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 580332004384 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 580332004385 P-loop; other site 580332004386 Magnesium ion binding site [ion binding]; other site 580332004387 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 580332004388 Magnesium ion binding site [ion binding]; other site 580332004389 Protein of unknown function (DUF1161); Region: DUF1161; pfam06649 580332004390 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 580332004391 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 580332004392 ligand binding site [chemical binding]; other site 580332004393 Protein of unknown function (DUF3025); Region: DUF3025; pfam11227 580332004394 MltA-interacting protein MipA; Region: MipA; cl01504 580332004395 squalene-associated FAD-dependent desaturase; Region: HpnE; TIGR03467 580332004396 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 580332004397 active site lid residues [active] 580332004398 substrate binding pocket [chemical binding]; other site 580332004399 catalytic residues [active] 580332004400 substrate-Mg2+ binding site; other site 580332004401 aspartate-rich region 1; other site 580332004402 aspartate-rich region 2; other site 580332004403 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 580332004404 active site lid residues [active] 580332004405 substrate binding pocket [chemical binding]; other site 580332004406 catalytic residues [active] 580332004407 substrate-Mg2+ binding site; other site 580332004408 aspartate-rich region 1; other site 580332004409 aspartate-rich region 2; other site 580332004410 HemK family putative methylases; Region: hemK_fam; TIGR00536 580332004411 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 580332004412 S-adenosylmethionine binding site [chemical binding]; other site 580332004413 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 580332004414 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 580332004415 metal binding site [ion binding]; metal-binding site 580332004416 dimer interface [polypeptide binding]; other site 580332004417 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 580332004418 ArsC family; Region: ArsC; pfam03960 580332004419 putative catalytic residues [active] 580332004420 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 580332004421 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 580332004422 Walker A motif; other site 580332004423 ATP binding site [chemical binding]; other site 580332004424 Walker B motif; other site 580332004425 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 580332004426 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 580332004427 active site 580332004428 substrate binding site [chemical binding]; other site 580332004429 trimer interface [polypeptide binding]; other site 580332004430 CoA binding site [chemical binding]; other site 580332004431 succinyldiaminopimelate transaminase; Provisional; Region: PRK09147 580332004432 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 580332004433 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332004434 homodimer interface [polypeptide binding]; other site 580332004435 catalytic residue [active] 580332004436 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 580332004437 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332004438 Zn2+ binding site [ion binding]; other site 580332004439 Mg2+ binding site [ion binding]; other site 580332004440 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 580332004441 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 580332004442 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 580332004443 binding surface 580332004444 TPR motif; other site 580332004445 fructose-bisphosphate aldolase; Provisional; Region: PRK09250 580332004446 Class I fructose-1,6-bisphosphate (FBP) aldolases of the archaeal type (DhnA homologs); Region: DhnA; cd00958 580332004447 putative active site; other site 580332004448 catalytic residue [active] 580332004449 Bacterial Ig-like domain (group 2); Region: Big_2; cl02708 580332004450 Galactose oxidase, central domain; Region: Kelch_4; pfam13418 580332004451 Galactose oxidase, central domain; Region: Kelch_3; cl02701 580332004452 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 580332004453 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332004454 ATP-grasp domain; Region: ATP-grasp; pfam02222 580332004455 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 580332004456 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 580332004457 dimer interface [polypeptide binding]; other site 580332004458 putative metal binding site [ion binding]; other site 580332004459 Predicted ATPase [General function prediction only]; Region: COG1485 580332004460 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 580332004461 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 580332004462 substrate binding pocket [chemical binding]; other site 580332004463 membrane-bound complex binding site; other site 580332004464 hinge residues; other site 580332004465 PAS fold; Region: PAS_4; pfam08448 580332004466 GAF domain; Region: GAF_2; pfam13185 580332004467 GAF domain; Region: GAF; pfam01590 580332004468 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 580332004469 PAS domain; Region: PAS_9; pfam13426 580332004470 putative active site [active] 580332004471 heme pocket [chemical binding]; other site 580332004472 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332004473 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332004474 metal binding site [ion binding]; metal-binding site 580332004475 active site 580332004476 I-site; other site 580332004477 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 580332004478 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 580332004479 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 580332004480 active site 580332004481 catalytic tetrad [active] 580332004482 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 580332004483 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 580332004484 putative active site [active] 580332004485 metal binding site [ion binding]; metal-binding site 580332004486 FIST N domain; Region: FIST; pfam08495 580332004487 FIST C domain; Region: FIST_C; pfam10442 580332004488 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 580332004489 PAS domain; Region: PAS_9; pfam13426 580332004490 putative active site [active] 580332004491 heme pocket [chemical binding]; other site 580332004492 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332004493 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332004494 metal binding site [ion binding]; metal-binding site 580332004495 active site 580332004496 I-site; other site 580332004497 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 580332004498 7-cyano-7-deazaguanine reductase; Provisional; Region: PRK13258 580332004499 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 580332004500 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 580332004501 Walker A/P-loop; other site 580332004502 ATP binding site [chemical binding]; other site 580332004503 Q-loop/lid; other site 580332004504 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; pfam06470 580332004505 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 580332004506 ABC transporter signature motif; other site 580332004507 Walker B; other site 580332004508 D-loop; other site 580332004509 H-loop/switch region; other site 580332004510 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 580332004511 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 580332004512 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 580332004513 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a...; Region: CBS_pair_IMPDH; cd04601 580332004514 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of...; Region: IMPDH; cd00381 580332004515 active site 580332004516 GMP synthase; Reviewed; Region: guaA; PRK00074 580332004517 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 580332004518 AMP/PPi binding site [chemical binding]; other site 580332004519 candidate oxyanion hole; other site 580332004520 catalytic triad [active] 580332004521 potential glutamine specificity residues [chemical binding]; other site 580332004522 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 580332004523 ATP Binding subdomain [chemical binding]; other site 580332004524 Ligand Binding sites [chemical binding]; other site 580332004525 Dimerization subdomain; other site 580332004526 MASE1; Region: MASE1; pfam05231 580332004527 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 580332004528 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 580332004529 putative active site [active] 580332004530 heme pocket [chemical binding]; other site 580332004531 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 580332004532 putative active site [active] 580332004533 heme pocket [chemical binding]; other site 580332004534 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332004535 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332004536 metal binding site [ion binding]; metal-binding site 580332004537 active site 580332004538 I-site; other site 580332004539 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 580332004540 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 580332004541 Interdomain contacts; other site 580332004542 Cytokine receptor motif; other site 580332004543 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 580332004544 Interdomain contacts; other site 580332004545 Cytokine receptor motif; other site 580332004546 Autotransporter beta-domain; Region: Autotransporter; pfam03797 580332004547 Protein of unknown function (DUF3281); Region: DUF3281; pfam11685 580332004548 FecR protein; Region: FecR; pfam04773 580332004549 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 580332004550 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 580332004551 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 580332004552 metal-binding site [ion binding] 580332004553 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 580332004554 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 580332004555 motif II; other site 580332004556 5'-methylthioadenosine phosphorylase; Provisional; Region: PRK08931 580332004557 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 580332004558 L-ribulose-5-phosphate 4-epimerase; Reviewed; Region: araD; PRK08193 580332004559 intersubunit interface [polypeptide binding]; other site 580332004560 active site 580332004561 Zn2+ binding site [ion binding]; other site 580332004562 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 580332004563 active site 580332004564 methylthioribose-1-phosphate isomerase; Reviewed; Region: mtnA; PRK05720 580332004565 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]; Region: COG0182 580332004566 ribosome maturation protein RimP; Reviewed; Region: PRK00092 580332004567 Sm and related proteins; Region: Sm_like; cl00259 580332004568 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 580332004569 putative oligomer interface [polypeptide binding]; other site 580332004570 putative RNA binding site [nucleotide binding]; other site 580332004571 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 580332004572 NusA N-terminal domain; Region: NusA_N; pfam08529 580332004573 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 580332004574 RNA binding site [nucleotide binding]; other site 580332004575 homodimer interface [polypeptide binding]; other site 580332004576 NusA-like KH domain; Region: KH_5; pfam13184 580332004577 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 580332004578 G-X-X-G motif; other site 580332004579 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 580332004580 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 580332004581 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 580332004582 translation initiation factor IF-2; Region: IF-2; TIGR00487 580332004583 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 580332004584 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 580332004585 G1 box; other site 580332004586 putative GEF interaction site [polypeptide binding]; other site 580332004587 GTP/Mg2+ binding site [chemical binding]; other site 580332004588 Switch I region; other site 580332004589 G2 box; other site 580332004590 G3 box; other site 580332004591 Switch II region; other site 580332004592 G4 box; other site 580332004593 G5 box; other site 580332004594 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 580332004595 Translation-initiation factor 2; Region: IF-2; pfam11987 580332004596 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 580332004597 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 580332004598 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 580332004599 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 580332004600 RNA binding site [nucleotide binding]; other site 580332004601 active site 580332004602 Pseudouridine synthase II TruB, C-terminal; Region: TruB-C_2; pfam09157 580332004603 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 580332004604 16S/18S rRNA binding site [nucleotide binding]; other site 580332004605 S13e-L30e interaction site [polypeptide binding]; other site 580332004606 25S rRNA binding site [nucleotide binding]; other site 580332004607 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 580332004608 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 580332004609 RNase E interface [polypeptide binding]; other site 580332004610 trimer interface [polypeptide binding]; other site 580332004611 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 580332004612 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 580332004613 RNase E interface [polypeptide binding]; other site 580332004614 trimer interface [polypeptide binding]; other site 580332004615 active site 580332004616 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 580332004617 putative nucleic acid binding region [nucleotide binding]; other site 580332004618 G-X-X-G motif; other site 580332004619 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 580332004620 RNA binding site [nucleotide binding]; other site 580332004621 domain interface; other site 580332004622 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 580332004623 macrolide transporter subunit MacA; Provisional; Region: PRK11578 580332004624 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 580332004625 HlyD family secretion protein; Region: HlyD_3; pfam13437 580332004626 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 580332004627 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 580332004628 Walker A/P-loop; other site 580332004629 ATP binding site [chemical binding]; other site 580332004630 Q-loop/lid; other site 580332004631 ABC transporter signature motif; other site 580332004632 Walker B; other site 580332004633 D-loop; other site 580332004634 H-loop/switch region; other site 580332004635 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 580332004636 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 580332004637 FtsX-like permease family; Region: FtsX; pfam02687 580332004638 Family-5 Uracil-DNA glycosylases (UDG), found in thermophilic organisms; Region: UDG_F5_TTUDGB_like; cd10031 580332004639 Fe-S cluster binding site [ion binding]; other site 580332004640 DNA binding site [nucleotide binding] 580332004641 active site 580332004642 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 580332004643 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 580332004644 GIY-YIG motif/motif A; other site 580332004645 active site 580332004646 catalytic site [active] 580332004647 putative DNA binding site [nucleotide binding]; other site 580332004648 metal binding site [ion binding]; metal-binding site 580332004649 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 580332004650 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 580332004651 DsrC like protein; Region: DsrC; cl01101 580332004652 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 580332004653 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 580332004654 global nitrogen regulator NtcA, cyanobacterial; Region: NtcA_cyano; TIGR03697 580332004655 ligand binding site [chemical binding]; other site 580332004656 flexible hinge region; other site 580332004657 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 580332004658 putative switch regulator; other site 580332004659 non-specific DNA interactions [nucleotide binding]; other site 580332004660 DNA binding site [nucleotide binding] 580332004661 sequence specific DNA binding site [nucleotide binding]; other site 580332004662 putative cAMP binding site [chemical binding]; other site 580332004663 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 580332004664 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 580332004665 dimer interface [polypeptide binding]; other site 580332004666 putative anticodon binding site; other site 580332004667 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 580332004668 motif 1; other site 580332004669 active site 580332004670 motif 2; other site 580332004671 motif 3; other site 580332004672 P-loop containing region of AAA domain; Region: AAA_29; pfam13555 580332004673 AAA domain; Region: AAA_23; pfam13476 580332004674 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 580332004675 AAA domain; Region: AAA_21; pfam13304 580332004676 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 580332004677 ABC transporter signature motif; other site 580332004678 Walker B; other site 580332004679 D-loop; other site 580332004680 H-loop/switch region; other site 580332004681 peptide chain release factor 2; Validated; Region: prfB; PRK00578 580332004682 This domain is found in peptide chain release factors; Region: PCRF; smart00937 580332004683 RF-1 domain; Region: RF-1; pfam00472 580332004684 MgtC family; Region: MgtC; pfam02308 580332004685 Predicted membrane protein [Function unknown]; Region: COG3174 580332004686 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 580332004687 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 580332004688 DHH family; Region: DHH; pfam01368 580332004689 DHHA1 domain; Region: DHHA1; pfam02272 580332004690 aspartate kinase; Reviewed; Region: PRK06635 580332004691 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 580332004692 putative nucleotide binding site [chemical binding]; other site 580332004693 putative catalytic residues [active] 580332004694 putative Mg ion binding site [ion binding]; other site 580332004695 putative aspartate binding site [chemical binding]; other site 580332004696 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 580332004697 putative allosteric regulatory site; other site 580332004698 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 580332004699 putative allosteric regulatory residue; other site 580332004700 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 580332004701 Methyltransferase domain; Region: Methyltransf_11; pfam08241 580332004702 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 580332004703 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 580332004704 RNA/DNA hybrid binding site [nucleotide binding]; other site 580332004705 active site 580332004706 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 580332004707 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 580332004708 active site 580332004709 catalytic site [active] 580332004710 substrate binding site [chemical binding]; other site 580332004711 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 580332004712 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 580332004713 putative FAD-binding dehydrogenase; Reviewed; Region: PRK12834 580332004714 HI0933-like protein; Region: HI0933_like; pfam03486 580332004715 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 580332004716 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 580332004717 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]; Region: COG1512 580332004718 Repair protein; Region: Repair_PSII; pfam04536 580332004719 Repair protein; Region: Repair_PSII; pfam04536 580332004720 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 580332004721 putative active site [active] 580332004722 putative metal binding residues [ion binding]; other site 580332004723 signature motif; other site 580332004724 putative triphosphate binding site [ion binding]; other site 580332004725 CHAD domain; Region: CHAD; pfam05235 580332004726 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 580332004727 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 580332004728 Part of AAA domain; Region: AAA_19; pfam13245 580332004729 Family description; Region: UvrD_C_2; pfam13538 580332004730 classical (c) SDRs; Region: SDR_c; cd05233 580332004731 short chain dehydrogenase; Provisional; Region: PRK08219 580332004732 NAD(P) binding site [chemical binding]; other site 580332004733 active site 580332004734 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 580332004735 Maf-like protein; Region: Maf; pfam02545 580332004736 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 580332004737 active site 580332004738 dimer interface [polypeptide binding]; other site 580332004739 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 580332004740 50S ribosomal protein L32; Validated; Region: rpmF; PRK01110 580332004741 putative phosphate acyltransferase; Provisional; Region: PRK05331 580332004742 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 580332004743 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 580332004744 dimer interface [polypeptide binding]; other site 580332004745 active site 580332004746 CoA binding pocket [chemical binding]; other site 580332004747 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 580332004748 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 580332004749 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 580332004750 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 580332004751 NAD(P) binding site [chemical binding]; other site 580332004752 homotetramer interface [polypeptide binding]; other site 580332004753 homodimer interface [polypeptide binding]; other site 580332004754 active site 580332004755 acyl carrier protein; Provisional; Region: acpP; PRK00982 580332004756 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 580332004757 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 580332004758 dimer interface [polypeptide binding]; other site 580332004759 active site 580332004760 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 580332004761 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 580332004762 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332004763 catalytic residue [active] 580332004764 YceG-like family; Region: YceG; pfam02618 580332004765 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 580332004766 dimerization interface [polypeptide binding]; other site 580332004767 thymidylate kinase; Validated; Region: tmk; PRK00698 580332004768 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 580332004769 TMP-binding site; other site 580332004770 ATP-binding site [chemical binding]; other site 580332004771 DNA polymerase III subunit delta'; Validated; Region: PRK06964 580332004772 DNA polymerase III subunit delta'; Validated; Region: PRK08485 580332004773 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 580332004774 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 580332004775 active site 580332004776 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 580332004777 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 580332004778 active site 580332004779 HIGH motif; other site 580332004780 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 580332004781 active site 580332004782 KMSKS motif; other site 580332004783 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 580332004784 Histone deacetylases and histone-like deacetylases, classII; Region: HDAC_classII_2; cd11599 580332004785 putative active site [active] 580332004786 Zn binding site [ion binding]; other site 580332004787 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 580332004788 CoA binding domain; Region: CoA_binding_2; pfam13380 580332004789 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 580332004790 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 580332004791 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 580332004792 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 580332004793 Adenylyl- / guanylyl cyclase, catalytic domain; Region: CYCc; smart00044 580332004794 cyclase homology domain; Region: CHD; cd07302 580332004795 nucleotidyl binding site; other site 580332004796 metal binding site [ion binding]; metal-binding site 580332004797 dimer interface [polypeptide binding]; other site 580332004798 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 580332004799 Coenzyme A binding pocket [chemical binding]; other site 580332004800 Protein of unknown function, DUF484; Region: DUF484; cl17449 580332004801 GAF domain; Region: GAF_2; pfam13185 580332004802 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332004803 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332004804 metal binding site [ion binding]; metal-binding site 580332004805 active site 580332004806 I-site; other site 580332004807 Fatty acid desaturase; Region: FA_desaturase; pfam00487 580332004808 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 580332004809 Di-iron ligands [ion binding]; other site 580332004810 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 580332004811 Transposase; Region: DDE_Tnp_ISL3; pfam01610 580332004812 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 580332004813 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 580332004814 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 580332004815 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 580332004816 RNA binding site [nucleotide binding]; other site 580332004817 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 580332004818 non-specific DNA binding site [nucleotide binding]; other site 580332004819 salt bridge; other site 580332004820 sequence-specific DNA binding site [nucleotide binding]; other site 580332004821 Uncharacterized protein conserved in bacteria (DUF2136); Region: DUF2136; cl01912 580332004822 Hemerythrin; Region: Hemerythrin; cd12107 580332004823 Fe binding site [ion binding]; other site 580332004824 Plasmid stabilisation system protein; Region: Plasmid_stabil; pfam05016 580332004825 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 580332004826 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 580332004827 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 580332004828 ligand binding site [chemical binding]; other site 580332004829 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332004830 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332004831 metal binding site [ion binding]; metal-binding site 580332004832 active site 580332004833 I-site; other site 580332004834 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 580332004835 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 580332004836 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332004837 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332004838 metal binding site [ion binding]; metal-binding site 580332004839 active site 580332004840 I-site; other site 580332004841 HDOD domain; Region: HDOD; pfam08668 580332004842 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 580332004843 hypothetical protein; Provisional; Region: PRK10621 580332004844 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 580332004845 Hemerythrin; Region: Hemerythrin; cd12107 580332004846 Fe binding site [ion binding]; other site 580332004847 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 580332004848 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 580332004849 catalytic triad [active] 580332004850 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 580332004851 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 580332004852 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 580332004853 Glycine-zipper containing OmpA-like membrane domain; Region: Gly-zipper_OmpA; pfam13436 580332004854 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 580332004855 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 580332004856 cyclase homology domain; Region: CHD; cd07302 580332004857 nucleotidyl binding site; other site 580332004858 metal binding site [ion binding]; metal-binding site 580332004859 dimer interface [polypeptide binding]; other site 580332004860 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 580332004861 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 580332004862 TM-ABC transporter signature motif; other site 580332004863 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 580332004864 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 580332004865 Walker A/P-loop; other site 580332004866 ATP binding site [chemical binding]; other site 580332004867 Q-loop/lid; other site 580332004868 ABC transporter signature motif; other site 580332004869 Walker B; other site 580332004870 D-loop; other site 580332004871 H-loop/switch region; other site 580332004872 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 580332004873 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 580332004874 Walker A/P-loop; other site 580332004875 ATP binding site [chemical binding]; other site 580332004876 Q-loop/lid; other site 580332004877 ABC transporter signature motif; other site 580332004878 Walker B; other site 580332004879 D-loop; other site 580332004880 H-loop/switch region; other site 580332004881 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 580332004882 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 580332004883 TM-ABC transporter signature motif; other site 580332004884 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 580332004885 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 580332004886 putative ligand binding site [chemical binding]; other site 580332004887 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 580332004888 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 580332004889 PAS domain; Region: PAS_9; pfam13426 580332004890 putative active site [active] 580332004891 heme pocket [chemical binding]; other site 580332004892 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332004893 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332004894 metal binding site [ion binding]; metal-binding site 580332004895 active site 580332004896 I-site; other site 580332004897 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 580332004898 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 580332004899 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 580332004900 active site 580332004901 phosphorylation site [posttranslational modification] 580332004902 intermolecular recognition site; other site 580332004903 dimerization interface [polypeptide binding]; other site 580332004904 CheB methylesterase; Region: CheB_methylest; pfam01339 580332004905 CheD chemotactic sensory transduction; Region: CheD; cl00810 580332004906 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 580332004907 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 580332004908 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 580332004909 S-adenosylmethionine binding site [chemical binding]; other site 580332004910 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 580332004911 ligand binding domain of Tar- and Tsr-related chemoreceptors; Region: Tar_Tsr_LBD; cl00144 580332004912 CHASE3 domain; Region: CHASE3; cl05000 580332004913 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 580332004914 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 580332004915 dimerization interface [polypeptide binding]; other site 580332004916 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332004917 dimer interface [polypeptide binding]; other site 580332004918 putative CheW interface [polypeptide binding]; other site 580332004919 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 580332004920 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 580332004921 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 580332004922 putative binding surface; other site 580332004923 active site 580332004924 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 580332004925 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 580332004926 ATP binding site [chemical binding]; other site 580332004927 Mg2+ binding site [ion binding]; other site 580332004928 G-X-G motif; other site 580332004929 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 580332004930 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 580332004931 anti sigma factor interaction site; other site 580332004932 regulatory phosphorylation site [posttranslational modification]; other site 580332004933 Response regulator receiver domain; Region: Response_reg; pfam00072 580332004934 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 580332004935 active site 580332004936 phosphorylation site [posttranslational modification] 580332004937 intermolecular recognition site; other site 580332004938 dimerization interface [polypeptide binding]; other site 580332004939 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332004940 dimer interface [polypeptide binding]; other site 580332004941 putative CheW interface [polypeptide binding]; other site 580332004942 PAS domain S-box; Region: sensory_box; TIGR00229 580332004943 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 580332004944 putative active site [active] 580332004945 heme pocket [chemical binding]; other site 580332004946 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 580332004947 Histidine kinase; Region: HisKA_3; pfam07730 580332004948 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 580332004949 ATP binding site [chemical binding]; other site 580332004950 Mg2+ binding site [ion binding]; other site 580332004951 G-X-G motif; other site 580332004952 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 580332004953 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 580332004954 active site 580332004955 phosphorylation site [posttranslational modification] 580332004956 intermolecular recognition site; other site 580332004957 dimerization interface [polypeptide binding]; other site 580332004958 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 580332004959 DNA binding residues [nucleotide binding] 580332004960 dimerization interface [polypeptide binding]; other site 580332004961 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 580332004962 dimerization interface [polypeptide binding]; other site 580332004963 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 580332004964 putative active site [active] 580332004965 heme pocket [chemical binding]; other site 580332004966 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 580332004967 GAF domain; Region: GAF; pfam01590 580332004968 Histidine kinase; Region: HisKA_3; pfam07730 580332004969 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 580332004970 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 580332004971 ATP binding site [chemical binding]; other site 580332004972 Mg2+ binding site [ion binding]; other site 580332004973 G-X-G motif; other site 580332004974 Ca2+/Na+ antiporter [Inorganic ion transport and metabolism]; Region: ECM27; COG0530 580332004975 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 580332004976 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 580332004977 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 580332004978 HlyD family secretion protein; Region: HlyD_3; pfam13437 580332004979 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 580332004980 Peptidase family M23; Region: Peptidase_M23; pfam01551 580332004981 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 580332004982 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 580332004983 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 580332004984 Cadherin repeat-like domain; Region: CA_like; cl15786 580332004985 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 580332004986 Ca2+ binding site [ion binding]; other site 580332004987 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 580332004988 Cadherin repeat-like domain; Region: CA_like; cl15786 580332004989 VCBS repeat; Region: VCBS_repeat; TIGR01965 580332004990 VCBS repeat; Region: VCBS_repeat; TIGR01965 580332004991 VCBS repeat; Region: VCBS_repeat; TIGR01965 580332004992 VCBS repeat; Region: VCBS_repeat; TIGR01965 580332004993 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 580332004994 Cadherin-like repeat domain of alpha dystroglycan; Region: Dystroglycan_repeat; cd11303 580332004995 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 580332004996 Cadherin repeat-like domain; Region: CA_like; cl15786 580332004997 Periplasmic component of the Tol biopolymer transport system [Intracellular trafficking and secretion]; Region: TolB; COG0823 580332004998 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 580332004999 Walker A/P-loop; other site 580332005000 ATP binding site [chemical binding]; other site 580332005001 ABC transporter; Region: ABC_tran; pfam00005 580332005002 Q-loop/lid; other site 580332005003 ABC transporter signature motif; other site 580332005004 Walker B; other site 580332005005 D-loop; other site 580332005006 H-loop/switch region; other site 580332005007 Transposase IS200 like; Region: Y1_Tnp; pfam01797 580332005008 Protein of unknown function (DUF497); Region: DUF497; cl01108 580332005009 Domain of unknown function (DUF4415); Region: DUF4415; pfam14384 580332005010 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 580332005011 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 580332005012 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 580332005013 Walker A/P-loop; other site 580332005014 ATP binding site [chemical binding]; other site 580332005015 Q-loop/lid; other site 580332005016 ABC transporter signature motif; other site 580332005017 Walker B; other site 580332005018 D-loop; other site 580332005019 H-loop/switch region; other site 580332005020 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 580332005021 catalytic residues [active] 580332005022 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 580332005023 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 580332005024 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 580332005025 SLBB domain; Region: SLBB; pfam10531 580332005026 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 580332005027 bidirectional hydrogenase complex protein HoxU; Validated; Region: PRK07569 580332005028 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 580332005029 catalytic loop [active] 580332005030 iron binding site [ion binding]; other site 580332005031 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 580332005032 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 580332005033 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 580332005034 Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion]; Region: FrhA; COG3259 580332005035 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 580332005036 nickel binding site [ion binding]; other site 580332005037 Protein of unknown function (DUF1311); Region: DUF1311; pfam07007 580332005038 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 580332005039 non-specific DNA binding site [nucleotide binding]; other site 580332005040 salt bridge; other site 580332005041 sequence-specific DNA binding site [nucleotide binding]; other site 580332005042 putative addiction module killer protein; Region: upstrm_HI1419; TIGR02683 580332005043 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 580332005044 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 580332005045 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 580332005046 Ni,Fe-hydrogenase I small subunit [Energy production and conversion]; Region: HyaA; COG1740 580332005047 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 580332005048 HupF/HypC family; Region: HupF_HypC; pfam01455 580332005049 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 580332005050 putative substrate-binding site; other site 580332005051 nickel binding site [ion binding]; other site 580332005052 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 580332005053 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 580332005054 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 580332005055 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 580332005056 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 580332005057 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 580332005058 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 580332005059 active site 580332005060 HIGH motif; other site 580332005061 dimer interface [polypeptide binding]; other site 580332005062 KMSKS motif; other site 580332005063 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 580332005064 Peptidase family M50; Region: Peptidase_M50; pfam02163 580332005065 active site 580332005066 putative substrate binding region [chemical binding]; other site 580332005067 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 580332005068 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 580332005069 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 580332005070 active site 580332005071 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 580332005072 hypothetical protein; Validated; Region: PRK01777 580332005073 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 580332005074 putative coenzyme Q binding site [chemical binding]; other site 580332005075 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 580332005076 SmpB-tmRNA interface; other site 580332005077 methionine sulfoxide reductase A; Provisional; Region: PRK14054 580332005078 Predicted integral membrane protein [Function unknown]; Region: COG5615 580332005079 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 580332005080 RNA/DNA hybrid binding site [nucleotide binding]; other site 580332005081 active site 580332005082 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 580332005083 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 580332005084 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 580332005085 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 580332005086 active site 580332005087 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 580332005088 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 580332005089 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 580332005090 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 580332005091 trimer interface [polypeptide binding]; other site 580332005092 active site 580332005093 UDP-GlcNAc binding site [chemical binding]; other site 580332005094 lipid binding site [chemical binding]; lipid-binding site 580332005095 periplasmic chaperone; Provisional; Region: PRK10780 580332005096 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 580332005097 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 580332005098 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 580332005099 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 580332005100 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 580332005101 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 580332005102 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 580332005103 Surface antigen; Region: Bac_surface_Ag; pfam01103 580332005104 zinc metallopeptidase RseP; Provisional; Region: PRK10779 580332005105 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 580332005106 active site 580332005107 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 580332005108 protein binding site [polypeptide binding]; other site 580332005109 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 580332005110 protein binding site [polypeptide binding]; other site 580332005111 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 580332005112 putative substrate binding region [chemical binding]; other site 580332005113 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 580332005114 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 580332005115 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 580332005116 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 580332005117 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 580332005118 CDP-diglyceride synthase; Provisional; Region: cdsA; PRK11624 580332005119 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 580332005120 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 580332005121 catalytic residue [active] 580332005122 putative FPP diphosphate binding site; other site 580332005123 putative FPP binding hydrophobic cleft; other site 580332005124 dimer interface [polypeptide binding]; other site 580332005125 putative IPP diphosphate binding site; other site 580332005126 ribosome recycling factor; Reviewed; Region: frr; PRK00083 580332005127 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another...; Region: RRF; cd00520 580332005128 hinge region; other site 580332005129 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 580332005130 putative nucleotide binding site [chemical binding]; other site 580332005131 uridine monophosphate binding site [chemical binding]; other site 580332005132 homohexameric interface [polypeptide binding]; other site 580332005133 elongation factor Ts; Provisional; Region: tsf; PRK09377 580332005134 UBA/TS-N domain; Region: UBA; pfam00627 580332005135 Elongation factor TS; Region: EF_TS; pfam00889 580332005136 Elongation factor TS; Region: EF_TS; pfam00889 580332005137 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 580332005138 rRNA interaction site [nucleotide binding]; other site 580332005139 S8 interaction site; other site 580332005140 putative laminin-1 binding site; other site 580332005141 Flagellar protein YcgR; Region: YcgR_2; pfam12945 580332005142 PilZ domain; Region: PilZ; pfam07238 580332005143 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 580332005144 Nitrogen regulatory protein P-II; Region: P-II; smart00938 580332005145 NAD synthetase; Provisional; Region: PRK13981 580332005146 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 580332005147 multimer interface [polypeptide binding]; other site 580332005148 active site 580332005149 catalytic triad [active] 580332005150 protein interface 1 [polypeptide binding]; other site 580332005151 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 580332005152 homodimer interface [polypeptide binding]; other site 580332005153 NAD binding pocket [chemical binding]; other site 580332005154 ATP binding pocket [chemical binding]; other site 580332005155 Mg binding site [ion binding]; other site 580332005156 active-site loop [active] 580332005157 RmuC family; Region: RmuC; pfam02646 580332005158 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 580332005159 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 580332005160 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 580332005161 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 580332005162 G1 box; other site 580332005163 putative GEF interaction site [polypeptide binding]; other site 580332005164 GTP/Mg2+ binding site [chemical binding]; other site 580332005165 Switch I region; other site 580332005166 G2 box; other site 580332005167 G3 box; other site 580332005168 Switch II region; other site 580332005169 G4 box; other site 580332005170 G5 box; other site 580332005171 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 580332005172 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 580332005173 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 580332005174 dimerization interface [polypeptide binding]; other site 580332005175 PAS domain S-box; Region: sensory_box; TIGR00229 580332005176 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 580332005177 putative active site [active] 580332005178 heme pocket [chemical binding]; other site 580332005179 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332005180 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332005181 metal binding site [ion binding]; metal-binding site 580332005182 active site 580332005183 I-site; other site 580332005184 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 580332005185 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 580332005186 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 580332005187 DEAD-like helicases superfamily; Region: DEXDc; smart00487 580332005188 ATP binding site [chemical binding]; other site 580332005189 Mg++ binding site [ion binding]; other site 580332005190 motif III; other site 580332005191 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 580332005192 nucleotide binding region [chemical binding]; other site 580332005193 ATP-binding site [chemical binding]; other site 580332005194 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 580332005195 active site 580332005196 PII uridylyl-transferase; Provisional; Region: PRK03059 580332005197 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 580332005198 metal binding triad; other site 580332005199 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 580332005200 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332005201 Zn2+ binding site [ion binding]; other site 580332005202 Mg2+ binding site [ion binding]; other site 580332005203 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 580332005204 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 580332005205 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 580332005206 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 580332005207 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 580332005208 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 580332005209 dimerization interface [polypeptide binding]; other site 580332005210 GAF domain; Region: GAF; pfam01590 580332005211 GAF domain; Region: GAF_2; pfam13185 580332005212 PAS domain S-box; Region: sensory_box; TIGR00229 580332005213 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 580332005214 putative active site [active] 580332005215 heme pocket [chemical binding]; other site 580332005216 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332005217 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332005218 metal binding site [ion binding]; metal-binding site 580332005219 active site 580332005220 I-site; other site 580332005221 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 580332005222 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 580332005223 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 580332005224 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 580332005225 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 580332005226 anthranilate dioxygenase reductase; Provisional; Region: antC; PRK11872 580332005227 catalytic loop [active] 580332005228 iron binding site [ion binding]; other site 580332005229 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 580332005230 FAD binding pocket [chemical binding]; other site 580332005231 conserved FAD binding motif [chemical binding]; other site 580332005232 phosphate binding motif [ion binding]; other site 580332005233 beta-alpha-beta structure motif; other site 580332005234 NAD binding pocket [chemical binding]; other site 580332005235 siroheme synthase; Provisional; Region: cysG; PRK10637 580332005236 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 580332005237 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 580332005238 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 580332005239 active site 580332005240 SAM binding site [chemical binding]; other site 580332005241 homodimer interface [polypeptide binding]; other site 580332005242 Domain of unknown function (DUF4202); Region: DUF4202; pfam13875 580332005243 Cobyrinic acid a,c-diamide synthase [Coenzyme metabolism]; Region: CobB; COG1797 580332005244 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 580332005245 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 580332005246 catalytic triad [active] 580332005247 Polysulphide reductase [Energy production and conversion]; Region: COG5557; cl17901 580332005248 Polysulphide reductase, NrfD; Region: NrfD; pfam03916 580332005249 TAT (twin-arginine translocation) pathway signal sequence; Region: TAT_signal; pfam10518 580332005250 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 580332005251 4Fe-4S binding domain; Region: Fer4; cl02805 580332005252 cytochrome c nitrate reductase, small subunit; Region: cytochr_NrfH; TIGR03153 580332005253 putative glutamate synthase (NADPH) small subunit; Provisional; Region: PRK12771 580332005254 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 580332005255 4Fe-4S binding domain; Region: Fer4; pfam00037 580332005256 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 580332005257 Cysteine-rich domain; Region: CCG; pfam02754 580332005258 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; cl00959 580332005259 Dissimilatory sulfite reductase (desulfoviridin), gamma subunit [Inorganic ion transport and metabolism]; Region: DsrC; COG2920 580332005260 DsrC like protein; Region: DsrC; pfam04358 580332005261 sulfur relay protein TusB/DsrH; Region: sulf_tusB_dsrH; TIGR03011 580332005262 sulfur relay protein TusC/DsrF; Region: sulf_tusC_dsrF; TIGR03010 580332005263 sulfur relay protein TusD/DsrE; Region: sulf_tusD_dsrE; TIGR03012 580332005264 sulfite reductase, dissimilatory-type beta subunit; Region: dsrB; TIGR02066 580332005265 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 580332005266 sulfite reductase, dissimilatory-type alpha subunit; Region: dsrA; TIGR02064 580332005267 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 580332005268 CRISPR/Cas system-associated RAMP superfamily protein Cas6; Region: Cas6-I-III; cd09733 580332005269 Dissimilatory sulfite reductase (desulfoviridin), gamma subunit [Inorganic ion transport and metabolism]; Region: DsrC; COG2920 580332005270 DsrC like protein; Region: DsrC; pfam04358 580332005271 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 580332005272 CPxP motif; other site 580332005273 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 580332005274 CPxP motif; other site 580332005275 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 580332005276 active site 580332005277 iron coordination sites [ion binding]; other site 580332005278 substrate binding pocket [chemical binding]; other site 580332005279 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 580332005280 DsrE/DsrF-like family; Region: DrsE; cl00672 580332005281 Predicted transporter component [General function prediction only]; Region: COG2391 580332005282 putative selenium metabolism protein, YedE family; Region: seleno_YedE; TIGR04112 580332005283 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 580332005284 Thermus thermophilus SoxB and related proteins, N-terminal metallophosphatase domain; Region: MPP_SoxB_N; cd07411 580332005285 active site 580332005286 metal binding site [ion binding]; metal-binding site 580332005287 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 580332005288 Cytochrome c [Energy production and conversion]; Region: COG3258 580332005289 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 580332005290 Predicted secreted protein [Function unknown]; Region: COG5501 580332005291 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 580332005292 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 580332005293 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 580332005294 DsrE/DsrF-like family; Region: DrsE; pfam02635 580332005295 RNA polymerase sigma factor RpoE; Provisional; Region: PRK09652 580332005296 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 580332005297 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 580332005298 DNA binding residues [nucleotide binding] 580332005299 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 580332005300 dimerization domain [polypeptide binding]; other site 580332005301 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 580332005302 dimer interface [polypeptide binding]; other site 580332005303 catalytic residues [active] 580332005304 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 580332005305 DsrE/DsrF/DrsH-like family; Region: DrsE_2; pfam13686 580332005306 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 580332005307 CPxP motif; other site 580332005308 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 580332005309 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 580332005310 Sulfate transporter family; Region: Sulfate_transp; pfam00916 580332005311 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 580332005312 DMSO reductase anchor subunit (DmsC); Region: DmsC; cl17519 580332005313 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 580332005314 4Fe-4S binding domain; Region: Fer4; pfam00037 580332005315 anaerobic dimethyl sulfoxide reductase, A subunit, DmsA/YnfE family; Region: dmsA_ynfE; TIGR02166 580332005316 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 580332005317 molybdopterin cofactor binding site; other site 580332005318 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 580332005319 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 580332005320 putative molybdopterin cofactor binding site; other site 580332005321 sulfate adenylyltransferase; Reviewed; Region: sat; PRK04149 580332005322 ATP-sulfurylase; Region: ATPS; cd00517 580332005323 active site 580332005324 HXXH motif; other site 580332005325 flexible loop; other site 580332005326 adenosine phosphosulphate reductase, beta subunit; Region: aprB; TIGR02060 580332005327 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 580332005328 Adenosine-5'-phosphosulfate reductase beta subunit; Region: APS-reductase_C; pfam12139 580332005329 adenylylsulfate reductase subunit alpha; Validated; Region: PRK06854 580332005330 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 580332005331 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 580332005332 Tetratricopeptide repeat; Region: TPR_12; pfam13424 580332005333 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 580332005334 nucleotide binding site/active site [active] 580332005335 HIT family signature motif; other site 580332005336 catalytic residue [active] 580332005337 Domain of unknown function (DUF4279); Region: DUF4279; pfam14106 580332005338 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 580332005339 active site residue [active] 580332005340 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 580332005341 active site 580332005342 metal binding site [ion binding]; metal-binding site 580332005343 homotetramer interface [polypeptide binding]; other site 580332005344 GAF domain; Region: GAF_3; pfam13492 580332005345 Histidine kinase; Region: HisKA_3; pfam07730 580332005346 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 580332005347 ATP binding site [chemical binding]; other site 580332005348 Mg2+ binding site [ion binding]; other site 580332005349 G-X-G motif; other site 580332005350 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 580332005351 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 580332005352 active site 580332005353 phosphorylation site [posttranslational modification] 580332005354 intermolecular recognition site; other site 580332005355 dimerization interface [polypeptide binding]; other site 580332005356 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 580332005357 DNA binding residues [nucleotide binding] 580332005358 dimerization interface [polypeptide binding]; other site 580332005359 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 580332005360 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 580332005361 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 580332005362 DNA binding residues [nucleotide binding] 580332005363 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 580332005364 IHF - DNA interface [nucleotide binding]; other site 580332005365 IHF dimer interface [polypeptide binding]; other site 580332005366 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 580332005367 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 580332005368 putative tRNA-binding site [nucleotide binding]; other site 580332005369 B3/4 domain; Region: B3_4; pfam03483 580332005370 tRNA synthetase B5 domain; Region: B5; smart00874 580332005371 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 580332005372 dimer interface [polypeptide binding]; other site 580332005373 motif 1; other site 580332005374 motif 3; other site 580332005375 motif 2; other site 580332005376 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 580332005377 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 580332005378 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 580332005379 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 580332005380 dimer interface [polypeptide binding]; other site 580332005381 motif 1; other site 580332005382 active site 580332005383 motif 2; other site 580332005384 motif 3; other site 580332005385 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 580332005386 23S rRNA binding site [nucleotide binding]; other site 580332005387 L21 binding site [polypeptide binding]; other site 580332005388 L13 binding site [polypeptide binding]; other site 580332005389 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 580332005390 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 580332005391 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 580332005392 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 580332005393 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 580332005394 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 580332005395 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 580332005396 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 580332005397 active site 580332005398 dimer interface [polypeptide binding]; other site 580332005399 motif 1; other site 580332005400 motif 2; other site 580332005401 motif 3; other site 580332005402 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 580332005403 anticodon binding site; other site 580332005404 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 580332005405 Permease; Region: Permease; pfam02405 580332005406 CHASE2 domain; Region: CHASE2; pfam05226 580332005407 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 580332005408 cyclase homology domain; Region: CHD; cd07302 580332005409 nucleotidyl binding site; other site 580332005410 metal binding site [ion binding]; metal-binding site 580332005411 dimer interface [polypeptide binding]; other site 580332005412 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 580332005413 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 580332005414 mce related protein; Region: MCE; pfam02470 580332005415 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 580332005416 Q-loop/lid; other site 580332005417 ABC transporter signature motif; other site 580332005418 Walker B; other site 580332005419 D-loop; other site 580332005420 replicative DNA helicase; Provisional; Region: PRK07004 580332005421 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 580332005422 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 580332005423 Walker A motif; other site 580332005424 ATP binding site [chemical binding]; other site 580332005425 Walker B motif; other site 580332005426 DNA binding loops [nucleotide binding] 580332005427 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 580332005428 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 580332005429 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 580332005430 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 580332005431 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 580332005432 generic binding surface I; other site 580332005433 generic binding surface II; other site 580332005434 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 580332005435 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 580332005436 FtsX-like permease family; Region: FtsX; pfam02687 580332005437 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 580332005438 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 580332005439 Walker A/P-loop; other site 580332005440 ATP binding site [chemical binding]; other site 580332005441 Q-loop/lid; other site 580332005442 ABC transporter signature motif; other site 580332005443 Walker B; other site 580332005444 D-loop; other site 580332005445 H-loop/switch region; other site 580332005446 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 580332005447 active site 580332005448 catalytic triad [active] 580332005449 oxyanion hole [active] 580332005450 switch loop; other site 580332005451 Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones]; Region: COG1331 580332005452 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 580332005453 catalytic residues [active] 580332005454 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 580332005455 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 580332005456 tandem repeat interface [polypeptide binding]; other site 580332005457 oligomer interface [polypeptide binding]; other site 580332005458 active site residues [active] 580332005459 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 580332005460 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 580332005461 motif II; other site 580332005462 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional; Region: PRK11760 580332005463 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 580332005464 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 580332005465 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 580332005466 RNA binding surface [nucleotide binding]; other site 580332005467 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 580332005468 active site 580332005469 Ribonucleases G and E [Translation, ribosomal structure and biogenesis]; Region: CafA; COG1530 580332005470 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 580332005471 homodimer interface [polypeptide binding]; other site 580332005472 oligonucleotide binding site [chemical binding]; other site 580332005473 Peptidase MA superfamily; Region: Peptidase_MA_2; pfam13485 580332005474 The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Region: NR_LBD; cl11397 580332005475 ligand binding site [chemical binding]; other site 580332005476 Surface antigen; Region: Bac_surface_Ag; pfam01103 580332005477 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 580332005478 Low molecular weight phosphatase family; Region: LMWPc; cd00115 580332005479 active site 580332005480 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 580332005481 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 580332005482 ATP binding site [chemical binding]; other site 580332005483 Mg2+ binding site [ion binding]; other site 580332005484 G-X-G motif; other site 580332005485 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 580332005486 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 580332005487 active site 580332005488 phosphorylation site [posttranslational modification] 580332005489 intermolecular recognition site; other site 580332005490 dimerization interface [polypeptide binding]; other site 580332005491 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 580332005492 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 580332005493 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 580332005494 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 580332005495 active site 580332005496 metal binding site [ion binding]; metal-binding site 580332005497 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 580332005498 excinuclease ABC subunit B; Provisional; Region: PRK05298 580332005499 Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes; Region: Motor_domain; cl00286 580332005500 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 580332005501 ATP-binding site [chemical binding]; other site 580332005502 ATP binding site [chemical binding]; other site 580332005503 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 580332005504 nucleotide binding region [chemical binding]; other site 580332005505 ATP-binding site [chemical binding]; other site 580332005506 Ultra-violet resistance protein B; Region: UvrB; pfam12344 580332005507 UvrB/uvrC motif; Region: UVR; pfam02151 580332005508 putative addiction module killer protein; Region: upstrm_HI1419; TIGR02683 580332005509 Predicted transcriptional regulator [Transcription]; Region: COG3636; cl17681 580332005510 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 580332005511 catalytic triad [active] 580332005512 Cytochrome c; Region: Cytochrom_C; cl11414 580332005513 Cytotoxic translational repressor of toxin-antitoxin stability system [Translation, ribosomal structure and biogenesis / Cell division and chromosome partitioning]; Region: RelE; COG2026 580332005514 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: StbD; COG2161 580332005515 fructokinase; Reviewed; Region: PRK09557 580332005516 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 580332005517 nucleotide binding site [chemical binding]; other site 580332005518 PAS fold; Region: PAS_4; pfam08448 580332005519 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332005520 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332005521 metal binding site [ion binding]; metal-binding site 580332005522 active site 580332005523 I-site; other site 580332005524 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 580332005525 putative active site [active] 580332005526 dimerization interface [polypeptide binding]; other site 580332005527 putative tRNAtyr binding site [nucleotide binding]; other site 580332005528 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 580332005529 Domain of unknown function (DUF427); Region: DUF427; pfam04248 580332005530 ergothioneine biosynthesis protein EgtB; Region: egtB_TIGR03440 580332005531 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 580332005532 dimethylhistidine N-methyltransferase; Region: egtD_ergothio; TIGR03438 580332005533 Uncharacterized conserved protein (DUF2260); Region: DUF2260; pfam10017 580332005534 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 580332005535 putative C-S lyase; Region: C_S_lyase_PatB; TIGR04350 580332005536 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 580332005537 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332005538 homodimer interface [polypeptide binding]; other site 580332005539 catalytic residue [active] 580332005540 Response regulator receiver domain; Region: Response_reg; pfam00072 580332005541 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 580332005542 active site 580332005543 phosphorylation site [posttranslational modification] 580332005544 intermolecular recognition site; other site 580332005545 dimerization interface [polypeptide binding]; other site 580332005546 Response regulator receiver domain; Region: Response_reg; pfam00072 580332005547 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 580332005548 active site 580332005549 phosphorylation site [posttranslational modification] 580332005550 intermolecular recognition site; other site 580332005551 dimerization interface [polypeptide binding]; other site 580332005552 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 580332005553 FOG: CBS domain [General function prediction only]; Region: COG0517 580332005554 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 580332005555 ATP binding site [chemical binding]; other site 580332005556 Mg2+ binding site [ion binding]; other site 580332005557 G-X-G motif; other site 580332005558 Putative glycerate kinase [Carbohydrate transport and metabolism]; Region: GckA; COG2379 580332005559 Domain of unknown function (DUF4147); Region: DUF4147; pfam13660 580332005560 MOFRL family; Region: MOFRL; pfam05161 580332005561 aspartate aminotransferase; Provisional; Region: PRK05764 580332005562 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 580332005563 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332005564 homodimer interface [polypeptide binding]; other site 580332005565 catalytic residue [active] 580332005566 HDOD domain; Region: HDOD; pfam08668 580332005567 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332005568 Zn2+ binding site [ion binding]; other site 580332005569 Mg2+ binding site [ion binding]; other site 580332005570 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 580332005571 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 580332005572 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 580332005573 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 580332005574 binding surface 580332005575 TPR motif; other site 580332005576 Cytochrome C biogenesis protein; Region: CcmH; pfam03918 580332005577 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 580332005578 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 580332005579 catalytic residues [active] 580332005580 central insert; other site 580332005581 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 580332005582 CcmE; Region: CcmE; pfam03100 580332005583 heme exporter protein CcmD; Region: cytochro_ccmD; TIGR03141 580332005584 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 580332005585 CcmB protein; Region: CcmB; pfam03379 580332005586 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13538 580332005587 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 580332005588 Walker A/P-loop; other site 580332005589 ATP binding site [chemical binding]; other site 580332005590 Q-loop/lid; other site 580332005591 ABC transporter signature motif; other site 580332005592 Walker B; other site 580332005593 D-loop; other site 580332005594 H-loop/switch region; other site 580332005595 Enoyl-[acyl-carrier-protein]; Region: FabI; COG0623 580332005596 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 580332005597 NAD binding site [chemical binding]; other site 580332005598 homotetramer interface [polypeptide binding]; other site 580332005599 homodimer interface [polypeptide binding]; other site 580332005600 substrate binding site [chemical binding]; other site 580332005601 active site 580332005602 SurA N-terminal domain; Region: SurA_N_3; cl07813 580332005603 periplasmic folding chaperone; Provisional; Region: PRK10788 580332005604 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 580332005605 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 580332005606 IHF dimer interface [polypeptide binding]; other site 580332005607 IHF - DNA interface [nucleotide binding]; other site 580332005608 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 580332005609 Found in ATP-dependent protease La (LON); Region: LON; smart00464 580332005610 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 580332005611 Walker A motif; other site 580332005612 ATP binding site [chemical binding]; other site 580332005613 Walker B motif; other site 580332005614 arginine finger; other site 580332005615 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 580332005616 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 580332005617 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 580332005618 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 580332005619 Walker A motif; other site 580332005620 ATP binding site [chemical binding]; other site 580332005621 Walker B motif; other site 580332005622 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 580332005623 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 580332005624 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 580332005625 oligomer interface [polypeptide binding]; other site 580332005626 active site residues [active] 580332005627 trigger factor; Provisional; Region: tig; PRK01490 580332005628 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 580332005629 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 580332005630 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 580332005631 homodimer interface [polypeptide binding]; other site 580332005632 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 580332005633 active site pocket [active] 580332005634 Catalytic domain of glycoside hydrolase (GH) families 38 and 57, lactam utilization protein LamB/YcsF family proteins, YdjC-family proteins, and similar proteins; Region: GH38-57_N_LamB_YdjC_SF; cl17191 580332005635 N-terminal catalytic domain of thermoactive amylopullulanases; glycoside hydrolase family 57 (GH57); Region: GH57N_APU; cd10796 580332005636 putative active site [active] 580332005637 catalytic site [active] 580332005638 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 580332005639 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 580332005640 ligand binding site; other site 580332005641 oligomer interface; other site 580332005642 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 580332005643 dimer interface [polypeptide binding]; other site 580332005644 N-terminal domain interface [polypeptide binding]; other site 580332005645 sulfate 1 binding site; other site 580332005646 glycogen synthase; Provisional; Region: glgA; PRK00654 580332005647 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 580332005648 ADP-binding pocket [chemical binding]; other site 580332005649 homodimer interface [polypeptide binding]; other site 580332005650 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 580332005651 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 580332005652 active site 580332005653 dimer interface [polypeptide binding]; other site 580332005654 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 580332005655 dimer interface [polypeptide binding]; other site 580332005656 active site 580332005657 glycogen branching enzyme; Provisional; Region: PRK05402 580332005658 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 580332005659 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 580332005660 active site 580332005661 catalytic site [active] 580332005662 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 580332005663 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 580332005664 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 580332005665 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 580332005666 Cu(I) binding site [ion binding]; other site 580332005667 Domain of unknown function (DUF4292); Region: DUF4292; pfam14125 580332005668 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 580332005669 Multicopper oxidase; Region: Cu-oxidase; pfam00394 580332005670 Middle domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; Region: RGL4_M; cd10316 580332005671 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 580332005672 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 580332005673 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 580332005674 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 580332005675 Response regulator receiver domain; Region: Response_reg; pfam00072 580332005676 active site 580332005677 phosphorylation site [posttranslational modification] 580332005678 intermolecular recognition site; other site 580332005679 dimerization interface [polypeptide binding]; other site 580332005680 PAS domain S-box; Region: sensory_box; TIGR00229 580332005681 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 580332005682 putative active site [active] 580332005683 heme pocket [chemical binding]; other site 580332005684 PAS domain S-box; Region: sensory_box; TIGR00229 580332005685 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 580332005686 putative active site [active] 580332005687 heme pocket [chemical binding]; other site 580332005688 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 580332005689 Histidine kinase; Region: HisKA_3; pfam07730 580332005690 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 580332005691 ATP binding site [chemical binding]; other site 580332005692 Mg2+ binding site [ion binding]; other site 580332005693 G-X-G motif; other site 580332005694 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 580332005695 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 580332005696 active site 580332005697 phosphorylation site [posttranslational modification] 580332005698 intermolecular recognition site; other site 580332005699 dimerization interface [polypeptide binding]; other site 580332005700 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 580332005701 DNA binding residues [nucleotide binding] 580332005702 dimerization interface [polypeptide binding]; other site 580332005703 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 580332005704 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 580332005705 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 580332005706 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 580332005707 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 580332005708 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 580332005709 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 580332005710 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 580332005711 binding surface 580332005712 TPR motif; other site 580332005713 Tetratricopeptide repeat; Region: TPR_16; pfam13432 580332005714 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 580332005715 Secretin and TonB N terminus short domain; Region: STN; smart00965 580332005716 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 580332005717 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 580332005718 Cohesin domain, interaction parter of dockerin; Region: cohesin_like; cd08546 580332005719 dockerin binding interface; other site 580332005720 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 580332005721 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 580332005722 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 580332005723 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 580332005724 Walker A motif; other site 580332005725 ATP binding site [chemical binding]; other site 580332005726 Walker B motif; other site 580332005727 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 580332005728 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 580332005729 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 580332005730 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 580332005731 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 580332005732 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 580332005733 Yhdh and yhfp-like putative quinone oxidoreductases; Region: MDR_yhdh_yhfp; cd05280 580332005734 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 580332005735 NADP binding site [chemical binding]; other site 580332005736 dimer interface [polypeptide binding]; other site 580332005737 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 580332005738 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 580332005739 E3 interaction surface; other site 580332005740 lipoyl attachment site [posttranslational modification]; other site 580332005741 e3 binding domain; Region: E3_binding; pfam02817 580332005742 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 580332005743 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 580332005744 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 580332005745 TPP-binding site [chemical binding]; other site 580332005746 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 580332005747 dimer interface [polypeptide binding]; other site 580332005748 PYR/PP interface [polypeptide binding]; other site 580332005749 TPP binding site [chemical binding]; other site 580332005750 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 580332005751 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 580332005752 dimer interface [polypeptide binding]; other site 580332005753 active site 580332005754 citrylCoA binding site [chemical binding]; other site 580332005755 NADH binding [chemical binding]; other site 580332005756 cationic pore residues; other site 580332005757 oxalacetate/citrate binding site [chemical binding]; other site 580332005758 coenzyme A binding site [chemical binding]; other site 580332005759 catalytic triad [active] 580332005760 Flavinator of succinate dehydrogenase; Region: Sdh5; pfam03937 580332005761 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 580332005762 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 580332005763 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK07057 580332005764 L-aspartate oxidase; Provisional; Region: PRK06175 580332005765 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 580332005766 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 580332005767 SdhC subunit interface [polypeptide binding]; other site 580332005768 proximal heme binding site [chemical binding]; other site 580332005769 cardiolipin binding site; other site 580332005770 Iron-sulfur protein interface; other site 580332005771 proximal quinone binding site [chemical binding]; other site 580332005772 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 580332005773 Iron-sulfur protein interface; other site 580332005774 proximal quinone binding site [chemical binding]; other site 580332005775 SdhD (CybS) interface [polypeptide binding]; other site 580332005776 proximal heme binding site [chemical binding]; other site 580332005777 malate dehydrogenase; Provisional; Region: PRK05442 580332005778 Chloroplast-like malate dehydrogenases; Region: MDH_choloroplast_like; cd01338 580332005779 NAD(P) binding site [chemical binding]; other site 580332005780 dimer interface [polypeptide binding]; other site 580332005781 malate binding site [chemical binding]; other site 580332005782 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 580332005783 putative ligand binding pocket/active site [active] 580332005784 putative metal binding site [ion binding]; other site 580332005785 AmmeMemoRadiSam system protein A; Region: AmmeMemoSam_A; TIGR04335 580332005786 AMMECR1; Region: AMMECR1; pfam01871 580332005787 AmmeMemoRadiSam system radical SAM enzyme; Region: AmmeMemoSam_rS; TIGR04337 580332005788 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 580332005789 FeS/SAM binding site; other site 580332005790 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332005791 Zn2+ binding site [ion binding]; other site 580332005792 Mg2+ binding site [ion binding]; other site 580332005793 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl17448 580332005794 Chalcone-flavanone isomerase; Region: Chalcone; cl03589 580332005795 acetyl-CoA acetyltransferase; Provisional; Region: PRK09052 580332005796 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 580332005797 dimer interface [polypeptide binding]; other site 580332005798 active site 580332005799 Uncharacterized conserved protein [Function unknown]; Region: COG2361 580332005800 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 580332005801 active site 580332005802 NTP binding site [chemical binding]; other site 580332005803 metal binding triad [ion binding]; metal-binding site 580332005804 antibiotic binding site [chemical binding]; other site 580332005805 Uncharacterized conserved protein [Function unknown]; Region: COG3791 580332005806 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 580332005807 ATP binding site [chemical binding]; other site 580332005808 G-X-G motif; other site 580332005809 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 580332005810 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 580332005811 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 580332005812 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 580332005813 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 580332005814 substrate binding site [chemical binding]; other site 580332005815 oxyanion hole (OAH) forming residues; other site 580332005816 trimer interface [polypeptide binding]; other site 580332005817 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 580332005818 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 580332005819 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 580332005820 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 580332005821 acyl-activating enzyme (AAE) consensus motif; other site 580332005822 putative AMP binding site [chemical binding]; other site 580332005823 putative active site [active] 580332005824 putative CoA binding site [chemical binding]; other site 580332005825 short chain dehydrogenase; Provisional; Region: PRK08278 580332005826 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332005827 NAD(P) binding site [chemical binding]; other site 580332005828 active site 580332005829 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 580332005830 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 580332005831 active site 580332005832 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 580332005833 Outer membrane efflux protein; Region: OEP; pfam02321 580332005834 Outer membrane efflux protein; Region: OEP; pfam02321 580332005835 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 580332005836 HlyD family secretion protein; Region: HlyD_3; pfam13437 580332005837 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 580332005838 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 580332005839 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 580332005840 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 580332005841 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 580332005842 S-adenosylmethionine binding site [chemical binding]; other site 580332005843 YHS domain; Region: YHS; pfam04945 580332005844 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 580332005845 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 580332005846 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 580332005847 motif II; other site 580332005848 Short C-terminal domain; Region: SHOCT; pfam09851 580332005849 Cytochrome c; Region: Cytochrom_C; pfam00034 580332005850 Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_1; cd02432 580332005851 Predicted integral membrane protein [Function unknown]; Region: COG3548 580332005852 ferredoxin-NADP+ reductase; Region: PLN02852 580332005853 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 580332005854 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 580332005855 4Fe-4S binding domain; Region: Fer4_5; pfam12801 580332005856 Cytochrome c553 [Energy production and conversion]; Region: COG2863 580332005857 Cytochrome c; Region: Cytochrom_C; cl11414 580332005858 Cytochrome c [Energy production and conversion]; Region: COG3258 580332005859 Cytochrome c; Region: Cytochrom_C; pfam00034 580332005860 hypothetical protein; Provisional; Region: PRK12378 580332005861 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 580332005862 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 580332005863 ATP binding site [chemical binding]; other site 580332005864 putative Mg++ binding site [ion binding]; other site 580332005865 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 580332005866 nucleotide binding region [chemical binding]; other site 580332005867 ATP-binding site [chemical binding]; other site 580332005868 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 580332005869 HRDC domain; Region: HRDC; pfam00570 580332005870 phosphoglucomutase; Region: PLN02307 580332005871 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 580332005872 substrate binding site [chemical binding]; other site 580332005873 dimer interface [polypeptide binding]; other site 580332005874 active site 580332005875 metal binding site [ion binding]; metal-binding site 580332005876 Septum formation initiator; Region: DivIC; cl17659 580332005877 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 580332005878 enolase; Provisional; Region: eno; PRK00077 580332005879 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 580332005880 dimer interface [polypeptide binding]; other site 580332005881 metal binding site [ion binding]; metal-binding site 580332005882 substrate binding pocket [chemical binding]; other site 580332005883 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 580332005884 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 580332005885 CTP synthetase; Validated; Region: pyrG; PRK05380 580332005886 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 580332005887 Catalytic site [active] 580332005888 active site 580332005889 UTP binding site [chemical binding]; other site 580332005890 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 580332005891 active site 580332005892 putative oxyanion hole; other site 580332005893 catalytic triad [active] 580332005894 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 580332005895 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 580332005896 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 580332005897 N-acetyl-D-glucosamine binding site [chemical binding]; other site 580332005898 catalytic residue [active] 580332005899 Protein of unknown function (DUF4063); Region: DUF4063; pfam13272 580332005900 Baseplate J-like protein; Region: Baseplate_J; cl01294 580332005901 coenzyme A disulfide reductase; Reviewed; Region: PRK09564 580332005902 Phage-related baseplate assembly protein; Region: Phage_base_V; cl17812 580332005903 Mu-like prophage tail protein gpP [General function prediction only]; Region: COG4379 580332005904 Bacteriophage protein of unknown function (DUF646); Region: DUF646; pfam04883 580332005905 Phage tail sheath protein; Region: Phage_sheath_1; cl01389 580332005906 Phage-related protein [Function unknown]; Region: COG4695; cl01923 580332005907 Phage portal protein; Region: Phage_portal; pfam04860 580332005908 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5410 580332005909 Terminase-like family; Region: Terminase_6; pfam03237 580332005910 Phage-related terminase [General function prediction only]; Region: COG5362; cl02216 580332005911 Uncharacterized conserved protein (DUF2280); Region: DUF2280; pfam10045 580332005912 Endodeoxyribonuclease RusA; Region: RusA; pfam05866 580332005913 Protein of unknown function (DUF1367); Region: DUF1367; pfam07105 580332005914 DNA methylase; Region: N6_N4_Mtase; cl17433 580332005915 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; cl17220 580332005916 putative DNA binding site [nucleotide binding]; other site 580332005917 putative Zn2+ binding site [ion binding]; other site 580332005918 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown]; Region: COG4197 580332005919 type 2 lantibiotic biosynthesis protein LanM; Region: lanti_2_LanM; TIGR03897 580332005920 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 580332005921 KTSC domain; Region: KTSC; pfam13619 580332005922 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 580332005923 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 580332005924 putative active site [active] 580332005925 putative NTP binding site [chemical binding]; other site 580332005926 putative nucleic acid binding site [nucleotide binding]; other site 580332005927 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 580332005928 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 580332005929 cofactor binding site; other site 580332005930 DNA binding site [nucleotide binding] 580332005931 substrate interaction site [chemical binding]; other site 580332005932 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 580332005933 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 580332005934 Active Sites [active] 580332005935 Phage protein Gp37/Gp68; Region: Gp37_Gp68; cl15384 580332005936 Protein of unknown function (DUF1643); Region: DUF1643; pfam07799 580332005937 Protein of unknown function (DUF3268); Region: DUF3268; pfam11672 580332005938 Protein of unknown function (DUF4031); Region: DUF4031; pfam13223 580332005939 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 580332005940 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 580332005941 dimer interface [polypeptide binding]; other site 580332005942 ssDNA binding site [nucleotide binding]; other site 580332005943 tetramer (dimer of dimers) interface [polypeptide binding]; other site 580332005944 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 580332005945 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 580332005946 catalytic residues [active] 580332005947 catalytic nucleophile [active] 580332005948 Recombinase; Region: Recombinase; pfam07508 580332005949 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 580332005950 Apolipophorin-III precursor (apoLp-III); Region: ApoLp-III; pfam07464 580332005951 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 580332005952 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 580332005953 HlyD family secretion protein; Region: HlyD_3; pfam13437 580332005954 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 580332005955 Protein of unknown function (DUF3240); Region: DUF3240; pfam11582 580332005956 Outer membrane efflux protein; Region: OEP; pfam02321 580332005957 Outer membrane efflux protein; Region: OEP; pfam02321 580332005958 Uncharacterized conserved protein [Function unknown]; Region: COG4095 580332005959 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 580332005960 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 580332005961 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332005962 Zn2+ binding site [ion binding]; other site 580332005963 Mg2+ binding site [ion binding]; other site 580332005964 acetyl-CoA synthetase; Provisional; Region: PRK00174 580332005965 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 580332005966 active site 580332005967 CoA binding site [chemical binding]; other site 580332005968 acyl-activating enzyme (AAE) consensus motif; other site 580332005969 AMP binding site [chemical binding]; other site 580332005970 acetate binding site [chemical binding]; other site 580332005971 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 580332005972 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 580332005973 N-acetyl-D-glucosamine binding site [chemical binding]; other site 580332005974 catalytic residue [active] 580332005975 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 580332005976 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 580332005977 YqjK-like protein; Region: YqjK; pfam13997 580332005978 Predicted membrane protein [Function unknown]; Region: COG5393 580332005979 Bacterial protein of unknown function (DUF883); Region: DUF883; pfam05957 580332005980 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 580332005981 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 580332005982 Walker A/P-loop; other site 580332005983 ATP binding site [chemical binding]; other site 580332005984 Q-loop/lid; other site 580332005985 ABC transporter signature motif; other site 580332005986 Walker B; other site 580332005987 D-loop; other site 580332005988 H-loop/switch region; other site 580332005989 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 580332005990 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 580332005991 Walker A/P-loop; other site 580332005992 ATP binding site [chemical binding]; other site 580332005993 Q-loop/lid; other site 580332005994 ABC transporter signature motif; other site 580332005995 Walker B; other site 580332005996 D-loop; other site 580332005997 H-loop/switch region; other site 580332005998 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 580332005999 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 580332006000 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 580332006001 dimer interface [polypeptide binding]; other site 580332006002 conserved gate region; other site 580332006003 putative PBP binding loops; other site 580332006004 ABC-ATPase subunit interface; other site 580332006005 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 580332006006 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 580332006007 dimer interface [polypeptide binding]; other site 580332006008 conserved gate region; other site 580332006009 putative PBP binding loops; other site 580332006010 ABC-ATPase subunit interface; other site 580332006011 Predicted dinucleotide-binding enzymes [General function prediction only]; Region: COG2085 580332006012 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; pfam03807 580332006013 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 580332006014 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 580332006015 catalytic residues [active] 580332006016 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 580332006017 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 580332006018 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; pfam01891 580332006019 Predicted membrane protein [Function unknown]; Region: COG3235 580332006020 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 580332006021 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 580332006022 Coenzyme A binding pocket [chemical binding]; other site 580332006023 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 580332006024 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 580332006025 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 580332006026 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 580332006027 nucleoside/Zn binding site; other site 580332006028 dimer interface [polypeptide binding]; other site 580332006029 catalytic motif [active] 580332006030 Predicted membrane protein, hemolysin III homolog [General function prediction only]; Region: COG1272 580332006031 channel protein, hemolysin III family; Region: hlyIII; TIGR01065 580332006032 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 580332006033 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 580332006034 catalytic triad [active] 580332006035 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 580332006036 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 580332006037 putative active site [active] 580332006038 PhoH-like protein; Region: PhoH; pfam02562 580332006039 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 580332006040 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 580332006041 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 580332006042 dimer interface [polypeptide binding]; other site 580332006043 N-terminal domain interface [polypeptide binding]; other site 580332006044 putative substrate binding pocket (H-site) [chemical binding]; other site 580332006045 methionine sulfoxide reductase B; Provisional; Region: PRK00222 580332006046 SelR domain; Region: SelR; pfam01641 580332006047 intracellular septation protein A; Reviewed; Region: PRK00259 580332006048 YciI-like protein; Reviewed; Region: PRK11370 580332006049 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 580332006050 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 580332006051 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 580332006052 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 580332006053 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 580332006054 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 580332006055 HlyD family secretion protein; Region: HlyD_3; pfam13437 580332006056 MASE1; Region: MASE1; cl17823 580332006057 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 580332006058 PAS domain; Region: PAS_9; pfam13426 580332006059 putative active site [active] 580332006060 heme pocket [chemical binding]; other site 580332006061 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332006062 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332006063 metal binding site [ion binding]; metal-binding site 580332006064 active site 580332006065 I-site; other site 580332006066 Dna-J like membrane chaperone protein; Provisional; Region: djlA; PRK09430 580332006067 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 580332006068 putative metal binding site [ion binding]; other site 580332006069 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 580332006070 HSP70 interaction site [polypeptide binding]; other site 580332006071 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 580332006072 Catalytic domain of Protein Kinases; Region: PKc; cd00180 580332006073 active site 580332006074 ATP binding site [chemical binding]; other site 580332006075 substrate binding site [chemical binding]; other site 580332006076 activation loop (A-loop); other site 580332006077 HDOD domain; Region: HDOD; pfam08668 580332006078 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 580332006079 GAF domain; Region: GAF_3; pfam13492 580332006080 PAS domain S-box; Region: sensory_box; TIGR00229 580332006081 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 580332006082 putative active site [active] 580332006083 heme pocket [chemical binding]; other site 580332006084 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 580332006085 putative active site [active] 580332006086 heme pocket [chemical binding]; other site 580332006087 RNase II stability modulator; Provisional; Region: PRK10060 580332006088 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 580332006089 putative active site [active] 580332006090 heme pocket [chemical binding]; other site 580332006091 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332006092 metal binding site [ion binding]; metal-binding site 580332006093 active site 580332006094 I-site; other site 580332006095 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 580332006096 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 580332006097 PAS domain; Region: PAS_9; pfam13426 580332006098 putative active site [active] 580332006099 heme pocket [chemical binding]; other site 580332006100 KTSC domain; Region: KTSC; pfam13619 580332006101 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 580332006102 active site residue [active] 580332006103 FOG: CBS domain [General function prediction only]; Region: COG0517 580332006104 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 580332006105 PBP superfamily domain; Region: PBP_like_2; cl17296 580332006106 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 580332006107 PAS fold; Region: PAS_4; pfam08448 580332006108 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 580332006109 PAS domain; Region: PAS_9; pfam13426 580332006110 putative active site [active] 580332006111 heme pocket [chemical binding]; other site 580332006112 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332006113 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332006114 metal binding site [ion binding]; metal-binding site 580332006115 active site 580332006116 I-site; other site 580332006117 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 580332006118 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 580332006119 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 580332006120 dimerization interface [polypeptide binding]; other site 580332006121 ATP binding site [chemical binding]; other site 580332006122 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 580332006123 dimerization interface [polypeptide binding]; other site 580332006124 ATP binding site [chemical binding]; other site 580332006125 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 580332006126 putative active site [active] 580332006127 catalytic triad [active] 580332006128 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 580332006129 putative substrate binding site [chemical binding]; other site 580332006130 putative ATP binding site [chemical binding]; other site 580332006131 Protein of unknown function (DUF2937); Region: DUF2937; pfam11157 580332006132 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 580332006133 S-adenosylmethionine binding site [chemical binding]; other site 580332006134 Uncharacterized ACR, COG1993; Region: DUF190; cl00872 580332006135 chromosome condensation membrane protein; Provisional; Region: PRK14196 580332006136 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 580332006137 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 580332006138 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 580332006139 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 580332006140 FeS/SAM binding site; other site 580332006141 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 580332006142 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 580332006143 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 580332006144 dimerization interface [polypeptide binding]; other site 580332006145 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332006146 dimer interface [polypeptide binding]; other site 580332006147 putative CheW interface [polypeptide binding]; other site 580332006148 PilZ domain; Region: PilZ; pfam07238 580332006149 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 580332006150 putative substrate translocation pore; other site 580332006151 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 580332006152 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 580332006153 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 580332006154 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 580332006155 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 580332006156 RNA binding surface [nucleotide binding]; other site 580332006157 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 580332006158 active site 580332006159 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 580332006160 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 580332006161 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 580332006162 nudix motif; other site 580332006163 Cytochrome c; Region: Cytochrom_C; cl11414 580332006164 FecR protein; Region: FecR; pfam04773 580332006165 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 580332006166 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 580332006167 IHF - DNA interface [nucleotide binding]; other site 580332006168 IHF dimer interface [polypeptide binding]; other site 580332006169 Peptidase family M48; Region: Peptidase_M48; pfam01435 580332006170 CHASE2 domain; Region: CHASE2; pfam05226 580332006171 Adenylyl- / guanylyl cyclase, catalytic domain; Region: CYCc; smart00044 580332006172 cyclase homology domain; Region: CHD; cd07302 580332006173 nucleotidyl binding site; other site 580332006174 metal binding site [ion binding]; metal-binding site 580332006175 dimer interface [polypeptide binding]; other site 580332006176 VacJ like lipoprotein; Region: VacJ; cl01073 580332006177 heat shock protein HtpX; Provisional; Region: PRK05457 580332006178 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 580332006179 Uncharacterized conserved protein [Function unknown]; Region: COG2353 580332006180 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 580332006181 Helix-hairpin-helix motif; Region: HHH; pfam00633 580332006182 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 580332006183 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 580332006184 NADP binding site [chemical binding]; other site 580332006185 homopentamer interface [polypeptide binding]; other site 580332006186 substrate binding site [chemical binding]; other site 580332006187 active site 580332006188 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 580332006189 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 580332006190 putative ribose interaction site [chemical binding]; other site 580332006191 putative ADP binding site [chemical binding]; other site 580332006192 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase...; Region: OMP_decarboxylase_like; cd04725 580332006193 active site 580332006194 dimer interface [polypeptide binding]; other site 580332006195 tetratricopeptide repeat protein; Provisional; Region: PRK11788 580332006196 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 580332006197 binding surface 580332006198 TPR motif; other site 580332006199 Protein of unknown function (DUF1049); Region: DUF1049; pfam06305 580332006200 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 580332006201 IHF dimer interface [polypeptide binding]; other site 580332006202 IHF - DNA interface [nucleotide binding]; other site 580332006203 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 580332006204 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 580332006205 RNA binding site [nucleotide binding]; other site 580332006206 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 580332006207 RNA binding site [nucleotide binding]; other site 580332006208 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec3; cd05688 580332006209 RNA binding site [nucleotide binding]; other site 580332006210 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...; Region: S1_RPS1_repeat_ec4; cd05689 580332006211 RNA binding site [nucleotide binding]; other site 580332006212 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...; Region: S1_RPS1_repeat_ec5; cd05690 580332006213 RNA binding site [nucleotide binding]; other site 580332006214 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...; Region: S1_RPS1_repeat_ec6; cd05691 580332006215 RNA binding site [nucleotide binding]; other site 580332006216 bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidine monophosphate kinase; Provisional; Region: PRK11860 580332006217 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 580332006218 hinge; other site 580332006219 active site 580332006220 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 580332006221 CMP-binding site; other site 580332006222 The sites determining sugar specificity; other site 580332006223 cyclohexadienyl dehydrogenase; Validated; Region: PRK07502 580332006224 prephenate dehydrogenase; Validated; Region: PRK08507 580332006225 3-deoxy-7-phosphoheptulonate synthase; Reviewed; Region: PRK08673 580332006226 phospho-2-dehydro-3-deoxyheptonate aldolase; Region: DAHP_synth_Bsub; TIGR01361 580332006227 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 580332006228 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 580332006229 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332006230 homodimer interface [polypeptide binding]; other site 580332006231 catalytic residue [active] 580332006232 Chorismate mutase type II; Region: CM_2; pfam01817 580332006233 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 580332006234 Prephenate dehydratase; Region: PDT; pfam00800 580332006235 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 580332006236 putative L-Phe binding site [chemical binding]; other site 580332006237 Putative D-3-Phosphoglycerate Dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_like_3; cd12174 580332006238 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 580332006239 putative ligand binding site [chemical binding]; other site 580332006240 putative NAD binding site [chemical binding]; other site 580332006241 putative catalytic site [active] 580332006242 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 580332006243 L-serine binding site [chemical binding]; other site 580332006244 ACT domain interface; other site 580332006245 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 580332006246 homodimer interface [polypeptide binding]; other site 580332006247 substrate-cofactor binding pocket; other site 580332006248 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332006249 catalytic residue [active] 580332006250 DNA gyrase subunit A; Validated; Region: PRK05560 580332006251 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 580332006252 CAP-like domain; other site 580332006253 active site 580332006254 primary dimer interface [polypeptide binding]; other site 580332006255 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 580332006256 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 580332006257 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 580332006258 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 580332006259 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 580332006260 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 580332006261 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 580332006262 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 580332006263 S-adenosylmethionine binding site [chemical binding]; other site 580332006264 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 580332006265 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 580332006266 motif II; other site 580332006267 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 580332006268 cyclase homology domain; Region: CHD; cd07302 580332006269 nucleotidyl binding site; other site 580332006270 metal binding site [ion binding]; metal-binding site 580332006271 dimer interface [polypeptide binding]; other site 580332006272 Hemerythrin; Region: Hemerythrin; cd12107 580332006273 Fe binding site [ion binding]; other site 580332006274 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 580332006275 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 580332006276 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 580332006277 Walker A motif; other site 580332006278 ATP binding site [chemical binding]; other site 580332006279 Walker B motif; other site 580332006280 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 580332006281 active site 580332006282 phosphate binding residues; other site 580332006283 catalytic residues [active] 580332006284 elongation factor P; Validated; Region: PRK00529 580332006285 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 580332006286 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 580332006287 RNA binding site [nucleotide binding]; other site 580332006288 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 580332006289 RNA binding site [nucleotide binding]; other site 580332006290 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4394 580332006291 Uncharacterized protein conserved in bacteria (DUF2331); Region: DUF2331; pfam10093 580332006292 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 580332006293 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 580332006294 FtsX-like permease family; Region: FtsX; pfam02687 580332006295 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 580332006296 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 580332006297 FtsX-like permease family; Region: FtsX; pfam02687 580332006298 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 580332006299 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 580332006300 Walker A/P-loop; other site 580332006301 ATP binding site [chemical binding]; other site 580332006302 Q-loop/lid; other site 580332006303 ABC transporter signature motif; other site 580332006304 Walker B; other site 580332006305 D-loop; other site 580332006306 H-loop/switch region; other site 580332006307 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 580332006308 HlyD family secretion protein; Region: HlyD_3; pfam13437 580332006309 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 580332006310 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 580332006311 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 580332006312 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 580332006313 type IV pilus modification protein PilV; Region: type_IV_pilV; TIGR02523 580332006314 PilX N-terminal; Region: PilX_N; pfam14341 580332006315 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 580332006316 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 580332006317 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 580332006318 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 580332006319 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 580332006320 lipoprotein signal peptidase; Provisional; Region: PRK14787 580332006321 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 580332006322 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 580332006323 active site 580332006324 HIGH motif; other site 580332006325 nucleotide binding site [chemical binding]; other site 580332006326 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 580332006327 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 580332006328 active site 580332006329 KMSKS motif; other site 580332006330 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 580332006331 tRNA binding surface [nucleotide binding]; other site 580332006332 anticodon binding site; other site 580332006333 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 580332006334 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 580332006335 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 580332006336 active site 580332006337 Riboflavin kinase; Region: Flavokinase; pfam01687 580332006338 Hemerythrin; Region: Hemerythrin; cd12107 580332006339 Fe binding site [ion binding]; other site 580332006340 protease TldD; Provisional; Region: tldD; PRK10735 580332006341 nitrilase; Region: PLN02798 580332006342 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 580332006343 putative active site [active] 580332006344 catalytic triad [active] 580332006345 dimer interface [polypeptide binding]; other site 580332006346 TIGR02099 family protein; Region: TIGR02099 580332006347 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 580332006348 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 580332006349 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 580332006350 metal binding triad; other site 580332006351 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 580332006352 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 580332006353 metal binding triad; other site 580332006354 Heme NO binding associated; Region: HNOBA; pfam07701 580332006355 Adenylyl- / guanylyl cyclase, catalytic domain; Region: CYCc; smart00044 580332006356 cyclase homology domain; Region: CHD; cd07302 580332006357 nucleotidyl binding site; other site 580332006358 metal binding site [ion binding]; metal-binding site 580332006359 dimer interface [polypeptide binding]; other site 580332006360 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 580332006361 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 580332006362 homodimer interface [polypeptide binding]; other site 580332006363 substrate-cofactor binding pocket; other site 580332006364 catalytic residue [active] 580332006365 Zinc-finger domain; Region: zf-CHCC; cl01821 580332006366 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 580332006367 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 580332006368 putative active site [active] 580332006369 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 580332006370 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 580332006371 active site 580332006372 substrate binding site [chemical binding]; other site 580332006373 metal binding site [ion binding]; metal-binding site 580332006374 Response regulator receiver domain; Region: Response_reg; pfam00072 580332006375 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 580332006376 active site 580332006377 phosphorylation site [posttranslational modification] 580332006378 intermolecular recognition site; other site 580332006379 dimerization interface [polypeptide binding]; other site 580332006380 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 580332006381 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: AlaRS_core; cd00673 580332006382 motif 1; other site 580332006383 active site 580332006384 motif 2; other site 580332006385 motif 3; other site 580332006386 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 580332006387 DHHA1 domain; Region: DHHA1; pfam02272 580332006388 recombination regulator RecX; Reviewed; Region: recX; PRK00117 580332006389 recombinase A; Provisional; Region: recA; PRK09354 580332006390 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 580332006391 hexamer interface [polypeptide binding]; other site 580332006392 Walker A motif; other site 580332006393 ATP binding site [chemical binding]; other site 580332006394 Walker B motif; other site 580332006395 Competence-damaged protein; Region: CinA; pfam02464 580332006396 O-succinylhomoserine sulfhydrylase; Validated; Region: PRK08133 580332006397 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 580332006398 homodimer interface [polypeptide binding]; other site 580332006399 substrate-cofactor binding pocket; other site 580332006400 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332006401 catalytic residue [active] 580332006402 amidophosphoribosyltransferase; Provisional; Region: PRK09246 580332006403 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 580332006404 active site 580332006405 tetramer interface [polypeptide binding]; other site 580332006406 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 580332006407 active site 580332006408 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 580332006409 Colicin V production protein; Region: Colicin_V; pfam02674 580332006410 Sporulation related domain; Region: SPOR; pfam05036 580332006411 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 580332006412 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 580332006413 hypothetical protein; Provisional; Region: PRK09272 580332006414 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 580332006415 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 580332006416 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 580332006417 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 580332006418 substrate binding site [chemical binding]; other site 580332006419 active site 580332006420 catalytic residues [active] 580332006421 heterodimer interface [polypeptide binding]; other site 580332006422 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 580332006423 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 580332006424 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332006425 catalytic residue [active] 580332006426 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are...; Region: PRAI; cd00405 580332006427 active site 580332006428 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 580332006429 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 580332006430 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 580332006431 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 580332006432 dimerization interface 3.5A [polypeptide binding]; other site 580332006433 active site 580332006434 FimV N-terminal domain; Region: FimV_core; TIGR03505 580332006435 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 580332006436 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 580332006437 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 580332006438 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 580332006439 tartrate dehydrogenase; Region: TTC; TIGR02089 580332006440 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 580332006441 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 580332006442 substrate binding site [chemical binding]; other site 580332006443 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 580332006444 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 580332006445 substrate binding site [chemical binding]; other site 580332006446 ligand binding site [chemical binding]; other site 580332006447 2-isopropylmalate synthase; Validated; Region: PRK03739 580332006448 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 580332006449 active site 580332006450 catalytic residues [active] 580332006451 metal binding site [ion binding]; metal-binding site 580332006452 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 580332006453 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 580332006454 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 580332006455 putative DNA binding site [nucleotide binding]; other site 580332006456 putative Zn2+ binding site [ion binding]; other site 580332006457 AsnC family; Region: AsnC_trans_reg; pfam01037 580332006458 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 580332006459 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 580332006460 putative substrate translocation pore; other site 580332006461 GrpE; Region: GrpE; pfam01025 580332006462 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 580332006463 dimer interface [polypeptide binding]; other site 580332006464 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 580332006465 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 580332006466 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 580332006467 nucleotide binding site [chemical binding]; other site 580332006468 chaperone protein DnaJ; Provisional; Region: PRK10767 580332006469 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 580332006470 HSP70 interaction site [polypeptide binding]; other site 580332006471 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 580332006472 substrate binding site [polypeptide binding]; other site 580332006473 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 580332006474 Zn binding sites [ion binding]; other site 580332006475 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 580332006476 dimer interface [polypeptide binding]; other site 580332006477 LemA family; Region: LemA; cl00742 580332006478 E3 Ubiquitin ligase; Region: GIDE; pfam12483 580332006479 Protein of unknown function, DUF482; Region: DUF482; pfam04339 580332006480 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; cl17497 580332006481 Domain of unknown function (DUF3393); Region: DUF3393; pfam11873 580332006482 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 580332006483 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 580332006484 N-acetyl-D-glucosamine binding site [chemical binding]; other site 580332006485 catalytic residue [active] 580332006486 ABC transporter ATPase component; Reviewed; Region: PRK11147 580332006487 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 580332006488 Walker A/P-loop; other site 580332006489 ATP binding site [chemical binding]; other site 580332006490 Q-loop/lid; other site 580332006491 ABC transporter signature motif; other site 580332006492 Walker B; other site 580332006493 D-loop; other site 580332006494 H-loop/switch region; other site 580332006495 ABC transporter; Region: ABC_tran_2; pfam12848 580332006496 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 580332006497 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 580332006498 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 580332006499 catalytic triad [active] 580332006500 alanine racemase; Reviewed; Region: dadX; PRK03646 580332006501 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 580332006502 active site 580332006503 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 580332006504 substrate binding site [chemical binding]; other site 580332006505 catalytic residues [active] 580332006506 dimer interface [polypeptide binding]; other site 580332006507 lysophospholipid transporter LplT; Provisional; Region: PRK11195 580332006508 Putative serine esterase (DUF676); Region: DUF676; pfam05057 580332006509 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 580332006510 Peptidase family M23; Region: Peptidase_M23; pfam01551 580332006511 Conserved hypothetical protein (DUF2461); Region: DUF2461; pfam09365 580332006512 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 580332006513 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 580332006514 hexamer interface [polypeptide binding]; other site 580332006515 ligand binding site [chemical binding]; other site 580332006516 putative active site [active] 580332006517 NAD(P) binding site [chemical binding]; other site 580332006518 Lecithin:cholesterol acyltransferase; Region: LACT; pfam02450 580332006519 Bacterial capsule synthesis protein PGA_cap; Region: PGA_cap; smart00854 580332006520 CapA and related proteins, metallophosphatase domain; Region: MPP_CapA; cd07381 580332006521 putative active site [active] 580332006522 putative metal binding site [ion binding]; other site 580332006523 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 580332006524 Ligand Binding Site [chemical binding]; other site 580332006525 AAA domain; Region: AAA_32; pfam13654 580332006526 lon-related putative ATP-dependent protease; Region: lon_rel; TIGR00764 580332006527 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 580332006528 RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal...; Region: RaiA; cd00552 580332006529 30S subunit binding site; other site 580332006530 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2187 580332006531 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 580332006532 AAA domain; Region: AAA_33; pfam13671 580332006533 active site 580332006534 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 580332006535 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 580332006536 Walker A motif; other site 580332006537 ATP binding site [chemical binding]; other site 580332006538 Walker B motif; other site 580332006539 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 580332006540 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332006541 Zn2+ binding site [ion binding]; other site 580332006542 Mg2+ binding site [ion binding]; other site 580332006543 MASE1; Region: MASE1; pfam05231 580332006544 CHASE domain; Region: CHASE; pfam03924 580332006545 PAS domain S-box; Region: sensory_box; TIGR00229 580332006546 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 580332006547 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 580332006548 putative active site [active] 580332006549 heme pocket [chemical binding]; other site 580332006550 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 580332006551 putative active site [active] 580332006552 heme pocket [chemical binding]; other site 580332006553 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332006554 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332006555 metal binding site [ion binding]; metal-binding site 580332006556 active site 580332006557 I-site; other site 580332006558 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 580332006559 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 580332006560 putative active site [active] 580332006561 putative metal binding site [ion binding]; other site 580332006562 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 580332006563 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 580332006564 Tfp pilus assembly protein PilV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilV; COG4967 580332006565 Type II transport protein GspH; Region: GspH; pfam12019 580332006566 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 580332006567 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 580332006568 Histidine kinase; Region: HisKA_3; pfam07730 580332006569 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 580332006570 ATP binding site [chemical binding]; other site 580332006571 Mg2+ binding site [ion binding]; other site 580332006572 G-X-G motif; other site 580332006573 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 580332006574 active site 580332006575 catalytic triad [active] 580332006576 oxyanion hole [active] 580332006577 switch loop; other site 580332006578 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 580332006579 putative active site [active] 580332006580 heme pocket [chemical binding]; other site 580332006581 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332006582 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332006583 metal binding site [ion binding]; metal-binding site 580332006584 active site 580332006585 I-site; other site 580332006586 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 580332006587 active site 580332006588 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 580332006589 dimer interface [polypeptide binding]; other site 580332006590 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 580332006591 HEAT repeats; Region: HEAT_2; pfam13646 580332006592 Uncharacterized protein family UPF0047; Region: UPF0047; pfam01894 580332006593 Domain of unknown function (DUF336); Region: DUF336; pfam03928 580332006594 multidrug efflux protein; Reviewed; Region: PRK01766 580332006595 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 580332006596 cation binding site [ion binding]; other site 580332006597 Predicted membrane protein [Function unknown]; Region: COG2259 580332006598 Bacterial protein of unknown function (DUF934); Region: DUF934; cl01526 580332006599 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 580332006600 Domain of unknown function (DUF4160); Region: DUF4160; pfam13711 580332006601 Protein of unknown function (DUF2442); Region: DUF2442; pfam10387 580332006602 Methyltransferase domain; Region: Methyltransf_31; pfam13847 580332006603 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 580332006604 S-adenosylmethionine binding site [chemical binding]; other site 580332006605 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 580332006606 Walker A/P-loop; other site 580332006607 ATP binding site [chemical binding]; other site 580332006608 AAA domain; Region: AAA_21; pfam13304 580332006609 Nuclease-related domain; Region: NERD; pfam08378 580332006610 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 580332006611 Family description; Region: UvrD_C_2; pfam13538 580332006612 aminomethyltransferase; Region: PLN02319 580332006613 Plasmid maintenance system antidote protein [General function prediction only]; Region: VapI; COG3093 580332006614 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 580332006615 sequence-specific DNA binding site [nucleotide binding]; other site 580332006616 salt bridge; other site 580332006617 Plasmid maintenance system killer protein; Region: Plasmid_killer; cl01422 580332006618 PAS domain S-box; Region: sensory_box; TIGR00229 580332006619 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 580332006620 putative active site [active] 580332006621 heme pocket [chemical binding]; other site 580332006622 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 580332006623 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 580332006624 Predicted transcriptional regulator [Transcription]; Region: COG2932 580332006625 Catalytic site [active] 580332006626 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 580332006627 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 580332006628 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 580332006629 cyclase homology domain; Region: CHD; cd07302 580332006630 nucleotidyl binding site; other site 580332006631 metal binding site [ion binding]; metal-binding site 580332006632 dimer interface [polypeptide binding]; other site 580332006633 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14464 580332006634 Membrane protein of unknown function; Region: DUF360; pfam04020 580332006635 DEDDy 3'-5' exonuclease domain of WRN and similar proteins; Region: WRN_exo; cd06141 580332006636 catalytic site [active] 580332006637 putative active site [active] 580332006638 putative substrate binding site [chemical binding]; other site 580332006639 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 580332006640 Clp amino terminal domain; Region: Clp_N; pfam02861 580332006641 Clp amino terminal domain; Region: Clp_N; pfam02861 580332006642 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 580332006643 Walker A motif; other site 580332006644 ATP binding site [chemical binding]; other site 580332006645 Walker B motif; other site 580332006646 arginine finger; other site 580332006647 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 580332006648 Walker A motif; other site 580332006649 ATP binding site [chemical binding]; other site 580332006650 Walker B motif; other site 580332006651 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 580332006652 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK06978 580332006653 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 580332006654 dimerization interface [polypeptide binding]; other site 580332006655 active site 580332006656 thioredoxin 2; Provisional; Region: PRK10996 580332006657 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 580332006658 catalytic residues [active] 580332006659 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 580332006660 Methyltransferase domain; Region: Methyltransf_31; pfam13847 580332006661 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 580332006662 S-adenosylmethionine binding site [chemical binding]; other site 580332006663 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 580332006664 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 580332006665 Membrane transport protein; Region: Mem_trans; cl09117 580332006666 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 580332006667 binding surface 580332006668 TPR motif; other site 580332006669 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 580332006670 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 580332006671 binding surface 580332006672 TPR motif; other site 580332006673 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 580332006674 FecR protein; Region: FecR; pfam04773 580332006675 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 580332006676 binding surface 580332006677 TPR motif; other site 580332006678 Tetratricopeptide repeat; Region: TPR_16; pfam13432 580332006679 Protein of unknown function (DUF560); Region: DUF560; pfam04575 580332006680 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 580332006681 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 580332006682 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 580332006683 active site 580332006684 phosphorylation site [posttranslational modification] 580332006685 intermolecular recognition site; other site 580332006686 dimerization interface [polypeptide binding]; other site 580332006687 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 580332006688 DNA binding residues [nucleotide binding] 580332006689 dimerization interface [polypeptide binding]; other site 580332006690 PAS fold; Region: PAS; pfam00989 580332006691 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 580332006692 putative active site [active] 580332006693 heme pocket [chemical binding]; other site 580332006694 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 580332006695 Histidine kinase; Region: HisKA_3; pfam07730 580332006696 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 580332006697 ATP binding site [chemical binding]; other site 580332006698 Mg2+ binding site [ion binding]; other site 580332006699 G-X-G motif; other site 580332006700 Protein of unknown function (DUF535); Region: DUF535; cl01128 580332006701 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 580332006702 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants; Region: Thr-synth_2; cd01560 580332006703 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332006704 catalytic residue [active] 580332006705 homoserine dehydrogenase; Provisional; Region: PRK06349 580332006706 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 580332006707 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 580332006708 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 580332006709 aminotransferase AlaT; Validated; Region: PRK09265 580332006710 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 580332006711 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332006712 homodimer interface [polypeptide binding]; other site 580332006713 catalytic residue [active] 580332006714 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 580332006715 MoxR-like ATPases [General function prediction only]; Region: COG0714 580332006716 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 580332006717 Walker A motif; other site 580332006718 ATP binding site [chemical binding]; other site 580332006719 Walker B motif; other site 580332006720 arginine finger; other site 580332006721 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 580332006722 Protein of unknown function DUF58; Region: DUF58; pfam01882 580332006723 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 580332006724 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 580332006725 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 580332006726 Domain of unknown function (DUF4129); Region: DUF4129; pfam13559 580332006727 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 580332006728 active site 580332006729 Response regulator receiver domain; Region: Response_reg; pfam00072 580332006730 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 580332006731 active site 580332006732 phosphorylation site [posttranslational modification] 580332006733 intermolecular recognition site; other site 580332006734 dimerization interface [polypeptide binding]; other site 580332006735 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332006736 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332006737 metal binding site [ion binding]; metal-binding site 580332006738 active site 580332006739 I-site; other site 580332006740 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 580332006741 dimerization interface [polypeptide binding]; other site 580332006742 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 580332006743 PAS domain; Region: PAS_9; pfam13426 580332006744 putative active site [active] 580332006745 heme pocket [chemical binding]; other site 580332006746 PAS domain S-box; Region: sensory_box; TIGR00229 580332006747 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 580332006748 putative active site [active] 580332006749 heme pocket [chemical binding]; other site 580332006750 PAS domain S-box; Region: sensory_box; TIGR00229 580332006751 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 580332006752 putative active site [active] 580332006753 heme pocket [chemical binding]; other site 580332006754 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 580332006755 PAS domain; Region: PAS_9; pfam13426 580332006756 putative active site [active] 580332006757 heme pocket [chemical binding]; other site 580332006758 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332006759 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332006760 metal binding site [ion binding]; metal-binding site 580332006761 active site 580332006762 I-site; other site 580332006763 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 580332006764 Fe-S cluster binding site [ion binding]; other site 580332006765 active site 580332006766 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 580332006767 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 580332006768 Coenzyme A binding pocket [chemical binding]; other site 580332006769 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 580332006770 Glycoprotease family; Region: Peptidase_M22; pfam00814 580332006771 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 580332006772 homotrimer interaction site [polypeptide binding]; other site 580332006773 zinc binding site [ion binding]; other site 580332006774 CDP-binding sites; other site 580332006775 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 580332006776 substrate binding site; other site 580332006777 dimer interface; other site 580332006778 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 580332006779 GAF domain; Region: GAF; pfam01590 580332006780 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 580332006781 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332006782 Zn2+ binding site [ion binding]; other site 580332006783 Mg2+ binding site [ion binding]; other site 580332006784 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 580332006785 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 580332006786 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 580332006787 ATP binding site [chemical binding]; other site 580332006788 putative Mg++ binding site [ion binding]; other site 580332006789 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 580332006790 nucleotide binding region [chemical binding]; other site 580332006791 ATP-binding site [chemical binding]; other site 580332006792 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 580332006793 Domain of unknown function (DUF4258); Region: DUF4258; pfam14076 580332006794 Protein of unknown function (DUF2283); Region: DUF2283; pfam10049 580332006795 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 580332006796 triphenylmethane reductase (TMR)-like proteins, NMRa-like, atypical (a) SDRs; Region: TMR_SDR_a; cd05269 580332006797 NADP binding site [chemical binding]; other site 580332006798 Predicted transcriptional regulators [Transcription]; Region: COG1733 580332006799 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 580332006800 Domain of unknown function (DUF4072); Region: DUF4072; pfam13284 580332006801 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 580332006802 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 580332006803 motif II; other site 580332006804 Galactose binding lectin domain; Region: Gal_Lectin; pfam02140 580332006805 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 580332006806 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; Region: NrdJ_Z; TIGR02504 580332006807 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 580332006808 active site 580332006809 dimer interface [polypeptide binding]; other site 580332006810 effector binding site; other site 580332006811 Predicted permeases [General function prediction only]; Region: COG0679 580332006812 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 580332006813 DEAD-like helicases superfamily; Region: DEXDc; smart00487 580332006814 ATP binding site [chemical binding]; other site 580332006815 Mg++ binding site [ion binding]; other site 580332006816 motif III; other site 580332006817 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 580332006818 nucleotide binding region [chemical binding]; other site 580332006819 ATP-binding site [chemical binding]; other site 580332006820 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 580332006821 uncharacterized flavoprotein, PP_4765 family; Region: flavo_PP4765; TIGR03862 580332006822 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 580332006823 Invasion gene expression up-regulator, SirB; Region: SirB; pfam04247 580332006824 Protein of unknown function (DUF2798); Region: DUF2798; pfam11391 580332006825 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 580332006826 Iron-sulphur cluster assembly; Region: Fe-S_assembly; pfam04384 580332006827 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 580332006828 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 580332006829 catalytic loop [active] 580332006830 iron binding site [ion binding]; other site 580332006831 chaperone protein HscA; Provisional; Region: hscA; PRK05183 580332006832 Nucleotide-binding domain of HscA and similar proteins; Region: HscA_like_NBD; cd10236 580332006833 nucleotide binding site [chemical binding]; other site 580332006834 putative NEF/HSP70 interaction site [polypeptide binding]; other site 580332006835 SBD interface [polypeptide binding]; other site 580332006836 co-chaperone HscB; Provisional; Region: hscB; PRK03578 580332006837 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 580332006838 HSP70 interaction site [polypeptide binding]; other site 580332006839 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 580332006840 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 580332006841 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 580332006842 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 580332006843 trimerization site [polypeptide binding]; other site 580332006844 active site 580332006845 cysteine desulfurase; Provisional; Region: PRK14012 580332006846 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 580332006847 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 580332006848 catalytic residue [active] 580332006849 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 580332006850 Rrf2 family protein; Region: rrf2_super; TIGR00738 580332006851 serine O-acetyltransferase; Region: cysE; TIGR01172 580332006852 Serine acetyltransferase, N-terminal; Region: SATase_N; cl05762 580332006853 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 580332006854 trimer interface [polypeptide binding]; other site 580332006855 active site 580332006856 substrate binding site [chemical binding]; other site 580332006857 CoA binding site [chemical binding]; other site 580332006858 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 580332006859 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 580332006860 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 580332006861 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 580332006862 active site 580332006863 dimerization interface [polypeptide binding]; other site 580332006864 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 580332006865 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 580332006866 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 580332006867 MutS domain I; Region: MutS_I; pfam01624 580332006868 MutS domain II; Region: MutS_II; pfam05188 580332006869 MutS domain III; Region: MutS_III; pfam05192 580332006870 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 580332006871 Walker A/P-loop; other site 580332006872 ATP binding site [chemical binding]; other site 580332006873 Q-loop/lid; other site 580332006874 ABC transporter signature motif; other site 580332006875 Walker B; other site 580332006876 D-loop; other site 580332006877 H-loop/switch region; other site 580332006878 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 580332006879 Uncharacterized conserved protein [Function unknown]; Region: COG0397 580332006880 hypothetical protein; Validated; Region: PRK00029 580332006881 Protein of unknown function (DUF3301); Region: DUF3301; pfam11743 580332006882 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 580332006883 Protein of unknown function (DUF1697); Region: DUF1697; pfam08002 580332006884 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332006885 Zn2+ binding site [ion binding]; other site 580332006886 Mg2+ binding site [ion binding]; other site 580332006887 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 580332006888 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 580332006889 Zn2+ binding site [ion binding]; other site 580332006890 Mg2+ binding site [ion binding]; other site 580332006891 transcriptional regulator TraR; Provisional; Region: PRK13870 580332006892 Autoinducer binding domain; Region: Autoind_bind; pfam03472 580332006893 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 580332006894 DNA binding residues [nucleotide binding] 580332006895 dimerization interface [polypeptide binding]; other site 580332006896 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332006897 metal binding site [ion binding]; metal-binding site 580332006898 active site 580332006899 I-site; other site 580332006900 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 580332006901 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; pfam13640 580332006902 Putative redox-active protein (C_GCAxxG_C_C); Region: C_GCAxxG_C_C; pfam09719 580332006903 Cache domain; Region: Cache_1; pfam02743 580332006904 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 580332006905 metal binding site [ion binding]; metal-binding site 580332006906 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 580332006907 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 580332006908 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 580332006909 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 580332006910 ATP binding site [chemical binding]; other site 580332006911 Walker B motif; other site 580332006912 glycerol-3-phosphate dehydrogenase (NAD(+)); Region: glycerol3P_DH; TIGR03376 580332006913 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 580332006914 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 580332006915 Glycosyl transferase family 1; Region: Glyco_trans_1_3; pfam13528 580332006916 Domain of unknown function (DUF1992); Region: DUF1992; cl08096 580332006917 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 580332006918 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 580332006919 Catalytic site [active] 580332006920 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 580332006921 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 580332006922 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 580332006923 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 580332006924 catalytic triad [active] 580332006925 Cupin superfamily protein; Region: Cupin_4; pfam08007 580332006926 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 580332006927 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]; Region: NlpB; COG3317 580332006928 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]; Region: NlpB; COG3317 580332006929 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 580332006930 dihydrodipicolinate synthase; Region: dapA; TIGR00674 580332006931 dimer interface [polypeptide binding]; other site 580332006932 active site 580332006933 catalytic residue [active] 580332006934 Fe2+ transport system protein A [Inorganic ion transport and metabolism]; Region: FeoA; COG1918 580332006935 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 580332006936 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 580332006937 G1 box; other site 580332006938 GTP/Mg2+ binding site [chemical binding]; other site 580332006939 Switch I region; other site 580332006940 G2 box; other site 580332006941 G3 box; other site 580332006942 Switch II region; other site 580332006943 G4 box; other site 580332006944 G5 box; other site 580332006945 Nucleoside recognition; Region: Gate; pfam07670 580332006946 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 580332006947 Nucleoside recognition; Region: Gate; pfam07670 580332006948 Polycystin cation channel protein; Provisional; Region: PLN03223 580332006949 YfaZ precursor; Region: YfaZ; pfam07437 580332006950 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 580332006951 YccA-like proteins; Region: YccA_like; cd10433 580332006952 HopJ type III effector protein; Region: HopJ; pfam08888 580332006953 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 580332006954 active site residue [active] 580332006955 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 580332006956 TRAM domain; Region: TRAM; cl01282 580332006957 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 580332006958 S-adenosylmethionine binding site [chemical binding]; other site 580332006959 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 580332006960 active site 580332006961 catalytic site [active] 580332006962 substrate binding site [chemical binding]; other site 580332006963 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 580332006964 SOS regulatory protein LexA; Region: lexA; TIGR00498 580332006965 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 580332006966 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 580332006967 Catalytic site [active] 580332006968 Lipase. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is "interfacial activation", the process of...; Region: Lipase; cl14883 580332006969 nucleophilic elbow; other site 580332006970 catalytic triad; other site 580332006971 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 580332006972 Transposase IS200 like; Region: Y1_Tnp; cl00848 580332006973 Protein of unknown function (DUF3617); Region: DUF3617; pfam12276 580332006974 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 580332006975 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 580332006976 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 580332006977 binding surface 580332006978 TPR motif; other site 580332006979 Peptidase family M48; Region: Peptidase_M48; cl12018 580332006980 Bacterial SH3 domain; Region: SH3_3; pfam08239 580332006981 CHASE2 domain; Region: CHASE2; pfam05226 580332006982 superoxide dismutase; Provisional; Region: PRK10543 580332006983 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 580332006984 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 580332006985 lipoyl synthase; Provisional; Region: PRK05481 580332006986 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 580332006987 FeS/SAM binding site; other site 580332006988 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 580332006989 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 580332006990 Walker A motif; other site 580332006991 ATP binding site [chemical binding]; other site 580332006992 DNA alkylation repair enzyme; Region: DNA_alkylation; pfam08713 580332006993 A new structural DNA glycosylase; Region: AlkD_like; cd06561 580332006994 active site 580332006995 hypothetical protein; Provisional; Region: PRK09256 580332006996 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 580332006997 S4 domain; Region: S4_2; pfam13275 580332006998 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 580332006999 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 580332007000 G1 box; other site 580332007001 putative GEF interaction site [polypeptide binding]; other site 580332007002 GTP/Mg2+ binding site [chemical binding]; other site 580332007003 Switch I region; other site 580332007004 G2 box; other site 580332007005 G3 box; other site 580332007006 Switch II region; other site 580332007007 G4 box; other site 580332007008 G5 box; other site 580332007009 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 580332007010 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 580332007011 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 580332007012 substrate binding pocket [chemical binding]; other site 580332007013 membrane-bound complex binding site; other site 580332007014 hinge residues; other site 580332007015 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 580332007016 cyclic-di-GMP phosphodiesterase; Provisional; Region: PRK11359 580332007017 putative active site [active] 580332007018 heme pocket [chemical binding]; other site 580332007019 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 580332007020 putative active site [active] 580332007021 heme pocket [chemical binding]; other site 580332007022 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 580332007023 putative active site [active] 580332007024 heme pocket [chemical binding]; other site 580332007025 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332007026 metal binding site [ion binding]; metal-binding site 580332007027 active site 580332007028 I-site; other site 580332007029 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 580332007030 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 580332007031 dimerization interface [polypeptide binding]; other site 580332007032 putative DNA binding site [nucleotide binding]; other site 580332007033 putative Zn2+ binding site [ion binding]; other site 580332007034 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_1; cd08894 580332007035 putative hydrophobic ligand binding site [chemical binding]; other site 580332007036 YCII-related domain; Region: YCII; cl00999 580332007037 RibD C-terminal domain; Region: RibD_C; cl17279 580332007038 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 580332007039 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 580332007040 hydrophobic ligand binding site; other site 580332007041 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 580332007042 hydrophobic ligand binding site; other site 580332007043 RibD C-terminal domain; Region: RibD_C; cl17279 580332007044 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins; Region: SRPBCC_1; cd07818 580332007045 putative hydrophobic ligand binding site [chemical binding]; other site 580332007046 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 580332007047 dimer interface [polypeptide binding]; other site 580332007048 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 580332007049 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 580332007050 dimer interface [polypeptide binding]; other site 580332007051 RibD C-terminal domain; Region: RibD_C; cl17279 580332007052 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 580332007053 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 580332007054 dimer interface [polypeptide binding]; other site 580332007055 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 580332007056 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 580332007057 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 580332007058 Bacterial protein of unknown function (DUF924); Region: DUF924; pfam06041 580332007059 B12 binding domain; Region: B12-binding; pfam02310 580332007060 B12 binding site [chemical binding]; other site 580332007061 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 580332007062 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 580332007063 FeS/SAM binding site; other site 580332007064 Protein of unknown function (DUF4080); Region: DUF4080; pfam13311 580332007065 Karyopherin (importin) beta [Intracellular trafficking and secretion]; Region: KAP95; COG5215 580332007066 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 580332007067 Transposase; Region: HTH_Tnp_1; cl17663 580332007068 putative transposase OrfB; Reviewed; Region: PHA02517 580332007069 HTH-like domain; Region: HTH_21; pfam13276 580332007070 Integrase core domain; Region: rve; pfam00665 580332007071 Integrase core domain; Region: rve_3; pfam13683 580332007072 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 580332007073 HDOD domain; Region: HDOD; pfam08668 580332007074 Hemerythrin; Region: Hemerythrin; cd12107 580332007075 Fe binding site [ion binding]; other site 580332007076 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 580332007077 PAS domain; Region: PAS_9; pfam13426 580332007078 putative active site [active] 580332007079 heme pocket [chemical binding]; other site 580332007080 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332007081 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332007082 metal binding site [ion binding]; metal-binding site 580332007083 active site 580332007084 I-site; other site 580332007085 Protein of unknown function (DUF3014); Region: DUF3014; pfam11219 580332007086 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 580332007087 metal ion-dependent adhesion site (MIDAS); other site 580332007088 MoxR-like ATPases [General function prediction only]; Region: COG0714 580332007089 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 580332007090 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 580332007091 SEC-C motif; Region: SEC-C; pfam02810 580332007092 hypothetical protein; Provisional; Region: PRK04233 580332007093 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 580332007094 nucleotide binding site/active site [active] 580332007095 HIT family signature motif; other site 580332007096 catalytic residue [active] 580332007097 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 580332007098 serine/threonine protein kinase; Provisional; Region: PRK11768 580332007099 Protein of unknown function (DUF1415); Region: DUF1415; pfam07209 580332007100 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 580332007101 DEAD-like helicases superfamily; Region: DEXDc; smart00487 580332007102 ATP binding site [chemical binding]; other site 580332007103 Mg++ binding site [ion binding]; other site 580332007104 motif III; other site 580332007105 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 580332007106 nucleotide binding region [chemical binding]; other site 580332007107 ATP-binding site [chemical binding]; other site 580332007108 GTP-binding protein YchF; Reviewed; Region: PRK09601 580332007109 YchF GTPase; Region: YchF; cd01900 580332007110 G1 box; other site 580332007111 GTP/Mg2+ binding site [chemical binding]; other site 580332007112 Switch I region; other site 580332007113 G2 box; other site 580332007114 Switch II region; other site 580332007115 G3 box; other site 580332007116 G4 box; other site 580332007117 G5 box; other site 580332007118 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 580332007119 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 580332007120 putative active site [active] 580332007121 catalytic residue [active] 580332007122 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 580332007123 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 580332007124 5S rRNA interface [nucleotide binding]; other site 580332007125 CTC domain interface [polypeptide binding]; other site 580332007126 L16 interface [polypeptide binding]; other site 580332007127 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 580332007128 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 580332007129 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 580332007130 active site 580332007131 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 580332007132 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 580332007133 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 580332007134 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 580332007135 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 580332007136 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 580332007137 TPR motif; other site 580332007138 binding surface 580332007139 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 580332007140 TPR motif; other site 580332007141 binding surface 580332007142 TPR repeat; Region: TPR_11; pfam13414 580332007143 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 580332007144 binding surface 580332007145 TPR motif; other site 580332007146 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 580332007147 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 580332007148 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 580332007149 Walker A/P-loop; other site 580332007150 ATP binding site [chemical binding]; other site 580332007151 Q-loop/lid; other site 580332007152 ABC transporter signature motif; other site 580332007153 Walker B; other site 580332007154 D-loop; other site 580332007155 H-loop/switch region; other site 580332007156 gliding motility-associated ABC transporter permease protein GldF; Region: ABC_perm_GldF; TIGR03518 580332007157 ABC-type uncharacterized transport system; Region: ABC_transp_aux; pfam09822 580332007158 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 580332007159 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 580332007160 DNA binding site [nucleotide binding] 580332007161 catalytic residue [active] 580332007162 H2TH interface [polypeptide binding]; other site 580332007163 putative catalytic residues [active] 580332007164 turnover-facilitating residue; other site 580332007165 intercalation triad [nucleotide binding]; other site 580332007166 8OG recognition residue [nucleotide binding]; other site 580332007167 putative reading head residues; other site 580332007168 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 580332007169 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 580332007170 PAS domain S-box; Region: sensory_box; TIGR00229 580332007171 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 580332007172 putative active site [active] 580332007173 heme pocket [chemical binding]; other site 580332007174 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332007175 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332007176 metal binding site [ion binding]; metal-binding site 580332007177 active site 580332007178 I-site; other site 580332007179 Hemerythrin; Region: Hemerythrin; cd12107 580332007180 Fe binding site [ion binding]; other site 580332007181 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 580332007182 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 580332007183 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 580332007184 active site 580332007185 (T/H)XGH motif; other site 580332007186 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 580332007187 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 580332007188 S-adenosylmethionine binding site [chemical binding]; other site 580332007189 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 580332007190 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 580332007191 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 580332007192 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 580332007193 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 580332007194 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 580332007195 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 580332007196 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 580332007197 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 580332007198 Walker A/P-loop; other site 580332007199 ATP binding site [chemical binding]; other site 580332007200 Q-loop/lid; other site 580332007201 ABC transporter signature motif; other site 580332007202 Walker B; other site 580332007203 D-loop; other site 580332007204 H-loop/switch region; other site 580332007205 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 580332007206 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 580332007207 Hemerythrin; Region: Hemerythrin; cd12107 580332007208 Fe binding site [ion binding]; other site 580332007209 Predicted transcriptional regulator [Transcription]; Region: COG1959 580332007210 Transcriptional regulator; Region: Rrf2; cl17282 580332007211 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 580332007212 apolar tunnel; other site 580332007213 heme binding site [chemical binding]; other site 580332007214 dimerization interface [polypeptide binding]; other site 580332007215 hypothetical protein; Provisional; Region: PRK05713 580332007216 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 580332007217 catalytic loop [active] 580332007218 iron binding site [ion binding]; other site 580332007219 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 580332007220 FAD binding pocket [chemical binding]; other site 580332007221 FAD binding motif [chemical binding]; other site 580332007222 phosphate binding motif [ion binding]; other site 580332007223 beta-alpha-beta structure motif; other site 580332007224 NAD binding pocket [chemical binding]; other site 580332007225 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 580332007226 peptidase PmbA; Provisional; Region: PRK11040 580332007227 hypothetical protein; Provisional; Region: PRK05255 580332007228 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 580332007229 PAS domain; Region: PAS_9; pfam13426 580332007230 putative active site [active] 580332007231 heme pocket [chemical binding]; other site 580332007232 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 580332007233 putative hydrolase; Provisional; Region: PRK11460 580332007234 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 580332007235 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 580332007236 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 580332007237 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 580332007238 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 580332007239 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 580332007240 quinone interaction residues [chemical binding]; other site 580332007241 active site 580332007242 catalytic residues [active] 580332007243 FMN binding site [chemical binding]; other site 580332007244 substrate binding site [chemical binding]; other site 580332007245 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 580332007246 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 580332007247 GAF domain; Region: GAF_3; pfam13492 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 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 580332007256 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 580332007257 active site 580332007258 phosphorylation site [posttranslational modification] 580332007259 intermolecular recognition site; other site 580332007260 dimerization interface [polypeptide binding]; other site 580332007261 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 580332007262 DNA binding site [nucleotide binding] 580332007263 K+ transporter [Inorganic ion transport and metabolism]; Region: Kup; COG3158 580332007264 potassium uptake protein; Region: kup; TIGR00794 580332007265 electron transport complex protein RsxA; Provisional; Region: PRK05151 580332007266 electron transport complex protein RnfB; Provisional; Region: PRK05113 580332007267 Putative Fe-S cluster; Region: FeS; pfam04060 580332007268 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 580332007269 SLBB domain; Region: SLBB; pfam10531 580332007270 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 580332007271 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 580332007272 FMN-binding domain; Region: FMN_bind; cl01081 580332007273 electron transport complex RsxE subunit; Provisional; Region: PRK12405 580332007274 endonuclease III; Provisional; Region: PRK10702 580332007275 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 580332007276 minor groove reading motif; other site 580332007277 helix-hairpin-helix signature motif; other site 580332007278 substrate binding pocket [chemical binding]; other site 580332007279 active site 580332007280 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 580332007281 Domain of unknown function (DUF1841); Region: DUF1841; pfam08897 580332007282 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 580332007283 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 580332007284 CDP-diacylglycerol--serine O-phosphatidyltransferase; Region: pssA; TIGR00473 580332007285 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 580332007286 ketol-acid reductoisomerase; Provisional; Region: PRK05479 580332007287 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 580332007288 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 580332007289 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 580332007290 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 580332007291 putative valine binding site [chemical binding]; other site 580332007292 dimer interface [polypeptide binding]; other site 580332007293 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 580332007294 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06965 580332007295 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 580332007296 PYR/PP interface [polypeptide binding]; other site 580332007297 dimer interface [polypeptide binding]; other site 580332007298 TPP binding site [chemical binding]; other site 580332007299 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 580332007300 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 580332007301 TPP-binding site [chemical binding]; other site 580332007302 dimer interface [polypeptide binding]; other site 580332007303 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 580332007304 RNA polymerase factor sigma-70; Validated; Region: PRK09047 580332007305 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 580332007306 DNA binding residues [nucleotide binding] 580332007307 Protein of unknown function (DUF3619); Region: DUF3619; pfam12279 580332007308 Protein of unknown function (DUF3106); Region: DUF3106; pfam11304 580332007309 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 580332007310 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 580332007311 Predicted permeases [General function prediction only]; Region: COG0795 580332007312 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 580332007313 multifunctional aminopeptidase A; Provisional; Region: PRK00913 580332007314 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 580332007315 interface (dimer of trimers) [polypeptide binding]; other site 580332007316 Substrate-binding/catalytic site; other site 580332007317 Zn-binding sites [ion binding]; other site 580332007318 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; pfam04364 580332007319 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 580332007320 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 580332007321 HIGH motif; other site 580332007322 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 580332007323 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 580332007324 active site 580332007325 KMSKS motif; other site 580332007326 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 580332007327 tRNA binding surface [nucleotide binding]; other site 580332007328 anticodon binding site; other site 580332007329 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 580332007330 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 580332007331 CPxP motif; other site 580332007332 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 580332007333 active site residue [active] 580332007334 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 580332007335 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 580332007336 active site 580332007337 ATP binding site [chemical binding]; other site 580332007338 substrate binding site [chemical binding]; other site 580332007339 activation loop (A-loop); other site 580332007340 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 580332007341 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 580332007342 ligand binding site [chemical binding]; other site 580332007343 flexible hinge region; other site 580332007344 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 580332007345 Peptidase family M48; Region: Peptidase_M48; cl12018 580332007346 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 580332007347 TPR motif; other site 580332007348 binding surface 580332007349 High-affinity nickel-transport protein; Region: NicO; cl00964 580332007350 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 580332007351 dimerization interface [polypeptide binding]; other site 580332007352 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 580332007353 ATP binding site [chemical binding]; other site 580332007354 hydrogenase isoenzymes formation protein HypD; Provisional; Region: PRK15062 580332007355 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 580332007356 HupF/HypC family; Region: HupF_HypC; pfam01455 580332007357 Acylphosphatase; Region: Acylphosphatase; pfam00708 580332007358 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 580332007359 HypF finger; Region: zf-HYPF; pfam07503 580332007360 HypF finger; Region: zf-HYPF; pfam07503 580332007361 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 580332007362 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 580332007363 Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]; Region: HybF; COG0375 580332007364 Hydrogenase expression/synthesis hypA family; Region: HypA; pfam01155 580332007365 Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion]; Region: FrhA; COG3259 580332007366 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 580332007367 dimerization interface [polypeptide binding]; other site 580332007368 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332007369 dimer interface [polypeptide binding]; other site 580332007370 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 580332007371 putative CheW interface [polypeptide binding]; other site 580332007372 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 580332007373 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 580332007374 tellurium resistance terB-like protein, subgroup 2; Region: terB_like_2; cd07313 580332007375 putative metal binding site [ion binding]; other site 580332007376 SlyX; Region: SlyX; pfam04102 580332007377 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 580332007378 Fic/DOC family; Region: Fic; pfam02661 580332007379 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 580332007380 Restriction endonuclease; Region: Mrr_cat; pfam04471 580332007381 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 580332007382 Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized proteins with a DEAD domain; Region: PLDc_Bfil_DEXD_like; cd09117 580332007383 PLD-like domain; Region: PLDc_2; pfam13091 580332007384 homodimer interface [polypeptide binding]; other site 580332007385 putative active site [active] 580332007386 catalytic site [active] 580332007387 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 580332007388 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 580332007389 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 580332007390 ATP binding site [chemical binding]; other site 580332007391 putative Mg++ binding site [ion binding]; other site 580332007392 Domain of unknown function (DUF3387); Region: DUF3387; pfam11867 580332007393 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 580332007394 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 580332007395 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 580332007396 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 580332007397 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 580332007398 HsdM N-terminal domain; Region: HsdM_N; pfam12161 580332007399 Methyltransferase domain; Region: Methyltransf_26; pfam13659 580332007400 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 580332007401 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 580332007402 non-specific DNA binding site [nucleotide binding]; other site 580332007403 salt bridge; other site 580332007404 sequence-specific DNA binding site [nucleotide binding]; other site 580332007405 Domain of unknown function (DUF955); Region: DUF955; cl01076 580332007406 Dodecin; Region: Dodecin; pfam07311 580332007407 Fic family protein [Function unknown]; Region: COG3177 580332007408 Fic/DOC family N-terminal; Region: Fic_N; pfam13784 580332007409 Fic/DOC family; Region: Fic; pfam02661 580332007410 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 580332007411 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 580332007412 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 580332007413 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 580332007414 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 580332007415 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 580332007416 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 580332007417 DNA binding residues [nucleotide binding] 580332007418 DNA primase; Validated; Region: dnaG; PRK05667 580332007419 CHC2 zinc finger; Region: zf-CHC2; pfam01807 580332007420 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 580332007421 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 580332007422 active site 580332007423 metal binding site [ion binding]; metal-binding site 580332007424 interdomain interaction site; other site 580332007425 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; cl07879 580332007426 Yqey-like protein; Region: YqeY; pfam09424 580332007427 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 580332007428 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 580332007429 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 580332007430 active site 580332007431 HIGH motif; other site 580332007432 dimer interface [polypeptide binding]; other site 580332007433 KMSKS motif; other site 580332007434 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 580332007435 RNA binding surface [nucleotide binding]; other site 580332007436 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 580332007437 Peptidase family M23; Region: Peptidase_M23; pfam01551 580332007438 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 580332007439 iron-sulfur cluster insertion protein ErpA; Provisional; Region: PRK13623 580332007440 Integral membrane protein CcmA involved in cell shape determination [Cell envelope biogenesis, outer membrane]; Region: CcmA; COG1664 580332007441 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 580332007442 Axonemal dynein light chain; Region: Ax_dynein_light; pfam10211 580332007443 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 580332007444 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 580332007445 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 580332007446 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 580332007447 23S rRNA interface [nucleotide binding]; other site 580332007448 L3 interface [polypeptide binding]; other site 580332007449 Glycerol kinase [Energy production and conversion]; Region: GlpK; COG0554 580332007450 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 580332007451 nucleotide binding site [chemical binding]; other site 580332007452 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 580332007453 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GlpA; COG0578 580332007454 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 580332007455 Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins; Region: GDPD; cd08556 580332007456 active site 580332007457 catalytic site [active] 580332007458 metal binding site [ion binding]; metal-binding site 580332007459 Esterase/lipase [General function prediction only]; Region: COG1647 580332007460 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 580332007461 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 580332007462 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332007463 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332007464 metal binding site [ion binding]; metal-binding site 580332007465 active site 580332007466 I-site; other site 580332007467 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 580332007468 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 580332007469 putative acyl-acceptor binding pocket; other site 580332007470 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; cl17496 580332007471 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 580332007472 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 580332007473 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 580332007474 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 580332007475 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 580332007476 active site 580332007477 HAMP domain; Region: HAMP; pfam00672 580332007478 dimerization interface [polypeptide binding]; other site 580332007479 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 580332007480 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332007481 dimer interface [polypeptide binding]; other site 580332007482 putative CheW interface [polypeptide binding]; other site 580332007483 Zinc dependent phospholipase C; Region: Zn_dep_PLPC; pfam00882 580332007484 Uncharacterized conserved protein [Function unknown]; Region: COG1434 580332007485 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 580332007486 putative active site [active] 580332007487 OsmC-like protein; Region: OsmC; cl00767 580332007488 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 580332007489 diiron binding motif [ion binding]; other site 580332007490 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4634 580332007491 Protein of unknown function (DUF433); Region: DUF433; pfam04255 580332007492 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 580332007493 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 580332007494 trimer interface [polypeptide binding]; other site 580332007495 eyelet of channel; other site 580332007496 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 580332007497 trimer interface [polypeptide binding]; other site 580332007498 eyelet of channel; other site 580332007499 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 580332007500 phosphoenolpyruvate synthase; Validated; Region: PRK06464 580332007501 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 580332007502 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 580332007503 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 580332007504 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 580332007505 electron transport complex RsxE subunit; Provisional; Region: PRK12405 580332007506 NADH:ubiquinone oxidoreductase, Na(+)-translocating, C subunit; Region: nqrC; TIGR01938 580332007507 FMN-binding domain; Region: FMN_bind; cl01081 580332007508 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; pfam03116 580332007509 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 580332007510 SLBB domain; Region: SLBB; pfam10531 580332007511 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 580332007512 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, alpha subunit [Energy production and conversion]; Region: PorA; COG0674 580332007513 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 580332007514 dimer interface [polypeptide binding]; other site 580332007515 PYR/PP interface [polypeptide binding]; other site 580332007516 TPP binding site [chemical binding]; other site 580332007517 substrate binding site [chemical binding]; other site 580332007518 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 580332007519 pyruvate/ketoisovalerate ferredoxin oxidoreductase subunit gamma; Provisional; Region: PRK14029 580332007520 4Fe-4S binding domain; Region: Fer4_6; pfam12837 580332007521 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 580332007522 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, beta subunit [Energy production and conversion]; Region: PorB; COG1013 580332007523 TPP-binding site [chemical binding]; other site 580332007524 4Fe-4S single cluster domain; Region: Fer4_15; pfam13459 580332007525 ferredoxin; Provisional; Region: PRK08764 580332007526 Putative Fe-S cluster; Region: FeS; cl17515 580332007527 Transcriptional regulator [Transcription]; Region: LysR; COG0583 580332007528 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 580332007529 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 580332007530 dimerization interface [polypeptide binding]; other site 580332007531 PEP synthetase regulatory protein; Provisional; Region: PRK05339 580332007532 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 580332007533 probable sodium:solute symporter, VC_2705 subfamily; Region: Na_symport_lg; TIGR03648 580332007534 Domain of unknown function (DUF4212); Region: DUF4212; pfam13937 580332007535 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 580332007536 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 580332007537 active site 580332007538 phosphorylation site [posttranslational modification] 580332007539 intermolecular recognition site; other site 580332007540 dimerization interface [polypeptide binding]; other site 580332007541 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 580332007542 DNA binding site [nucleotide binding] 580332007543 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 580332007544 HAMP domain; Region: HAMP; pfam00672 580332007545 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 580332007546 dimer interface [polypeptide binding]; other site 580332007547 phosphorylation site [posttranslational modification] 580332007548 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 580332007549 ATP binding site [chemical binding]; other site 580332007550 Mg2+ binding site [ion binding]; other site 580332007551 G-X-G motif; other site 580332007552 Planctomycete cytochrome C; Region: PSCyt1; pfam07635 580332007553 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 580332007554 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 580332007555 Protein of unknown function (DUF3374); Region: DUF3374; cl11904 580332007556 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 580332007557 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 580332007558 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 580332007559 Cytochrome c; Region: Cytochrom_C; cl11414 580332007560 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 580332007561 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 580332007562 ATP binding site [chemical binding]; other site 580332007563 Mg2+ binding site [ion binding]; other site 580332007564 G-X-G motif; other site 580332007565 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 580332007566 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 580332007567 active site 580332007568 phosphorylation site [posttranslational modification] 580332007569 intermolecular recognition site; other site 580332007570 dimerization interface [polypeptide binding]; other site 580332007571 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 580332007572 DNA binding residues [nucleotide binding] 580332007573 dimerization interface [polypeptide binding]; other site 580332007574 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 580332007575 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 580332007576 Na binding site [ion binding]; other site 580332007577 Protein of unknown function, DUF485; Region: DUF485; pfam04341 580332007578 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 580332007579 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 580332007580 active site 580332007581 catalytic site [active] 580332007582 substrate binding site [chemical binding]; other site 580332007583 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 580332007584 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 580332007585 ligand binding site [chemical binding]; other site 580332007586 flexible hinge region; other site 580332007587 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 580332007588 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 580332007589 metal binding triad; other site 580332007590 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 580332007591 active site 580332007592 ribulose/triose binding site [chemical binding]; other site 580332007593 phosphate binding site [ion binding]; other site 580332007594 substrate (anthranilate) binding pocket [chemical binding]; other site 580332007595 product (indole) binding pocket [chemical binding]; other site 580332007596 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 580332007597 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 580332007598 putative catalytic cysteine [active] 580332007599 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 580332007600 E3 interaction surface; other site 580332007601 lipoyl attachment site [posttranslational modification]; other site 580332007602 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 580332007603 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 580332007604 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 580332007605 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 580332007606 Protein of unknown function (DUF4197); Region: DUF4197; pfam13852 580332007607 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 580332007608 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 580332007609 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 580332007610 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 580332007611 HlyD family secretion protein; Region: HlyD_3; pfam13437 580332007612 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 580332007613 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 580332007614 Walker A/P-loop; other site 580332007615 ATP binding site [chemical binding]; other site 580332007616 Q-loop/lid; other site 580332007617 ABC transporter signature motif; other site 580332007618 Walker B; other site 580332007619 D-loop; other site 580332007620 H-loop/switch region; other site 580332007621 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 580332007622 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 580332007623 Walker A/P-loop; other site 580332007624 ATP binding site [chemical binding]; other site 580332007625 Q-loop/lid; other site 580332007626 ABC transporter signature motif; other site 580332007627 Walker B; other site 580332007628 D-loop; other site 580332007629 H-loop/switch region; other site 580332007630 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 580332007631 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 580332007632 ABC-2 family transporter protein; Region: ABC2_membrane_2; pfam12679 580332007633 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 580332007634 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 580332007635 Predicted membrane protein [Function unknown]; Region: COG1238 580332007636 PAS domain S-box; Region: sensory_box; TIGR00229 580332007637 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 580332007638 putative active site [active] 580332007639 heme pocket [chemical binding]; other site 580332007640 PAS domain S-box; Region: sensory_box; TIGR00229 580332007641 PAS domain S-box; Region: sensory_box; TIGR00229 580332007642 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 580332007643 putative active site [active] 580332007644 heme pocket [chemical binding]; other site 580332007645 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 580332007646 PAS domain; Region: PAS_9; pfam13426 580332007647 putative active site [active] 580332007648 heme pocket [chemical binding]; other site 580332007649 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332007650 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332007651 metal binding site [ion binding]; metal-binding site 580332007652 active site 580332007653 I-site; other site 580332007654 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 580332007655 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 580332007656 putative catalytic site [active] 580332007657 putative metal binding site [ion binding]; other site 580332007658 putative phosphate binding site [ion binding]; other site 580332007659 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 580332007660 interface (dimer of trimers) [polypeptide binding]; other site 580332007661 Substrate-binding/catalytic site; other site 580332007662 Zn-binding sites [ion binding]; other site 580332007663 thymidylate synthase; Reviewed; Region: thyA; PRK01827 580332007664 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 580332007665 dimerization interface [polypeptide binding]; other site 580332007666 active site 580332007667 S23 ribosomal protein; Region: Ribosomal_S23p; pfam05635 580332007668 four helix bundle protein; Region: TIGR02436 580332007669 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 580332007670 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 580332007671 folate binding site [chemical binding]; other site 580332007672 NADP+ binding site [chemical binding]; other site 580332007673 Trehalose-6-phosphate synthase [Carbohydrate transport and metabolism]; Region: OtsA; COG0380 580332007674 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 580332007675 active site 580332007676 homotetramer interface [polypeptide binding]; other site 580332007677 trehalose-6-phosphate phosphatase; Provisional; Region: PRK10187; cl17105 580332007678 Trehalose-phosphatase; Region: Trehalose_PPase; pfam02358 580332007679 Glucoamylase and related glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: SGA1; COG3387 580332007680 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 580332007681 Ca2+/H+ antiporter [Inorganic ion transport and metabolism]; Region: ChaA; COG0387 580332007682 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 580332007683 Iron permease FTR1 family; Region: FTR1; cl00475 580332007684 Cupredoxin-like domain; Region: Cupredoxin_1; pfam13473 580332007685 ferric uptake regulator; Provisional; Region: fur; PRK09462 580332007686 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 580332007687 metal binding site 2 [ion binding]; metal-binding site 580332007688 putative DNA binding helix; other site 580332007689 metal binding site 1 [ion binding]; metal-binding site 580332007690 dimer interface [polypeptide binding]; other site 580332007691 structural Zn2+ binding site [ion binding]; other site 580332007692 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 580332007693 Peptidase family U32; Region: Peptidase_U32; pfam01136 580332007694 Collagenase; Region: DUF3656; pfam12392 580332007695 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 580332007696 dimerization interface [polypeptide binding]; other site 580332007697 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 580332007698 PAS domain; Region: PAS_9; pfam13426 580332007699 putative active site [active] 580332007700 heme pocket [chemical binding]; other site 580332007701 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332007702 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332007703 metal binding site [ion binding]; metal-binding site 580332007704 active site 580332007705 I-site; other site 580332007706 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 580332007707 alpha-L-glutamate ligases, RimK family; Region: rimK_fam; TIGR00768 580332007708 phosphoserine aminotransferase; Provisional; Region: PRK12462 580332007709 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 580332007710 catalytic residue [active] 580332007711 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 580332007712 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 580332007713 catalytic residues [active] 580332007714 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 580332007715 RNA binding surface [nucleotide binding]; other site 580332007716 Orn/Lys/Arg decarboxylase, N-terminal domain; Region: OKR_DC_1_N; pfam03709 580332007717 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 580332007718 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 580332007719 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 580332007720 catalytic residue [active] 580332007721 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 580332007722 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 580332007723 trimer interface [polypeptide binding]; other site 580332007724 active site 580332007725 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 580332007726 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 580332007727 active site 580332007728 HIGH motif; other site 580332007729 KMSKS motif; other site 580332007730 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 580332007731 tRNA binding surface [nucleotide binding]; other site 580332007732 anticodon binding site; other site 580332007733 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 580332007734 dimer interface [polypeptide binding]; other site 580332007735 putative tRNA-binding site [nucleotide binding]; other site 580332007736 soluble pyridine nucleotide transhydrogenase; Provisional; Region: PRK05249 580332007737 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 580332007738 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 580332007739 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 580332007740 putative zinc finger/helix-turn-helix protein, YgiT family; Region: CxxCG_CxxCG_HTH; TIGR03830 580332007741 YgiT-type zinc finger domain; Region: YgiT_finger; TIGR03831 580332007742 Zn binding site [ion binding]; other site 580332007743 toxin interface [polypeptide binding]; other site 580332007744 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 580332007745 non-specific DNA binding site [nucleotide binding]; other site 580332007746 salt bridge; other site 580332007747 sequence-specific DNA binding site [nucleotide binding]; other site 580332007748 Motility quorum-sensing regulator (MqsR); Region: MqsR; cd12869 580332007749 peptide binding site [polypeptide binding]; other site 580332007750 Hemerythrin; Region: Hemerythrin; cd12107 580332007751 Fe binding site [ion binding]; other site 580332007752 ATP synthase subunit D; Region: ATP-synt_D; pfam01813 580332007753 V-type ATP synthase subunit B; Provisional; Region: PRK04196 580332007754 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 580332007755 Walker A motif homologous position; other site 580332007756 Walker B motif; other site 580332007757 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 580332007758 V-type ATP synthase subunit A; Provisional; Region: PRK04192 580332007759 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 580332007760 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 580332007761 Walker A motif/ATP binding site; other site 580332007762 Walker B motif; other site 580332007763 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 580332007764 V-type ATP synthase subunit E; Provisional; Region: PRK03963; cl17074 580332007765 ATP synthase (F/14-kDa) subunit; Region: ATP-synt_F; pfam01990 580332007766 ATP synthase subunit C; Region: ATP-synt_C; cl00466 580332007767 V-type ATP synthase subunit I; Validated; Region: PRK05771 580332007768 V-type ATP synthase subunit C; Provisional; Region: PRK01198; cl00660 580332007769 Archaeal/vacuolar-type H+-ATPase subunit C [Energy production and conversion]; Region: NtpC; COG1527 580332007770 Ni,Fe-hydrogenase III small subunit [Energy production and conversion]; Region: COG3260 580332007771 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; pfam00329 580332007772 Ni,Fe-hydrogenase III large subunit [Energy production and conversion]; Region: HycE; COG3261 580332007773 NADH dehydrogenase subunit D; Validated; Region: PRK06075; cl17338 580332007774 hydrogenase 4 subunit F; Validated; Region: PRK06458 580332007775 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 580332007776 Hydrogenase 4 membrane component (E) [Energy production and conversion]; Region: HyfE; cl17899 580332007777 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 580332007778 hydrogenase 4 subunit B; Validated; Region: PRK06521 580332007779 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 580332007780 FOG: CBS domain [General function prediction only]; Region: COG0517 580332007781 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 580332007782 FOG: CBS domain [General function prediction only]; Region: COG0517 580332007783 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 580332007784 PAS fold; Region: PAS_4; pfam08448 580332007785 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 580332007786 putative active site [active] 580332007787 heme pocket [chemical binding]; other site 580332007788 PAS domain S-box; Region: sensory_box; TIGR00229 580332007789 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 580332007790 putative active site [active] 580332007791 heme pocket [chemical binding]; other site 580332007792 PAS domain S-box; Region: sensory_box; TIGR00229 580332007793 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 580332007794 putative active site [active] 580332007795 heme pocket [chemical binding]; other site 580332007796 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 580332007797 PAS domain; Region: PAS_9; pfam13426 580332007798 putative active site [active] 580332007799 heme pocket [chemical binding]; other site 580332007800 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332007801 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332007802 metal binding site [ion binding]; metal-binding site 580332007803 active site 580332007804 I-site; other site 580332007805 Cyclic nucleotide-binding domain; Region: cNMP_binding; pfam00027 580332007806 global nitrogen regulator NtcA, cyanobacterial; Region: NtcA_cyano; TIGR03697 580332007807 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 580332007808 putative switch regulator; other site 580332007809 non-specific DNA interactions [nucleotide binding]; other site 580332007810 DNA binding site [nucleotide binding] 580332007811 sequence specific DNA binding site [nucleotide binding]; other site 580332007812 putative cAMP binding site [chemical binding]; other site 580332007813 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 580332007814 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 580332007815 putative active site [active] 580332007816 putative PHP Thumb interface [polypeptide binding]; other site 580332007817 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 580332007818 generic binding surface II; other site 580332007819 generic binding surface I; other site 580332007820 Dihaem cytochrome c; Region: DHC; pfam09626 580332007821 membrane-bound lytic transglycosylase F; Provisional; Region: PRK10859 580332007822 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 580332007823 substrate binding pocket [chemical binding]; other site 580332007824 membrane-bound complex binding site; other site 580332007825 hinge residues; other site 580332007826 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 580332007827 N-acetyl-D-glucosamine binding site [chemical binding]; other site 580332007828 catalytic residue [active] 580332007829 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 580332007830 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332007831 NAD(P) binding site [chemical binding]; other site 580332007832 active site 580332007833 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 580332007834 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 580332007835 FtsX-like permease family; Region: FtsX; pfam02687 580332007836 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 580332007837 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 580332007838 Walker A/P-loop; other site 580332007839 ATP binding site [chemical binding]; other site 580332007840 Q-loop/lid; other site 580332007841 ABC transporter signature motif; other site 580332007842 Walker B; other site 580332007843 D-loop; other site 580332007844 H-loop/switch region; other site 580332007845 seryl-tRNA synthetase; Provisional; Region: PRK05431 580332007846 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 580332007847 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme...; Region: SerRS_core; cd00770 580332007848 dimer interface [polypeptide binding]; other site 580332007849 active site 580332007850 motif 1; other site 580332007851 motif 2; other site 580332007852 motif 3; other site 580332007853 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_3; pfam13366 580332007854 recombination factor protein RarA; Reviewed; Region: PRK13342 580332007855 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 580332007856 Walker A motif; other site 580332007857 ATP binding site [chemical binding]; other site 580332007858 Walker B motif; other site 580332007859 arginine finger; other site 580332007860 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 580332007861 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 580332007862 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 580332007863 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 580332007864 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 580332007865 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 580332007866 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 580332007867 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 580332007868 active site 580332007869 phosphorylation site [posttranslational modification] 580332007870 intermolecular recognition site; other site 580332007871 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 580332007872 DNA binding residues [nucleotide binding] 580332007873 dimerization interface [polypeptide binding]; other site 580332007874 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 580332007875 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 580332007876 dimer interface [polypeptide binding]; other site 580332007877 phosphorylation site [posttranslational modification] 580332007878 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 580332007879 ATP binding site [chemical binding]; other site 580332007880 Mg2+ binding site [ion binding]; other site 580332007881 G-X-G motif; other site 580332007882 Response regulator receiver domain; Region: Response_reg; pfam00072 580332007883 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 580332007884 active site 580332007885 phosphorylation site [posttranslational modification] 580332007886 intermolecular recognition site; other site 580332007887 dimerization interface [polypeptide binding]; other site 580332007888 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 580332007889 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 580332007890 Cu(I) binding site [ion binding]; other site 580332007891 Family description; Region: DsbD_2; pfam13386 580332007892 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 580332007893 AAA domain; Region: AAA_26; pfam13500 580332007894 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 580332007895 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 580332007896 S-adenosylmethionine binding site [chemical binding]; other site 580332007897 pimelyl-[acyl-carrier protein] methyl ester esterase; Region: bioH; TIGR01738 580332007898 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 580332007899 TAP-like protein; Region: Abhydrolase_4; pfam08386 580332007900 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 580332007901 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 580332007902 substrate-cofactor binding pocket; other site 580332007903 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332007904 catalytic residue [active] 580332007905 biotin synthase; Region: bioB; TIGR00433 580332007906 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 580332007907 FeS/SAM binding site; other site 580332007908 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 580332007909 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 580332007910 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 580332007911 active site 580332007912 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 580332007913 binding surface 580332007914 TPR motif; other site 580332007915 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 580332007916 binding surface 580332007917 TPR motif; other site 580332007918 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 580332007919 AAA ATPase domain; Region: AAA_16; pfam13191 580332007920 Secretin and TonB N terminus short domain; Region: STN; pfam07660 580332007921 Secretin N-terminal domain; Region: Secretin_N_2; pfam07655 580332007922 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 580332007923 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 580332007924 Type II secretory pathway, component PulL [Intracellular trafficking and secretion]; Region: PulL; COG3297 580332007925 type IV pilus assembly protein PilM; Region: pilM; TIGR01175 580332007926 legume lectins; Region: lectin_L-type; cl14058 580332007927 homotetramer interaction site [polypeptide binding]; other site 580332007928 homodimer interaction site [polypeptide binding]; other site 580332007929 carbohydrate binding site [chemical binding]; other site 580332007930 metal binding site [ion binding]; metal-binding site 580332007931 Tfp pilus assembly protein PilV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilV; COG4967 580332007932 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 580332007933 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 580332007934 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 580332007935 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 580332007936 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 580332007937 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 580332007938 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 580332007939 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 580332007940 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 580332007941 Walker A motif; other site 580332007942 ATP binding site [chemical binding]; other site 580332007943 Walker B motif; other site 580332007944 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 580332007945 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 580332007946 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 580332007947 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 580332007948 Bacterial SH3 domain; Region: SH3_4; pfam06347 580332007949 preprotein translocase subunit SecB; Validated; Region: PRK05751 580332007950 SecA binding site; other site 580332007951 Preprotein binding site; other site 580332007952 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 580332007953 GSH binding site [chemical binding]; other site 580332007954 catalytic residues [active] 580332007955 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 580332007956 active site residue [active] 580332007957 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 580332007958 O-Antigen ligase; Region: Wzy_C; pfam04932 580332007959 Domain of unknown function (DUF3366); Region: DUF3366; pfam11846 580332007960 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 580332007961 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 580332007962 Protein export membrane protein; Region: SecD_SecF; cl14618 580332007963 Protein export membrane protein; Region: SecD_SecF; cl14618 580332007964 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 580332007965 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 580332007966 HlyD family secretion protein; Region: HlyD_3; pfam13437 580332007967 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 580332007968 dimerization interface [polypeptide binding]; other site 580332007969 putative DNA binding site [nucleotide binding]; other site 580332007970 putative Zn2+ binding site [ion binding]; other site 580332007971 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 580332007972 phosphoglyceromutase; Provisional; Region: PRK05434 580332007973 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 580332007974 Peptidase family M23; Region: Peptidase_M23; pfam01551 580332007975 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 580332007976 C-terminal peptidase (prc); Region: prc; TIGR00225 580332007977 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 580332007978 protein binding site [polypeptide binding]; other site 580332007979 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 580332007980 Catalytic dyad [active] 580332007981 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332007982 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332007983 metal binding site [ion binding]; metal-binding site 580332007984 active site 580332007985 I-site; other site 580332007986 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 580332007987 Beta-lactamase; Region: Beta-lactamase; pfam00144 580332007988 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 580332007989 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 580332007990 NodB motif; other site 580332007991 active site 580332007992 catalytic site [active] 580332007993 metal binding site [ion binding]; metal-binding site 580332007994 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 580332007995 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 580332007996 S-adenosylmethionine binding site [chemical binding]; other site 580332007997 ribonucleotide-diphosphate reductase subunit beta; Provisional; Region: nrdF2; PRK13966 580332007998 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 580332007999 dimer interface [polypeptide binding]; other site 580332008000 putative radical transfer pathway; other site 580332008001 diiron center [ion binding]; other site 580332008002 tyrosyl radical; other site 580332008003 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07207 580332008004 ATP cone domain; Region: ATP-cone; pfam03477 580332008005 Class I ribonucleotide reductase; Region: RNR_I; cd01679 580332008006 active site 580332008007 dimer interface [polypeptide binding]; other site 580332008008 catalytic residues [active] 580332008009 effector binding site; other site 580332008010 R2 peptide binding site; other site 580332008011 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 580332008012 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 580332008013 amidase catalytic site [active] 580332008014 Zn binding residues [ion binding]; other site 580332008015 substrate binding site [chemical binding]; other site 580332008016 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 580332008017 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 580332008018 active site 580332008019 phosphorylation site [posttranslational modification] 580332008020 intermolecular recognition site; other site 580332008021 dimerization interface [polypeptide binding]; other site 580332008022 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 580332008023 Walker A motif; other site 580332008024 ATP binding site [chemical binding]; other site 580332008025 Walker B motif; other site 580332008026 arginine finger; other site 580332008027 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 580332008028 PAS domain; Region: PAS; smart00091 580332008029 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 580332008030 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 580332008031 dimer interface [polypeptide binding]; other site 580332008032 phosphorylation site [posttranslational modification] 580332008033 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 580332008034 ATP binding site [chemical binding]; other site 580332008035 Mg2+ binding site [ion binding]; other site 580332008036 G-X-G motif; other site 580332008037 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 580332008038 Protein of unknown function (DUF1418); Region: DUF1418; cl11648 580332008039 4Fe-4S binding domain; Region: Fer4_5; pfam12801 580332008040 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 580332008041 Major Facilitator Superfamily; Region: MFS_1; pfam07690 580332008042 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 580332008043 S-adenosylmethionine binding site [chemical binding]; other site 580332008044 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 580332008045 Uncharacterized conserved protein [Function unknown]; Region: COG1262 580332008046 Cytochrome c; Region: Cytochrom_C; pfam00034 580332008047 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 580332008048 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 580332008049 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 580332008050 Low-spin heme binding site [chemical binding]; other site 580332008051 D-pathway; other site 580332008052 Putative water exit pathway; other site 580332008053 Binuclear center (active site) [active] 580332008054 K-pathway; other site 580332008055 Putative proton exit pathway; other site 580332008056 Cytochrome c; Region: Cytochrom_C; cl11414 580332008057 Cytochrome c; Region: Cytochrom_C; cl11414 580332008058 Cytochrome c; Region: Cytochrom_C; pfam00034 580332008059 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 580332008060 Thiol-disulfide isomerase and thioredoxins [Posttranslational modification, protein turnover, chaperones / Energy production and conversion]; Region: TrxA; COG0526 580332008061 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 580332008062 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 580332008063 MPT binding site; other site 580332008064 trimer interface [polypeptide binding]; other site 580332008065 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 580332008066 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 580332008067 dimer interface [polypeptide binding]; other site 580332008068 putative functional site; other site 580332008069 putative MPT binding site; other site 580332008070 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 580332008071 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 580332008072 GTP binding site; other site 580332008073 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 580332008074 Walker A motif; other site 580332008075 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 580332008076 MoaE homodimer interface [polypeptide binding]; other site 580332008077 MoaD interaction [polypeptide binding]; other site 580332008078 active site residues [active] 580332008079 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 580332008080 MoaE interaction surface [polypeptide binding]; other site 580332008081 MoeB interaction surface [polypeptide binding]; other site 580332008082 thiocarboxylated glycine; other site 580332008083 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 580332008084 trimer interface [polypeptide binding]; other site 580332008085 dimer interface [polypeptide binding]; other site 580332008086 putative active site [active] 580332008087 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 580332008088 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 580332008089 ATP binding site [chemical binding]; other site 580332008090 substrate interface [chemical binding]; other site 580332008091 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 580332008092 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 580332008093 FeS/SAM binding site; other site 580332008094 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 580332008095 twin arginine translocase protein A; Provisional; Region: tatA; PRK02958 580332008096 Domain of unknown function DUF59; Region: DUF59; pfam01883 580332008097 antiporter inner membrane protein; Provisional; Region: PRK11670 580332008098 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 580332008099 Walker A motif; other site 580332008100 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 580332008101 NlpC/P60 family; Region: NLPC_P60; pfam00877 580332008102 Transglycosylase SLT domain; Region: SLT_2; pfam13406 580332008103 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 580332008104 N-acetyl-D-glucosamine binding site [chemical binding]; other site 580332008105 catalytic residue [active] 580332008106 thioredoxin reductase; Provisional; Region: PRK10262 580332008107 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 580332008108 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 580332008109 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 580332008110 Smr domain; Region: Smr; pfam01713 580332008111 peroxidase; Provisional; Region: PRK15000 580332008112 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 580332008113 dimer interface [polypeptide binding]; other site 580332008114 decamer (pentamer of dimers) interface [polypeptide binding]; other site 580332008115 catalytic triad [active] 580332008116 peroxidatic and resolving cysteines [active] 580332008117 Hemerythrin; Region: Hemerythrin; cd12107 580332008118 Fe binding site [ion binding]; other site 580332008119 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 580332008120 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 580332008121 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 580332008122 Walker A/P-loop; other site 580332008123 ATP binding site [chemical binding]; other site 580332008124 Q-loop/lid; other site 580332008125 ABC transporter signature motif; other site 580332008126 Walker B; other site 580332008127 D-loop; other site 580332008128 H-loop/switch region; other site 580332008129 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 580332008130 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 580332008131 N-terminal plug; other site 580332008132 ligand-binding site [chemical binding]; other site 580332008133 Protein of unknown function (DUF972); Region: DUF972; pfam06156 580332008134 Cell division protein ZapA; Region: ZapA; pfam05164 580332008135 EVE domain; Region: EVE; cl00728 580332008136 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 580332008137 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 580332008138 4Fe-4S binding domain; Region: Fer4_5; pfam12801 580332008139 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 580332008140 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 580332008141 Walker A/P-loop; other site 580332008142 ATP binding site [chemical binding]; other site 580332008143 Q-loop/lid; other site 580332008144 ABC transporter signature motif; other site 580332008145 Walker B; other site 580332008146 D-loop; other site 580332008147 H-loop/switch region; other site 580332008148 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 580332008149 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 580332008150 Walker A/P-loop; other site 580332008151 ATP binding site [chemical binding]; other site 580332008152 Q-loop/lid; other site 580332008153 ABC transporter signature motif; other site 580332008154 Walker B; other site 580332008155 D-loop; other site 580332008156 H-loop/switch region; other site 580332008157 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 580332008158 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 580332008159 TM-ABC transporter signature motif; other site 580332008160 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 580332008161 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 580332008162 TM-ABC transporter signature motif; other site 580332008163 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 580332008164 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 580332008165 dimerization interface [polypeptide binding]; other site 580332008166 ligand binding site [chemical binding]; other site 580332008167 Cytochrome c; Region: Cytochrom_C; cl11414 580332008168 Cytochrome c; Region: Cytochrom_C; cl11414 580332008169 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 580332008170 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 580332008171 P-loop; other site 580332008172 Magnesium ion binding site [ion binding]; other site 580332008173 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 580332008174 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 580332008175 Domain of unknown function DUF21; Region: DUF21; pfam01595 580332008176 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 580332008177 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 580332008178 Transporter associated domain; Region: CorC_HlyC; smart01091 580332008179 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 580332008180 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 580332008181 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 580332008182 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 580332008183 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 580332008184 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 580332008185 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 580332008186 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 580332008187 CoA-binding site [chemical binding]; other site 580332008188 ATP-binding [chemical binding]; other site 580332008189 hypothetical protein; Provisional; Region: PRK05287 580332008190 Domain of unknown function (DUF329); Region: DUF329; pfam03884 580332008191 hypothetical protein; Provisional; Region: PRK08999 580332008192 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 580332008193 active site 580332008194 8-oxo-dGMP binding site [chemical binding]; other site 580332008195 nudix motif; other site 580332008196 metal binding site [ion binding]; metal-binding site 580332008197 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 580332008198 thiamine phosphate binding site [chemical binding]; other site 580332008199 active site 580332008200 pyrophosphate binding site [ion binding]; other site 580332008201 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 580332008202 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 580332008203 Walker A motif; other site 580332008204 ATP binding site [chemical binding]; other site 580332008205 Walker B motif; other site 580332008206 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 580332008207 heterotetramer interface [polypeptide binding]; other site 580332008208 active site pocket [active] 580332008209 cleavage site 580332008210 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 580332008211 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 580332008212 ligand binding site [chemical binding]; other site 580332008213 flexible hinge region; other site 580332008214 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 580332008215 DEAD/DEAH box helicase; Region: DEAD; pfam00270 580332008216 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 580332008217 SEC-C motif; Region: SEC-C; pfam02810 580332008218 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 580332008219 Peptidase family M23; Region: Peptidase_M23; pfam01551 580332008220 Protein of unknown function (DUF721); Region: DUF721; cl02324 580332008221 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 580332008222 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 580332008223 cell division protein FtsZ; Validated; Region: PRK09330 580332008224 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 580332008225 nucleotide binding site [chemical binding]; other site 580332008226 SulA interaction site; other site 580332008227 cell division protein FtsA; Region: ftsA; TIGR01174 580332008228 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 580332008229 nucleotide binding site [chemical binding]; other site 580332008230 SHS2 domain inserted in FTSA; Region: SHS2_FTSA; pfam02491 580332008231 Cell division protein FtsA; Region: FtsA; pfam14450 580332008232 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 580332008233 Cell division protein FtsQ; Region: FtsQ; pfam03799 580332008234 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 580332008235 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 580332008236 ATP-grasp domain; Region: ATP-grasp_4; cl17255 580332008237 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 580332008238 FAD binding domain; Region: FAD_binding_4; pfam01565 580332008239 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 580332008240 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 580332008241 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 580332008242 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 580332008243 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 580332008244 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 580332008245 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 580332008246 active site 580332008247 homodimer interface [polypeptide binding]; other site 580332008248 cell division protein FtsW; Region: ftsW; TIGR02614 580332008249 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK02006 580332008250 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 580332008251 NAD binding site [chemical binding]; other site 580332008252 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 580332008253 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 580332008254 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 580332008255 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 580332008256 Mg++ binding site [ion binding]; other site 580332008257 putative catalytic motif [active] 580332008258 putative substrate binding site [chemical binding]; other site 580332008259 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 580332008260 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 580332008261 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 580332008262 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 580332008263 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 580332008264 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 580332008265 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 580332008266 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 580332008267 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 580332008268 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 580332008269 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 580332008270 Cell division protein FtsL; Region: FtsL; pfam04999 580332008271 MraW methylase family; Region: Methyltransf_5; pfam01795 580332008272 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 580332008273 cell division protein MraZ; Reviewed; Region: PRK00326 580332008274 MraZ protein; Region: MraZ; pfam02381 580332008275 MraZ protein; Region: MraZ; pfam02381 580332008276 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 580332008277 ligand binding site [chemical binding]; other site 580332008278 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 580332008279 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 580332008280 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 580332008281 transcriptional regulator PhoU; Provisional; Region: PRK11115 580332008282 PhoU domain; Region: PhoU; pfam01895 580332008283 PhoU domain; Region: PhoU; pfam01895 580332008284 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 580332008285 tetramer (dimer of dimers) interface [polypeptide binding]; other site 580332008286 active site 580332008287 dimer interface [polypeptide binding]; other site 580332008288 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 580332008289 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 580332008290 active site 580332008291 Int/Topo IB signature motif; other site 580332008292 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 580332008293 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 580332008294 DNA binding site [nucleotide binding] 580332008295 active site 580332008296 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 580332008297 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 580332008298 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 580332008299 RimM N-terminal domain; Region: RimM; pfam01782 580332008300 PRC-barrel domain; Region: PRC; pfam05239 580332008301 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 580332008302 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 580332008303 signal recognition particle protein; Provisional; Region: PRK10867 580332008304 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 580332008305 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 580332008306 P loop; other site 580332008307 GTP binding site [chemical binding]; other site 580332008308 Signal peptide binding domain; Region: SRP_SPB; pfam02978 580332008309 beta-phosphoglucomutase family hydrolase; Region: PGMB-YQAB-SF; TIGR02009 580332008310 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 580332008311 motif II; other site 580332008312 threonine dehydratase; Reviewed; Region: PRK09224 580332008313 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 580332008314 tetramer interface [polypeptide binding]; other site 580332008315 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332008316 catalytic residue [active] 580332008317 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 580332008318 putative Ile/Val binding site [chemical binding]; other site 580332008319 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 580332008320 putative Ile/Val binding site [chemical binding]; other site 580332008321 TfoX N-terminal domain; Region: TfoX_N; pfam04993 580332008322 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 580332008323 5,10-methenyltetrahydrofolate synthetase; Region: MTHFS_bact; TIGR02727 580332008324 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 580332008325 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 580332008326 dimer interface [polypeptide binding]; other site 580332008327 TPP-binding site [chemical binding]; other site 580332008328 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 580332008329 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 580332008330 E3 interaction surface; other site 580332008331 lipoyl attachment site [posttranslational modification]; other site 580332008332 e3 binding domain; Region: E3_binding; pfam02817 580332008333 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 580332008334 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 580332008335 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 580332008336 active site 580332008337 (T/H)XGH motif; other site 580332008338 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 580332008339 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 580332008340 Maf-like protein; Region: Maf; pfam02545 580332008341 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 580332008342 active site 580332008343 dimer interface [polypeptide binding]; other site 580332008344 ribonuclease G; Provisional; Region: PRK11712 580332008345 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 580332008346 homodimer interface [polypeptide binding]; other site 580332008347 oligonucleotide binding site [chemical binding]; other site 580332008348 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 580332008349 IHF dimer interface [polypeptide binding]; other site 580332008350 IHF - DNA interface [nucleotide binding]; other site 580332008351 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 580332008352 hydrophobic ligand binding site; other site 580332008353 Uncharacterized ACR, YggU family COG1872; Region: DUF167; cl00811 580332008354 YGGT family; Region: YGGT; cl00508 580332008355 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 580332008356 pyrroline-5-carboxylate reductase; Region: PLN02688 580332008357 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 580332008358 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 580332008359 catalytic residue [active] 580332008360 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 580332008361 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 580332008362 Walker A motif; other site 580332008363 ATP binding site [chemical binding]; other site 580332008364 Walker B motif; other site 580332008365 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 580332008366 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 580332008367 Walker A motif; other site 580332008368 ATP binding site [chemical binding]; other site 580332008369 Walker B motif; other site 580332008370 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; pfam09836 580332008371 hypothetical protein; Provisional; Region: PRK05409 580332008372 Predicted integral membrane protein (DUF2282); Region: DUF2282; pfam10048 580332008373 methionine sulfoxide reductase A; Provisional; Region: PRK13014 580332008374 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 580332008375 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 580332008376 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 580332008377 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 580332008378 catalytic residues [active] 580332008379 methionine sulfoxide reductase B; Provisional; Region: PRK00222 580332008380 SelR domain; Region: SelR; pfam01641 580332008381 FecR protein; Region: FecR; pfam04773 580332008382 RNA polymerase sigma factor; Provisional; Region: PRK12536 580332008383 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 580332008384 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 580332008385 DNA binding residues [nucleotide binding] 580332008386 Protein of unknown function (DUF1109); Region: DUF1109; pfam06532 580332008387 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 580332008388 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 580332008389 active site 580332008390 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332008391 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 580332008392 NAD(P) binding site [chemical binding]; other site 580332008393 active site 580332008394 Acylphosphatase; Region: Acylphosphatase; pfam00708 580332008395 Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]; Region: NfeD; COG1030 580332008396 Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Region: Clp_protease_NfeD_1; cd07020 580332008397 dimer interface [polypeptide binding]; other site 580332008398 active site residues [active] 580332008399 NfeD-like C-terminal, partner-binding; Region: NfeD; pfam01957 580332008400 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 580332008401 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 580332008402 Transcription elongation factor Spt4; Region: Spt4; cl12033 580332008403 Cytochrome c; Region: Cytochrom_C; cl11414 580332008404 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 580332008405 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 580332008406 ATP binding site [chemical binding]; other site 580332008407 Mg2+ binding site [ion binding]; other site 580332008408 G-X-G motif; other site 580332008409 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 580332008410 anchoring element; other site 580332008411 dimer interface [polypeptide binding]; other site 580332008412 ATP binding site [chemical binding]; other site 580332008413 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 580332008414 active site 580332008415 metal binding site [ion binding]; metal-binding site 580332008416 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 580332008417 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 580332008418 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 580332008419 CAP-like domain; other site 580332008420 active site 580332008421 primary dimer interface [polypeptide binding]; other site 580332008422 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c_3; pfam13589 580332008423 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 580332008424 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 580332008425 ATP binding site [chemical binding]; other site 580332008426 Mg2+ binding site [ion binding]; other site 580332008427 G-X-G motif; other site 580332008428 Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]; Region: ComEC; COG2333 580332008429 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 580332008430 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 580332008431 Transposase; Region: HTH_Tnp_1; cl17663 580332008432 putative transposase OrfB; Reviewed; Region: PHA02517 580332008433 HTH-like domain; Region: HTH_21; pfam13276 580332008434 Integrase core domain; Region: rve; pfam00665 580332008435 Integrase core domain; Region: rve_3; pfam13683 580332008436 putative addiction module killer protein; Region: upstrm_HI1419; TIGR02683 580332008437 Predicted transcriptional regulator [Transcription]; Region: COG3636; cl17681 580332008438 Protein of unknown function (DUF1398); Region: DUF1398; cl11576 580332008439 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 580332008440 S-adenosylmethionine binding site [chemical binding]; other site 580332008441 Uncharacterized protein conserved in bacteria (DUF2136); Region: DUF2136; pfam09907 580332008442 Predicted transcription regulator containing HTH domain [Transcription]; Region: COG5499 580332008443 hypothetical protein; Provisional; Region: PRK10396 580332008444 Uncharacterized protein family (UPF0149); Region: UPF0149; cl01173 580332008445 SEC-C motif; Region: SEC-C; pfam02810 580332008446 dUTPase; Region: dUTPase_2; pfam08761 580332008447 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in dimeric 2-Deoxyuridine 5'-triphosphate nucleotidohydrolase and similar proteins; Region: NTP-PPase_dUTPase; cd11527 580332008448 active site 580332008449 homodimer interface [polypeptide binding]; other site 580332008450 metal binding site [ion binding]; metal-binding site 580332008451 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 580332008452 S-adenosylmethionine binding site [chemical binding]; other site 580332008453 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 580332008454 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 580332008455 ligand binding site [chemical binding]; other site 580332008456 flexible hinge region; other site 580332008457 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 580332008458 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 580332008459 ligand binding site [chemical binding]; other site 580332008460 flexible hinge region; other site 580332008461 Protein of unknown function (DUF2934); Region: DUF2934; pfam11154 580332008462 Isochorismatase family; Region: Isochorismatase; pfam00857 580332008463 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 580332008464 catalytic triad [active] 580332008465 dimer interface [polypeptide binding]; other site 580332008466 conserved cis-peptide bond; other site 580332008467 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 580332008468 substrate binding site [chemical binding]; other site 580332008469 PAS domain S-box; Region: sensory_box; TIGR00229 580332008470 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 580332008471 putative active site [active] 580332008472 heme pocket [chemical binding]; other site 580332008473 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332008474 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332008475 metal binding site [ion binding]; metal-binding site 580332008476 active site 580332008477 I-site; other site 580332008478 PAS fold; Region: PAS_4; pfam08448 580332008479 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332008480 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332008481 metal binding site [ion binding]; metal-binding site 580332008482 active site 580332008483 I-site; other site 580332008484 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 580332008485 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 580332008486 putative active site [active] 580332008487 PAS fold; Region: PAS_3; pfam08447 580332008488 heme pocket [chemical binding]; other site 580332008489 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 580332008490 PAS domain; Region: PAS_9; pfam13426 580332008491 putative active site [active] 580332008492 heme pocket [chemical binding]; other site 580332008493 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 580332008494 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 580332008495 metal binding site [ion binding]; metal-binding site 580332008496 active site 580332008497 I-site; other site 580332008498 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 580332008499 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 580332008500 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 580332008501 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 580332008502 Uncharacterized protein family (UPF0093); Region: UPF0093; pfam03653 580332008503 ABC-2 type transporter; Region: ABC2_membrane; cl17235 580332008504 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 580332008505 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 580332008506 active site 580332008507 nodulation ABC transporter NodI; Provisional; Region: PRK13537 580332008508 ATP-binding cassette domain of the lipid transporters, subfamily A; Region: ABC_subfamily_A; cd03263 580332008509 Walker A/P-loop; other site 580332008510 ATP binding site [chemical binding]; other site 580332008511 Q-loop/lid; other site 580332008512 ABC transporter signature motif; other site 580332008513 Walker B; other site 580332008514 D-loop; other site 580332008515 H-loop/switch region; other site 580332008516 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 580332008517 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 580332008518 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 580332008519 dimer interface [polypeptide binding]; other site 580332008520 [2Fe-2S] cluster binding site [ion binding]; other site 580332008521 Predicted integral membrane protein [Function unknown]; Region: COG5652 580332008522 Hemerythrin; Region: Hemerythrin; cd12107 580332008523 Fe binding site [ion binding]; other site 580332008524 Uncharacterized ACR, YggU family COG1872; Region: DUF167; cl00811 580332008525 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 580332008526 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 580332008527 RNA binding surface [nucleotide binding]; other site 580332008528 Pseudouridine synthase, a subgroup of the RsuA family; Region: PSSA_1; cd02555 580332008529 active site 580332008530 Uncharacterized conserved protein (DUF2132); Region: DUF2132; pfam09905 580332008531 Response regulator receiver domain; Region: Response_reg; pfam00072 580332008532 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 580332008533 active site 580332008534 phosphorylation site [posttranslational modification] 580332008535 intermolecular recognition site; other site 580332008536 dimerization interface [polypeptide binding]; other site 580332008537 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 580332008538 PAS fold; Region: PAS_3; pfam08447 580332008539 putative active site [active] 580332008540 heme pocket [chemical binding]; other site 580332008541 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 580332008542 PAS domain; Region: PAS_9; pfam13426 580332008543 putative active site [active] 580332008544 heme pocket [chemical binding]; other site 580332008545 Response regulator receiver domain; Region: Response_reg; pfam00072 580332008546 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 580332008547 active site 580332008548 phosphorylation site [posttranslational modification] 580332008549 intermolecular recognition site; other site 580332008550 dimerization interface [polypeptide binding]; other site 580332008551 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 580332008552 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 580332008553 putative active site [active] 580332008554 heme pocket [chemical binding]; other site 580332008555 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 580332008556 dimer interface [polypeptide binding]; other site 580332008557 phosphorylation site [posttranslational modification] 580332008558 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 580332008559 ATP binding site [chemical binding]; other site 580332008560 Mg2+ binding site [ion binding]; other site 580332008561 G-X-G motif; other site 580332008562 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 580332008563 heme-binding site [chemical binding]; other site 580332008564 DsrC like protein; Region: DsrC; pfam04358 580332008565 DNA polymerase I; Provisional; Region: PRK05755 580332008566 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 580332008567 active site 580332008568 metal binding site 1 [ion binding]; metal-binding site 580332008569 putative 5' ssDNA interaction site; other site 580332008570 metal binding site 3; metal-binding site 580332008571 metal binding site 2 [ion binding]; metal-binding site 580332008572 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 580332008573 putative DNA binding site [nucleotide binding]; other site 580332008574 putative metal binding site [ion binding]; other site 580332008575 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 580332008576 active site 580332008577 catalytic site [active] 580332008578 substrate binding site [chemical binding]; other site 580332008579 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 580332008580 active site 580332008581 DNA binding site [nucleotide binding] 580332008582 catalytic site [active] 580332008583 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 580332008584 Protein of unknown function (DUF2782); Region: DUF2782; pfam11191 580332008585 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 580332008586 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 580332008587 putative active site [active] 580332008588 putative substrate binding site [chemical binding]; other site 580332008589 ATP binding site [chemical binding]; other site 580332008590 lipoprotein; Provisional; Region: PRK11443 580332008591 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 580332008592 active site residue [active] 580332008593 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 580332008594 MEKHLA domain; Region: MEKHLA; pfam08670 580332008595 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 580332008596 Part of AAA domain; Region: AAA_19; pfam13245 580332008597 Family description; Region: UvrD_C_2; pfam13538 580332008598 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in mouse RS21-C6 protein and its homologs; Region: NTP-PPase_RS21-C6_like; cd11537 580332008599 homodimer interface [polypeptide binding]; other site 580332008600 chemical substrate binding site [chemical binding]; other site 580332008601 oligomer interface [polypeptide binding]; other site 580332008602 metal binding site [ion binding]; metal-binding site 580332008603 phosphoribulokinase; Provisional; Region: PRK15453 580332008604 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 580332008605 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 580332008606 HIGH motif; other site 580332008607 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 580332008608 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 580332008609 active site 580332008610 KMSKS motif; other site 580332008611 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 580332008612 tRNA binding surface [nucleotide binding]; other site 580332008613 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 580332008614 Lipopolysaccharide-assembly; Region: LptE; cl01125 580332008615 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 580332008616 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 580332008617 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 580332008618 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 580332008619 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 580332008620 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 580332008621 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 580332008622 DsbD alpha interface [polypeptide binding]; other site 580332008623 catalytic residues [active] 580332008624 Domain of unknown function (DUF202); Region: DUF202; pfam02656 580332008625 Dehydroquinase class II; Region: DHquinase_II; pfam01220 580332008626 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 580332008627 trimer interface [polypeptide binding]; other site 580332008628 active site 580332008629 dimer interface [polypeptide binding]; other site 580332008630 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 580332008631 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 580332008632 carboxyltransferase (CT) interaction site; other site 580332008633 biotinylation site [posttranslational modification]; other site 580332008634 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 580332008635 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 580332008636 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 580332008637 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 580332008638 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 580332008639 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 580332008640 DNA methylase; Region: N6_N4_Mtase; cl17433 580332008641 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 580332008642 S-adenosylmethionine binding site [chemical binding]; other site 580332008643 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 580332008644 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 580332008645 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 580332008646 POPLD (NUC188) domain; Region: POPLD; pfam08170 580332008647 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 580332008648 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 580332008649 lipoyl attachment site [posttranslational modification]; other site 580332008650 glycine dehydrogenase; Provisional; Region: PRK05367 580332008651 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 580332008652 tetramer interface [polypeptide binding]; other site 580332008653 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332008654 catalytic residue [active] 580332008655 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 580332008656 tetramer interface [polypeptide binding]; other site 580332008657 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332008658 catalytic residue [active] 580332008659 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 580332008660 dimer interface [polypeptide binding]; other site 580332008661 catalytic triad [active] 580332008662 peroxidatic and resolving cysteines [active] 580332008663 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; smart00831 580332008664 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 580332008665 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 580332008666 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 580332008667 Soluble P-type ATPase [General function prediction only]; Region: COG4087 580332008668 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 580332008669 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 580332008670 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 580332008671 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 580332008672 substrate binding site [chemical binding]; other site 580332008673 ATP binding site [chemical binding]; other site 580332008674 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 580332008675 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 580332008676 Fructosamine kinase; Region: Fructosamin_kin; pfam03881 580332008677 Phosphotransferase enzyme family; Region: APH; pfam01636 580332008678 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 580332008679 DNA-binding site [nucleotide binding]; DNA binding site 580332008680 RNA-binding motif; other site 580332008681 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 580332008682 rRNA binding site [nucleotide binding]; other site 580332008683 predicted 30S ribosome binding site; other site 580332008684 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 580332008685 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 580332008686 active site 580332008687 metal binding site [ion binding]; metal-binding site 580332008688 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 580332008689 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 580332008690 Glycosyl transferase family 2; Region: Glycos_transf_2; pfam00535 580332008691 active site 580332008692 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 580332008693 O-Antigen ligase; Region: Wzy_C; pfam04932 580332008694 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 580332008695 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 580332008696 Methyltransferase domain; Region: Methyltransf_23; pfam13489 580332008697 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 580332008698 S-adenosylmethionine binding site [chemical binding]; other site 580332008699 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 580332008700 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 580332008701 active site 580332008702 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 580332008703 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 580332008704 putative metal binding site; other site 580332008705 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 580332008706 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 580332008707 NAD(P) binding site [chemical binding]; other site 580332008708 homodimer interface [polypeptide binding]; other site 580332008709 substrate binding site [chemical binding]; other site 580332008710 active site 580332008711 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 580332008712 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 580332008713 Mg++ binding site [ion binding]; other site 580332008714 putative catalytic motif [active] 580332008715 putative substrate binding site [chemical binding]; other site 580332008716 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 580332008717 UDP-glucose 4 epimerase, subgroup 4, extended (e) SDRs; Region: UDP_G4E_4_SDR_e; cd05232 580332008718 putative NAD(P) binding site [chemical binding]; other site 580332008719 active site 580332008720 putative substrate binding site [chemical binding]; other site 580332008721 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 580332008722 Methyltransferase domain; Region: Methyltransf_24; pfam13578 580332008723 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 580332008724 active site 580332008725 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 580332008726 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 580332008727 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 580332008728 active site 580332008729 Glycosyl transferase family 2; Region: Glycos_transf_2; pfam00535 580332008730 active site 580332008731 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 580332008732 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 580332008733 NAD(P) binding site [chemical binding]; other site 580332008734 active site 580332008735 Alpha-1,2-fucosyltransferase; Region: Fut1_Fut2_like; cd11301 580332008736 GDP-Fucose binding site [chemical binding]; other site 580332008737 Glycosyltransferase family 10 (fucosyltransferase); Region: Glyco_transf_10; pfam00852 580332008738 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 580332008739 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 580332008740 active site 580332008741 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 580332008742 Wzx, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_Wzx_like; cd13128 580332008743 Cephalosporin hydroxylase; Region: CmcI; pfam04989 580332008744 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 580332008745 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 580332008746 putative trimer interface [polypeptide binding]; other site 580332008747 putative CoA binding site [chemical binding]; other site 580332008748 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 580332008749 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 580332008750 inhibitor-cofactor binding pocket; inhibition site 580332008751 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332008752 catalytic residue [active] 580332008753 Putative zinc binding domain; Region: Methyltransf_13; pfam08421 580332008754 Methyltransferase domain; Region: Methyltransf_23; pfam13489 580332008755 C-methyltransferase C-terminal domain; Region: Methyltransf_14; pfam08484 580332008756 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; pfam00908 580332008757 CDP-glucose 4,6-dehydratase; Region: CDP_4_6_dhtase; TIGR02622 580332008758 CDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: CDP_GD_SDR_e; cd05252 580332008759 NAD binding site [chemical binding]; other site 580332008760 homotetramer interface [polypeptide binding]; other site 580332008761 homodimer interface [polypeptide binding]; other site 580332008762 substrate binding site [chemical binding]; other site 580332008763 active site 580332008764 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 580332008765 G1P_cytidylyltransferase catalyzes the production of CDP-D-Glucose; Region: G1P_cytidylyltransferase; cd02524 580332008766 substrate binding site; other site 580332008767 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 580332008768 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 580332008769 inhibitor-cofactor binding pocket; inhibition site 580332008770 pyridoxal 5'-phosphate binding site [chemical binding]; other site 580332008771 catalytic residue [active] 580332008772 GDP-fucose synthetase, extended (e) SDRs; Region: GDP_FS_SDR_e; cd05239 580332008773 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 580332008774 NADP binding site [chemical binding]; other site 580332008775 active site 580332008776 putative substrate binding site [chemical binding]; other site 580332008777 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 580332008778 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 580332008779 NADP-binding site; other site 580332008780 homotetramer interface [polypeptide binding]; other site 580332008781 substrate binding site [chemical binding]; other site 580332008782 homodimer interface [polypeptide binding]; other site 580332008783 active site 580332008784 mannose-1-phosphate guanyltransferase; Provisional; Region: cpsB; PRK15460 580332008785 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 580332008786 active site 580332008787 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 580332008788 Cupin domain; Region: Cupin_2; cl17218 580332008789 EPS-associated transcriptional regulator, MarR family; Region: MarR_EPS; TIGR04176 580332008790 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 580332008791 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 580332008792 putative active site [active] 580332008793 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 580332008794 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 580332008795 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 580332008796 dTDP-glucose 4,6 dehydratase; Provisional; Region: PRK10084 580332008797 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 580332008798 NAD binding site [chemical binding]; other site 580332008799 substrate binding site [chemical binding]; other site 580332008800 homodimer interface [polypeptide binding]; other site 580332008801 active site 580332008802 S23 ribosomal protein; Region: Ribosomal_S23p; pfam05635 580332008803 four helix bundle protein; Region: TIGR02436 580332008804 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 580332008805 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 580332008806 substrate binding site; other site 580332008807 tetramer interface; other site 580332008808 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: rmlC; TIGR01221 580332008809 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 580332008810 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 580332008811 NADP binding site [chemical binding]; other site 580332008812 active site 580332008813 putative substrate binding site [chemical binding]; other site 580332008814 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 580332008815 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 580332008816 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 580332008817 S-adenosylmethionine binding site [chemical binding]; other site 580332008818 ThiC-associated domain; Region: ThiC-associated; pfam13667 580332008819 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 580332008820 Thiamine biosynthesis protein ThiC [Coenzyme metabolism]; Region: ThiC; COG0422 580332008821 HNH endonuclease; Region: HNH_2; pfam13391 580332008822 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 580332008823 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 580332008824 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 580332008825 active site residue [active] 580332008826 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 580332008827 Cation efflux family; Region: Cation_efflux; pfam01545 580332008828 glutamine synthetase; Provisional; Region: glnA; PRK09469 580332008829 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 580332008830 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 580332008831 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 580332008832 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 580332008833 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 580332008834 putative active site [active] 580332008835 heme pocket [chemical binding]; other site 580332008836 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 580332008837 dimer interface [polypeptide binding]; other site 580332008838 phosphorylation site [posttranslational modification] 580332008839 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 580332008840 ATP binding site [chemical binding]; other site 580332008841 Mg2+ binding site [ion binding]; other site 580332008842 G-X-G motif; other site 580332008843 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 580332008844 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 580332008845 active site 580332008846 phosphorylation site [posttranslational modification] 580332008847 intermolecular recognition site; other site 580332008848 dimerization interface [polypeptide binding]; other site 580332008849 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 580332008850 Walker A motif; other site 580332008851 ATP binding site [chemical binding]; other site 580332008852 Walker B motif; other site 580332008853 arginine finger; other site 580332008854 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 580332008855 Phosphoesterase family; Region: Phosphoesterase; pfam04185 580332008856 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 580332008857 putative catalytic site [active] 580332008858 putative phosphate binding site [ion binding]; other site 580332008859 active site 580332008860 metal binding site A [ion binding]; metal-binding site 580332008861 DNA binding site [nucleotide binding] 580332008862 putative AP binding site [nucleotide binding]; other site 580332008863 putative metal binding site B [ion binding]; other site 580332008864 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 580332008865 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 580332008866 catalytic residues [active] 580332008867 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 580332008868 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 580332008869 active site 580332008870 Zn binding site [ion binding]; other site 580332008871 dihydroorotase; Provisional; Region: PRK07627 580332008872 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 580332008873 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 580332008874 active site 580332008875 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 580332008876 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 580332008877 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 580332008878 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 580332008879 hypothetical protein; Validated; Region: PRK00228 580332008880 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 580332008881 putative binding surface; other site 580332008882 active site 580332008883 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 580332008884 putative binding surface; other site 580332008885 active site 580332008886 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 580332008887 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 580332008888 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 580332008889 ATP binding site [chemical binding]; other site 580332008890 Mg2+ binding site [ion binding]; other site 580332008891 G-X-G motif; other site 580332008892 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 580332008893 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 580332008894 Response regulator receiver domain; Region: Response_reg; pfam00072 580332008895 active site 580332008896 phosphorylation site [posttranslational modification] 580332008897 intermolecular recognition site; other site 580332008898 dimerization interface [polypeptide binding]; other site 580332008899 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 580332008900 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 580332008901 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 580332008902 dimer interface [polypeptide binding]; other site 580332008903 putative CheW interface [polypeptide binding]; other site 580332008904 CheW-like domain; Region: CheW; pfam01584 580332008905 Response regulator receiver domain; Region: Response_reg; pfam00072 580332008906 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 580332008907 active site 580332008908 phosphorylation site [posttranslational modification] 580332008909 intermolecular recognition site; other site 580332008910 dimerization interface [polypeptide binding]; other site 580332008911 Response regulator receiver domain; Region: Response_reg; pfam00072 580332008912 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 580332008913 active site 580332008914 phosphorylation site [posttranslational modification] 580332008915 intermolecular recognition site; other site 580332008916 dimerization interface [polypeptide binding]; other site 580332008917 Cation transport protein; Region: TrkH; cl17365 580332008918 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 580332008919 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 580332008920 TrkA-N domain; Region: TrkA_N; pfam02254 580332008921 TrkA-C domain; Region: TrkA_C; pfam02080 580332008922 TrkA-N domain; Region: TrkA_N; pfam02254 580332008923 TrkA-C domain; Region: TrkA_C; pfam02080 580332008924 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 580332008925 putative catalytic residue [active] 580332008926 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 580332008927 RNA methyltransferase, RsmE family; Region: TIGR00046 580332008928 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 580332008929 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 580332008930 ligand binding site [chemical binding]; other site 580332008931 FecR protein; Region: FecR; pfam04773 580332008932 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]; Region: COG1942 580332008933 active site 1 [active] 580332008934 dimer interface [polypeptide binding]; other site 580332008935 hexamer interface [polypeptide binding]; other site 580332008936 active site 2 [active] 580332008937 N-acetylglutamate synthase; Validated; Region: PRK05279 580332008938 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 580332008939 putative feedback inhibition sensing region; other site 580332008940 putative nucleotide binding site [chemical binding]; other site 580332008941 putative substrate binding site [chemical binding]; other site 580332008942 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 580332008943 Coenzyme A binding pocket [chemical binding]; other site 580332008944 oxidative damage protection protein; Provisional; Region: PRK05408 580332008945 polyphosphate kinase; Provisional; Region: PRK05443 580332008946 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 580332008947 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 580332008948 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 580332008949 putative domain interface [polypeptide binding]; other site 580332008950 putative active site [active] 580332008951 catalytic site [active] 580332008952 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 580332008953 putative domain interface [polypeptide binding]; other site 580332008954 putative active site [active] 580332008955 catalytic site [active] 580332008956 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 580332008957 catalytic core [active] 580332008958 polyphosphate:AMP phosphotransferase; Region: poly_P_AMP_trns; TIGR03708 580332008959 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 580332008960 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 580332008961 Protein of unknown function (DUF2288); Region: DUF2288; pfam10052 580332008962 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 580332008963 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 580332008964 trimer interface [polypeptide binding]; other site 580332008965 putative metal binding site [ion binding]; other site 580332008966 Plasmid stabilisation system protein; Region: Plasmid_stabil; pfam05016 580332008967 Predicted transcriptional regulator [Transcription]; Region: COG3905 580332008968 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 580332008969 active site 580332008970 substrate binding pocket [chemical binding]; other site 580332008971 dimer interface [polypeptide binding]; other site 580332008972 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 580332008973 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 580332008974 Predicted methyltransferases [General function prediction only]; Region: COG0313 580332008975 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 580332008976 putative SAM binding site [chemical binding]; other site 580332008977 putative homodimer interface [polypeptide binding]; other site 580332008978 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 580332008979 putative ligand binding site [chemical binding]; other site 580332008980 hypothetical protein; Reviewed; Region: PRK12497 580332008981 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 580332008982 dimer interface [polypeptide binding]; other site 580332008983 active site 580332008984 BON domain; Region: BON; pfam04972 580332008985 BON domain; Region: BON; pfam04972 580332008986 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 580332008987 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 580332008988 active site 580332008989 nucleotide binding site [chemical binding]; other site 580332008990 HIGH motif; other site 580332008991 KMSKS motif; other site 580332008992 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3536 580332008993 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 580332008994 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 580332008995 S-adenosylmethionine binding site [chemical binding]; other site 580332008996 Plasmid stabilisation system protein; Region: Plasmid_stabil; pfam05016 580332008997 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 580332008998 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 580332008999 PhnA protein; Region: PhnA; pfam03831 580332009000 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 580332009001 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 580332009002 active site 580332009003 Tim44-like domain; Region: Tim44; pfam04280 580332009004 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 580332009005 ABC1 family; Region: ABC1; pfam03109 580332009006 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 580332009007 active site 580332009008 ATP binding site [chemical binding]; other site 580332009009 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 580332009010 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 580332009011 P-loop; other site 580332009012 Magnesium ion binding site [ion binding]; other site 580332009013 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 580332009014 Magnesium ion binding site [ion binding]; other site 580332009015 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 580332009016 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 580332009017 glutaminase active site [active] 580332009018 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 580332009019 dimer interface [polypeptide binding]; other site 580332009020 active site 580332009021 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 580332009022 dimer interface [polypeptide binding]; other site 580332009023 active site 580332009024 N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]; Region: GlmU; COG1207 580332009025 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 580332009026 Substrate binding site; other site 580332009027 Mg++ binding site; other site 580332009028 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 580332009029 active site 580332009030 substrate binding site [chemical binding]; other site 580332009031 CoA binding site [chemical binding]; other site 580332009032 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 580332009033 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 580332009034 gamma subunit interface [polypeptide binding]; other site 580332009035 epsilon subunit interface [polypeptide binding]; other site 580332009036 LBP interface [polypeptide binding]; other site 580332009037 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 580332009038 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 580332009039 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 580332009040 alpha subunit interaction interface [polypeptide binding]; other site 580332009041 Walker A motif; other site 580332009042 ATP binding site [chemical binding]; other site 580332009043 Walker B motif; other site 580332009044 inhibitor binding site; inhibition site 580332009045 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 580332009046 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 580332009047 core domain interface [polypeptide binding]; other site 580332009048 delta subunit interface [polypeptide binding]; other site 580332009049 epsilon subunit interface [polypeptide binding]; other site 580332009050 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 580332009051 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 580332009052 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 580332009053 beta subunit interaction interface [polypeptide binding]; other site 580332009054 Walker A motif; other site 580332009055 ATP binding site [chemical binding]; other site 580332009056 Walker B motif; other site 580332009057 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 580332009058 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 580332009059 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 580332009060 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 580332009061 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 580332009062 F0F1 ATP synthase subunit C; Validated; Region: PRK06876 580332009063 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 580332009064 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 580332009065 ATP synthase I chain; Region: ATP_synt_I; pfam03899 580332009066 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 580332009067 ParB-like nuclease domain; Region: ParB; smart00470 580332009068 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 580332009069 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 580332009070 P-loop; other site 580332009071 Magnesium ion binding site [ion binding]; other site 580332009072 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 580332009073 Magnesium ion binding site [ion binding]; other site 580332009074 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 580332009075 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 580332009076 S-adenosylmethionine binding site [chemical binding]; other site 580332009077 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 580332009078 tRNA:m(5)U-54 methyltransferase; Region: gid_trmFO; TIGR00137 580332009079 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 580332009080 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 580332009081 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 580332009082 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 580332009083 Circularly permuted YlqF-related GTPases; Region: YlqF_related_GTPase; cl17249 580332009084 G4 box; other site 580332009085 GTP/Mg2+ binding site [chemical binding]; other site 580332009086 G5 box; other site 580332009087 trmE is a tRNA modification GTPase; Region: trmE; cd04164 580332009088 G1 box; other site 580332009089 G1 box; other site 580332009090 GTP/Mg2+ binding site [chemical binding]; other site 580332009091 Switch I region; other site 580332009092 Switch I region; other site 580332009093 G2 box; other site 580332009094 G2 box; other site 580332009095 Switch II region; other site 580332009096 G3 box; other site 580332009097 G4 box; other site 580332009098 G5 box; other site 580332009099 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 580332009100 membrane protein insertase; Provisional; Region: PRK01318 580332009101 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 580332009102 Haemolytic domain; Region: Haemolytic; pfam01809 580332009103 Ribonuclease P; Region: Ribonuclease_P; pfam00825 580332009104 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399